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  • 1
    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
    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: 2011-05-14
    Description: We describe a general computational method for designing proteins that bind a surface patch of interest on a target macromolecule. Favorable interactions between disembodied amino acid residues and the target surface are identified and used to anchor de novo designed interfaces. The method was used to design proteins that bind a conserved surface patch on the stem of the influenza hemagglutinin (HA) from the 1918 H1N1 pandemic virus. After affinity maturation, two of the designed proteins, HB36 and HB80, bind H1 and H5 HAs with low nanomolar affinity. Further, HB80 inhibits the HA fusogenic conformational changes induced at low pH. The crystal structure of HB36 in complex with 1918/H1 HA revealed that the actual binding interface is nearly identical to that in the computational design model. Such designed binding proteins may be useful for both diagnostics and therapeutics.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3164876/" 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/PMC3164876/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fleishman, Sarel J -- Whitehead, Timothy A -- Ekiert, Damian C -- Dreyfus, Cyrille -- Corn, Jacob E -- Strauch, Eva-Maria -- Wilson, Ian A -- Baker, David -- AI057141/AI/NIAID NIH HHS/ -- AI058113/AI/NIAID NIH HHS/ -- GM080209/GM/NIGMS NIH HHS/ -- P01 AI058113/AI/NIAID NIH HHS/ -- P01 AI058113-07/AI/NIAID NIH HHS/ -- Y1-CO-1020/CO/NCI NIH HHS/ -- Y1-GM-1104/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2011 May 13;332(6031):816-21. doi: 10.1126/science.1202617.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21566186" target="_blank"〉PubMed〈/a〉
    Keywords: Algorithms ; Amino Acid Sequence ; Binding Sites ; Computational Biology ; *Computer Simulation ; Hemagglutinin Glycoproteins, Influenza Virus/chemistry/*metabolism ; Hydrogen Bonding ; Hydrogen-Ion Concentration ; Hydrophobic and Hydrophilic Interactions ; *Models, Molecular ; Molecular Sequence Data ; Mutation ; Peptide Library ; Protein Binding ; Protein Conformation ; *Protein Engineering ; Protein Interaction Domains and Motifs ; Protein Structure, Secondary ; Proteins/*chemistry/genetics/*metabolism ; Software
    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: 2015-03-21
    Description: 〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4394183/" 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/PMC4394183/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Baltimore, David -- Berg, Paul -- Botchan, Michael -- Carroll, Dana -- Charo, R Alta -- Church, George -- Corn, Jacob E -- Daley, George Q -- Doudna, Jennifer A -- Fenner, Marsha -- Greely, Henry T -- Jinek, Martin -- Martin, G Steven -- Penhoet, Edward -- Puck, Jennifer -- Sternberg, Samuel H -- Weissman, Jonathan S -- Yamamoto, Keith R -- P50 HG005550/HG/NHGRI NIH HHS/ -- T32 GM066698/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2015 Apr 3;348(6230):36-8. doi: 10.1126/science.aab1028. Epub 2015 Mar 19.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉California Institute of Technology, Mail Code 147-75, Pasadena, CA 91125, USA. ; Stanford University School of Medicine, 291 Campus Drive, Stanford, CA 94305, USA. ; University of California, Berkeley, 450 Li Ka Shing no. 3370, Berkeley, CA 94720-3370, USA. Innovative Genomics Initiative, University of California, Berkeley, 188 Li Ka Shing Center, Berkeley, CA 94720-3370, USA. ; Department of Biochemistry, University of Utah School of Medicine, 15 North Medical Drive East, Room 4100, Salt Lake City, UT 84112-5650, USA. ; Department of Medical History and Bioethics, School of Medicine and Public Health, University of Wisconsin Law School, 975 Bascom Mall, Madison, WI 53706, USA. ; Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA. ; Innovative Genomics Initiative, University of California, Berkeley, 188 Li Ka Shing Center, Berkeley, CA 94720-3370, USA. ; Boston Children's Hospital, 300 Longwood Avenue, Karp Family Building, 7th Floor, Boston, MA 02115, USA. Howard Hughes Medical Institute, 4000 Jones Bridge Road, Chevy Chase, MD 20815, USA. ; Innovative Genomics Initiative, University of California, Berkeley, 188 Li Ka Shing Center, Berkeley, CA 94720-3370, USA. Departments of Molecular and Cell Biology and Chemistry, Howard Hughes Medical Institute, 731 Stanley Hall, MS 3220, University of California, Berkeley, Berkeley, CA 94720-3220, USA. doudna@berkeley.edu. ; Center for Law and the Biosciences, Crown Quadrangle 559 Nathan Abbott Way Stanford, CA 94305-8610, USA. ; Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland. ; Department of Molecular and Cell Biology, College of Letters and Science, University of California, Berkeley, 210K Durant Hall, Berkeley, CA 94720-2920, USA. ; Alta Partners, One Embarcadero Center, 37th Floor, San Francisco, CA 94111, USA. ; Department of Pediatrics UCSF School of Medicine, 513 Parnassus Avenue, San Francisco, CA 94143, USA. ; Department of Chemistry, 731 Stanley Hall, MS 3220, University of California, Berkeley, CA 94720-3220, USA. ; Innovative Genomics Initiative, University of California, Berkeley, 188 Li Ka Shing Center, Berkeley, CA 94720-3370, USA. Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, Byers Hall, 1700 4th Street, San Francisco, CA 94158-2330, USA. ; Innovative Genomics Initiative, University of California, Berkeley, 188 Li Ka Shing Center, Berkeley, CA 94720-3370, USA. UCSF School of Medicine, 600 16th Street, San Francisco, CA 94158, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25791083" target="_blank"〉PubMed〈/a〉
    Keywords: Biotechnology/ethics ; *Caspase 9 ; *Clustered Regularly Interspaced Short Palindromic Repeats ; Gene Transfer, Horizontal ; Genetic Engineering/*ethics ; Genetic Predisposition to Disease/*prevention & control ; Genome, Human/genetics ; Genomics ; *Germ Cells ; Humans ; Risk Management ; Targeted Gene Repair/*ethics
    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
    ISSN: 0021-8995
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Notes: Bisphenol fluorenone carbonate-dimethylsiloxane block polymers have been synthesized by interfacial condensation of phosgene with various mixtures of BPF-endcapped silicone oligomers and free BPF or its monosodium salt. The multisequence block polymers described here contain 7% to 27% silicone consisting of blocks of number-average degree of polymerization 10 to 40. Cast films are clear and colorless. Two glass temperatures are evident in each resin, one at about -100°C for the silicone microdomains and one at temperatures as high as 275°C for the polycarbonate matrix. While BPF polycarbonate is brittle, block polymers with as little as 10% silicone yield by shear deformation before breaking. Ultimate elongations are increased by preorientation at silicone contents above 15%. At temperatures far removed from BPF carbonate domain Tg's, both modulus and yield stress decrease with increasing silicone content, independent of block length, in a manner rationalized quantitatively by hard phase-soft phase continuum models. Ultimate tensile elongation, impact toughness, and plane strain stress intensity factors increase with silicone content, through a stress whitening mechanism. At higher silicone contents, shear deformation enhances tensile elongation and impact toughness. Heat distortion temperatures of 200°C or more are achieved. Flame resistance exceeds that of any known nonhalogenated resin. The resins are extrudable and injection moldable with only minor changes in color, transparency, and strength properties. Resins with 15% to 20% silicone can have a balance of properties that makes them attractive as tough, transparent heat- and flame- resistant engineering plastics.
    Additional Material: 14 Ill.
    Type of Medium: Electronic Resource
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  • 5
    ISSN: 0030-493X
    Keywords: Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A new method of general applicability for determining the percentage deuterium labeling in organic compounds is described. It uses the heights of ‘metastable peaks’ in the mass spectrum to determine the relative amounts of deuterated and undeuterated species. The method is illustrated by describing the analysis of mixtures of toluene-o-d1 and toluene, of toluene α-d1 and toluene, and of toluene-2,6-d2, toluene-o-d1 and toluene.
    Additional Material: 1 Ill.
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  • 6
    Electronic Resource
    Electronic Resource
    Chichester : Wiley-Blackwell
    Biological Mass Spectrometry 3 (1970), S. 1371-1377 
    ISSN: 0030-493X
    Keywords: Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Metastable ion decompositions involving the loss of hydrogen and deuterium from partially deuterated toluene ions were studied using a double focusing mass spectrometer. The electric sector voltage was adjusted so that the only ions transmitted were those which lost a particular fraction of their kinetic energy in decompositions taking place in front of the electric sector. Transitions involving loss of mass 1 or mass 2 from the molecular ions of toluene-α-d3 and toluene-2,3,4,5,6-d5 were studied. The results showed that in these slow reactions, the ‘preference factor’ defined as the ratio of the probability of loss of a hydrogen atom from a side-chain position to loss of a hydrogen atom from a ring position was 1.00. The ‘isotope factor,’ defined as the ratio of the probability of loss of a hydrogen atom from any position to that for the loss of a deuterium atom from the same position was found to be 3·50.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
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  • 7
  • 8
    Publication Date: 2019
    Description: 〈p〉CRISPR-Cas genome editing induces targeted DNA damage but can also affect off-target sites. Current off-target discovery methods work using purified DNA or specific cellular models but are incapable of direct detection in vivo. We developed DISCOVER-Seq (discovery of in situ Cas off-targets and verification by sequencing), a universally applicable approach for unbiased off-target identification that leverages the recruitment of DNA repair factors in cells and organisms. Tracking the precise recruitment of MRE11 uncovers the molecular nature of Cas activity in cells with single-base resolution. DISCOVER-Seq works with multiple guide RNA formats and types of Cas enzymes, allowing characterization of new editing tools. Off-targets can be identified in cell lines and patient-derived induced pluripotent stem cells and during adenoviral editing of mice, paving the way for in situ off-target discovery within individual patient genotypes during therapeutic genome editing.〈/p〉
    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
    Publication Date: 2013-07-10
    Description: Ubiquitin is a highly conserved eukaryotic protein that interacts with a diverse set of partners to act as a cellular signaling hub. Ubiquitin’s conformational flexibility has been postulated to underlie its multifaceted recognition. Here we use computational and library-based means to interrogate core mutations that modulate the conformational dynamics of...
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
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  • 10
    Publication Date: 2017-07-13
    Description: CRISPR (clustered regularly interspaced short palindromic repeats)–Cas9 gene editing technology is derived from a microbial adaptive immune system, where bacteriophages are often the intended target. Natural inhibitors of CRISPR-Cas9 enable phages to evade immunity and show promise in controlling Cas9-mediated gene editing in human cells. However, the mechanism of CRISPR-Cas9 inhibition is not known, and the potential applications for Cas9 inhibitor proteins in mammalian cells have not been fully established. We show that the anti-CRISPR protein AcrIIA4 binds only to assembled Cas9–single-guide RNA (sgRNA) complexes and not to Cas9 protein alone. A 3.9 Å resolution cryo–electron microscopy structure of the Cas9-sgRNA-AcrIIA4 complex revealed that the surface of AcrIIA4 is highly acidic and binds with a 1:1 stoichiometry to a region of Cas9 that normally engages the DNA protospacer adjacent motif. Consistent with this binding mode, order-of-addition experiments showed that AcrIIA4 interferes with DNA recognition but has no effect on preformed Cas9-sgRNA-DNA complexes. Timed delivery of AcrIIA4 into human cells as either protein or expression plasmid allows on-target Cas9-mediated gene editing while reducing off-target edits. These results provide a mechanistic understanding of AcrIIA4 function and demonstrate that inhibitors can modulate the extent and outcomes of Cas9-mediated gene editing.
    Electronic ISSN: 2375-2548
    Topics: Natural Sciences in General
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