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  • Articles  (1,770)
  • Escherichia coli
  • Industrial Chemistry and Chemical Engineering
  • Wiley-Blackwell  (1,686)
  • American Association for the Advancement of Science (AAAS)  (70)
  • Nature Publishing Group (NPG)  (14)
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  • Articles  (1,770)
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  • 1
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    Ribosome-catalyzed peptide-bond formation with an A-site substrate covalently linked to 23S ribosomal RNA (1998)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1998-05-02
    Description: In the ribosome, the aminoacyl-transfer RNA (tRNA) analog 4-thio-dT-p-C-p-puromycin crosslinks photochemically with G2553 of 23S ribosomal RNA (rRNA). This covalently linked substrate reacts with a peptidyl-tRNA analog to form a peptide bond in a peptidyl transferase-catalyzed reaction. This result places the conserved 2555 loop of 23S rRNA at the peptidyl transferase A site and suggests that peptide bond formation can occur uncoupled from movement of the A-site tRNA. Crosslink formation depends on occupancy of the P site by a tRNA carrying an intact CCA acceptor end, indicating that peptidyl-tRNA, directly or indirectly, helps to create the peptidyl transferase A site.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Green, R -- Switzer, C -- Noller, H F -- New York, N.Y. -- Science. 1998 Apr 10;280(5361):286-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Molecular Biology of RNA, Sinsheimer Laboratories, University of California, Santa Cruz, CA 95064, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9535658" target="_blank"〉PubMed〈/a〉
    Keywords: Anti-Bacterial Agents/pharmacology ; Binding Sites ; Catalysis ; Enzyme Inhibitors/pharmacology ; Escherichia coli ; Nucleic Acid Conformation ; Peptidyl Transferases/antagonists & inhibitors/*metabolism ; Puromycin/analogs & derivatives/chemical synthesis/chemistry/*metabolism ; RNA, Bacterial/chemistry/metabolism ; RNA, Ribosomal, 23S/chemistry/*metabolism ; RNA, Transfer, Amino Acyl/chemistry/*metabolism ; RNA, Transfer, Phe/chemistry/genetics/*metabolism ; Ribosomes/*metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
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  • 2
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    Bacterial rhodopsin: evidence for a new type of phototrophy in the sea (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2000-09-16
    Description: Extremely halophilic archaea contain retinal-binding integral membrane proteins called bacteriorhodopsins that function as light-driven proton pumps. So far, bacteriorhodopsins capable of generating a chemiosmotic membrane potential in response to light have been demonstrated only in halophilic archaea. We describe here a type of rhodopsin derived from bacteria that was discovered through genomic analyses of naturally occuring marine bacterioplankton. The bacterial rhodopsin was encoded in the genome of an uncultivated gamma-proteobacterium and shared highest amino acid sequence similarity with archaeal rhodopsins. The protein was functionally expressed in Escherichia coli and bound retinal to form an active, light-driven proton pump. The new rhodopsin exhibited a photochemical reaction cycle with intermediates and kinetics characteristic of archaeal proton-pumping rhodopsins. Our results demonstrate that archaeal-like rhodopsins are broadly distributed among different taxa, including members of the domain Bacteria. Our data also indicate that a previously unsuspected mode of bacterially mediated light-driven energy generation may commonly occur in oceanic surface waters worldwide.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Beja, O -- Aravind, L -- Koonin, E V -- Suzuki, M T -- Hadd, A -- Nguyen, L P -- Jovanovich, S B -- Gates, C M -- Feldman, R A -- Spudich, J L -- Spudich, E N -- DeLong, E F -- HG01775-02S1/HG/NHGRI NIH HHS/ -- R01GM27750/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2000 Sep 15;289(5486):1902-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Monterey Bay Aquarium Research Institute, Moss Landing, CA 95039-0628, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10988064" target="_blank"〉PubMed〈/a〉
    Keywords: Aerobiosis ; Amino Acid Sequence ; Archaea/classification/physiology ; Bacteria/genetics ; *Bacterial Physiological Phenomena ; Cloning, Molecular ; Escherichia coli ; Gammaproteobacteria/classification/genetics/*physiology ; Molecular Sequence Data ; Oceans and Seas ; Photochemistry ; Photosynthesis ; Phylogeny ; Phytoplankton/genetics/physiology ; Protein Binding ; Proton Pumps/physiology ; Retinaldehyde/metabolism ; Rhodopsin/*physiology ; Rhodopsins, Microbial ; *Water Microbiology
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 3
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    Structural basis of chaperone function and pilus biogenesis (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-08-14
    Description: Many Gram-negative pathogens assemble architecturally and functionally diverse adhesive pili on their surfaces by the chaperone-usher pathway. Immunoglobulin-like periplasmic chaperones escort pilus subunits to the usher, a large protein complex that facilitates the translocation and assembly of subunits across the outer membrane. The crystal structure of the PapD-PapK chaperone-subunit complex, determined at 2.4 angstrom resolution, reveals that the chaperone functions by donating its G(1) beta strand to complete the immunoglobulin-like fold of the subunit via a mechanism termed donor strand complementation. The structure of the PapD-PapK complex also suggests that during pilus biogenesis, every subunit completes the immunoglobulin-like fold of its neighboring subunit via a mechanism termed donor strand exchange.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sauer, F G -- Futterer, K -- Pinkner, J S -- Dodson, K W -- Hultgren, S J -- Waksman, G -- R01AI29549/AI/NIAID NIH HHS/ -- R01DK51406/DK/NIDDK NIH HHS/ -- R01GM54033/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1999 Aug 13;285(5430):1058-61.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Microbiology, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO 63110, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10446050" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacterial Proteins/*chemistry/*metabolism ; Crystallography, X-Ray ; Escherichia coli ; *Escherichia coli Proteins ; Fimbriae Proteins ; Fimbriae, Bacterial/chemistry/*metabolism/ultrastructure ; Models, Molecular ; Molecular Chaperones/*chemistry/*metabolism ; Molecular Sequence Data ; *Periplasmic Proteins ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Sequence Alignment
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 4
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    Arabidopsis NPH3: A NPH1 photoreceptor-interacting protein essential for phototropism (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-11-05
    Description: Phototropism of Arabidopsis thaliana seedlings in response to a blue light source is initiated by nonphototropic hypocotyl 1 (NPH1), a light-activated serine-threonine protein kinase. Mutations in three loci [NPH2, root phototropism 2 (RPT2), and NPH3] disrupt early signaling occurring downstream of the NPH1 photoreceptor. The NPH3 gene, now cloned, encodes a NPH1-interacting protein. NPH3 is a member of a large protein family, apparently specific to higher plants, and may function as an adapter or scaffold protein to bring together the enzymatic components of a NPH1-activated phosphorelay.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Motchoulski, A -- Liscum, E -- New York, N.Y. -- Science. 1999 Oct 29;286(5441):961-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10542152" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Arabidopsis/genetics/*metabolism ; *Arabidopsis Proteins ; Cell Membrane/metabolism ; Cloning, Molecular ; Escherichia coli ; Molecular Sequence Data ; Phosphoproteins/genetics/*metabolism ; Photoreceptor Cells, Invertebrate/*metabolism ; Phototropism ; Plant Proteins/genetics/*metabolism ; Protein Binding ; Two-Hybrid System Techniques
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  • 5
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    Recognition of the codon-anticodon helix by ribosomal RNA (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-09-11
    Description: Translational fidelity is established by ribosomal recognition of the codon-anticodon interaction within the aminoacyl-transfer RNA (tRNA) site (A site) of the ribosome. Experiments are presented that reveal possible contacts between 16S ribosomal RNA and the codon-anticodon complex. N1 methylation of adenine at position 1492 (A1492) and A1493 interfered with A-site tRNA binding. Mutation of A1492 and A1493 to guanine or cytosine also impaired A-site tRNA binding. The deleterious effects of A1492G or A1493G (or both) mutations were compensated by 2'fluorine substitutions in the mRNA codon. The results suggest that the ribosome recognizes the codon-anticodon complex by adenine contacts to the messenger RNA backbone and provide a mechanism for molecular discrimination of correct versus incorrect codon-anticodon pairs.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yoshizawa, S -- Fourmy, D -- Puglisi, J D -- GM51266/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1999 Sep 10;285(5434):1722-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5126, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10481006" target="_blank"〉PubMed〈/a〉
    Keywords: Adenine/analogs & derivatives/metabolism ; Anticodon/chemistry/*metabolism ; Binding Sites ; Biotin ; Codon/chemistry/*metabolism ; Escherichia coli ; Hydrogen Bonding ; Methylation ; Mutagenesis, Site-Directed ; *Nucleic Acid Conformation ; Paromomycin/pharmacology ; Protein Biosynthesis ; RNA, Bacterial/chemistry/metabolism ; RNA, Ribosomal, 16S/chemistry/genetics/*metabolism ; RNA, Transfer, Met/metabolism ; RNA, Transfer, Phe/metabolism ; Ribosomes/*metabolism
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  • 6
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    An anti-apoptotic role for the p53 family member, p73, during developmental neuron death (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2000-07-15
    Description: p53 plays an essential pro-apoptotic role, a function thought to be shared with its family members p73 and p63. Here, we show that p73 is primarily present in developing neurons as a truncated isoform whose levels are dramatically decreased when sympathetic neurons apoptose after nerve growth factor (NGF) withdrawal. Increased expression of truncated p73 rescues these neurons from apoptosis induced by NGF withdrawal or p53 overexpression. In p73-/- mice, all isoforms of p73 are deleted and the apoptosis of developing sympathetic neurons is greatly enhanced. Thus, truncated p73 is an essential anti-apoptotic protein in neurons, serving to counteract the pro-apoptotic function of p53.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pozniak, C D -- Radinovic, S -- Yang, A -- McKeon, F -- Kaplan, D R -- Miller, F D -- New York, N.Y. -- Science. 2000 Jul 14;289(5477):304-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Neuronal Survival, Brain Tumor Research Center, Montreal Neurological Institute, McGill University, Montreal, Canada H3A 2B4.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10894779" target="_blank"〉PubMed〈/a〉
    Keywords: Adenoviridae/genetics ; Animals ; Apoptosis/*physiology ; Cells, Cultured ; DNA-Binding Proteins/biosynthesis/chemistry/*physiology ; Escherichia coli ; Genes, Tumor Suppressor ; Humans ; Mice ; Mice, Inbred BALB C ; Nerve Growth Factor/pharmacology ; Neurons/*physiology ; Nuclear Proteins/biosynthesis/chemistry/*physiology ; Protein Isoforms/biosynthesis/chemistry/physiology ; Recombinant Proteins ; Sympathetic Nervous System/cytology/*physiology ; Tumor Suppressor Protein p53/antagonists & inhibitors/*physiology ; Tumor Suppressor Proteins
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  • 7
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    A single adenosine with a neutral pKa in the ribosomal peptidyl transferase center (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2000-08-11
    Description: Biochemical and crystallographic evidence suggests that 23S ribosomal RNA (rRNA) is the catalyst of peptide bond formation. To explore the mechanism of this reaction, we screened for nucleotides in Escherichia coli 23S rRNA that may have a perturbed pKa (where Ka is the acid constant) based on the pH dependence of dimethylsulfate modification. A single universally conserved A (number 2451) within the central loop of domain V has a near neutral pKa of 7.6 +/- 0.2, which is about the same as that reported for the peptidyl transferase reaction. In vivo mutational analysis of this nucleotide indicates that it has an essential role in ribosomal function. These results are consistent with a mechanism wherein the nucleotide base of A2451 serves as a general acid base during peptide bond formation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Muth, G W -- Ortoleva-Donnelly, L -- Strobel, S A -- GM54839/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2000 Aug 11;289(5481):947-50.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biophysics and Biochemistry, Yale University, 260 Whitney Avenue, New Haven, CT 06520-8114, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10937997" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine/chemistry/*metabolism ; Binding Sites ; Catalysis ; Dimethyl Sulfoxide ; Escherichia coli ; Hydrogen Bonding ; Methylation ; Mutation ; *Peptide Biosynthesis ; Peptidyl Transferases/*chemistry/*metabolism ; Protons ; RNA, Bacterial/chemistry/genetics/metabolism ; RNA, Ribosomal, 23S/*chemistry/genetics/*metabolism ; Ribosomes/chemistry/*metabolism ; Tubercidin/metabolism
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  • 8
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    Control of the selectivity of the aquaporin water channel family by global orientational tuning (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-04-20
    Description: Aquaporins are transmembrane channels found in cell membranes of all life forms. We examine their apparently paradoxical property, facilitation of efficient permeation of water while excluding protons, which is of critical importance to preserving the electrochemical potential across the cell membrane. We have determined the structure of the Escherichia coli aquaglyceroporin GlpF with bound water, in native (2.7 angstroms) and in W48F/F200T mutant (2.1 angstroms) forms, and carried out 12-nanosecond molecular dynamics simulations that define the spatial and temporal probability distribution and orientation of a single file of seven to nine water molecules inside the channel. Two conserved asparagines force a central water molecule to serve strictly as a hydrogen bond donor to its neighboring water molecules. Assisted by the electrostatic potential generated by two half-membrane spanning loops, this dictates opposite orientations of water molecules in the two halves of the channel, and thus prevents the formation of a "proton wire," while permitting rapid water diffusion. Both simulations and observations revealed a more regular distribution of channel water and an increased water permeability for the W48F/F200T mutant.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tajkhorshid, Emad -- Nollert, Peter -- Jensen, Morten O -- Miercke, Larry J W -- O'Connell, Joseph -- Stroud, Robert M -- Schulten, Klaus -- New York, N.Y. -- Science. 2002 Apr 19;296(5567):525-30.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Theoretical Biophysics Group, Beckman Institute, University of Illinois at Urbana-Champaign, 405 North Mathews, Urbana, IL 61801, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11964478" target="_blank"〉PubMed〈/a〉
    Keywords: Aquaporins/*chemistry/genetics/metabolism ; Asparagine/chemistry ; Chemistry, Physical ; Computer Simulation ; Crystallography, X-Ray ; Diffusion ; Electrochemistry ; Escherichia coli ; Escherichia coli Proteins/*chemistry/genetics/metabolism ; Glycerol/metabolism ; Hydrogen Bonding ; Models, Molecular ; Mutation ; Physicochemical Phenomena ; Protein Conformation ; Protein Structure, Secondary ; Protons ; Static Electricity ; Water/chemistry/*metabolism
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  • 9
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    Discrete determinants in transfer RNA for editing and aminoacylation (1997)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1997-05-23
    Description: During translation errors of aminoacylation are corrected in editing reactions which ensure that an amino acid is stably attached to its corresponding transfer RNA (tRNA). Previous studies have not shown whether the tRNA nucleotides needed for effecting translational editing are the same as or distinct from those required for aminoacylation, but several considerations have suggested that they are the same. Here, designed tRNAs that are highly active for aminoacylation but are not active in translational editing are presented. The editing reaction can be controlled by manipulation of nucleotides at the corner of the L-shaped tRNA. In contrast, these manipulations do not affect aminoacylation. These results demonstrate the segregation of nucleotide determinants for the editing and aminoacylation functions of tRNA.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hale, S P -- Auld, D S -- Schmidt, E -- Schimmel, P -- GM15539/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1997 May 23;276(5316):1250-2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9157882" target="_blank"〉PubMed〈/a〉
    Keywords: Acetylation ; Base Sequence ; Binding Sites ; Cloning, Molecular ; Escherichia coli ; Molecular Sequence Data ; Nucleic Acid Conformation ; *RNA Editing ; RNA, Transfer/*metabolism ; RNA, Transfer, Ile/chemistry/metabolism ; RNA, Transfer, Val/chemistry/metabolism
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  • 10
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    Metal ion chaperone function of the soluble Cu(I) receptor Atx1 (1997)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1997-11-05
    Description: Reactive and potentially toxic cofactors such as copper ions are imported into eukaryotic cells and incorporated into target proteins by unknown mechanisms. Atx1, a prototypical copper chaperone protein from yeast, has now been shown to act as a soluble cytoplasmic copper(I) receptor that can adopt either a two- or three-coordinate metal center in the active site. Atx1 also associated directly with the Atx1-like cytosolic domains of Ccc2, a vesicular protein defined in genetic studies as a member of the copper-trafficking pathway. The unusual structure and dynamics of Atx1 suggest a copper exchange function for this protein and related domains in the Menkes and Wilson disease proteins.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pufahl, R A -- Singer, C P -- Peariso, K L -- Lin, S J -- Schmidt, P J -- Fahrni, C J -- Culotta, V C -- Penner-Hahn, J E -- O'Halloran, T V -- GM-38047/GM/NIGMS NIH HHS/ -- GM-50016/GM/NIGMS NIH HHS/ -- GM-54111/GM/NIGMS NIH HHS/ -- R01 GM054111/GM/NIGMS NIH HHS/ -- etc. -- New York, N.Y. -- Science. 1997 Oct 31;278(5339):853-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Northwestern University, Evanston, IL 60208, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9346482" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; *Carrier Proteins ; *Cation Transport Proteins ; Copper/*metabolism ; Escherichia coli ; Fungal Proteins/metabolism/*physiology ; Humans ; Molecular Chaperones/*physiology ; Molecular Sequence Data ; Recombinant Proteins ; Saccharomyces cerevisiae/metabolism/*physiology ; *Saccharomyces cerevisiae Proteins ; Sequence Homology, Amino Acid
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  • 11
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    Anticodon switching changes the identity of methionine and valine transfer RNAs (1988)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1988-11-04
    Description: The anticodon has previously been shown to play a role in recognition of certain transfer RNAs by aminoacyl-tRNA synthetases; however, the extent to which this sequence dictates tRNA identity is generally unknown. To investigate the contribution of the anticodon to the identity of Escherichia coli methionine and valine tRNAs, in vitro transcripts of these tRNAs were prepared that contained normal and interchanged anticodon sequences. Transcripts containing wild-type tRNA sequences were excellent substrates for their respective cognate aminoacyl-tRNA synthetases and were effectively discriminated against by a variety of noncognate enzymes. The mutant tRNAs produced by switching the anticodon sequences lost their original tRNA identity and assumed an identity corresponding to the acquired anticodon sequence. These results indicate that the anticodon contains sufficient information to distinguish methionine and valine tRNAs with high fidelity.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schulman, L H -- Pelka, H -- New York, N.Y. -- Science. 1988 Nov 4;242(4879):765-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Developmental Biology and Cancer, Albert Einstein College of Medicine, Bronx, New York 10461.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3055296" target="_blank"〉PubMed〈/a〉
    Keywords: *Anticodon ; Escherichia coli ; Kinetics ; Methionine-tRNA Ligase/metabolism ; *RNA, Transfer ; RNA, Transfer, Amino Acid-Specific/*physiology ; RNA, Transfer, Met/*physiology ; RNA, Transfer, Val/*physiology ; Substrate Specificity ; *Transfer RNA Aminoacylation ; Valine-tRNA Ligase/metabolism
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  • 12
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    Sugar and signal-transducer binding sites of the Escherichia coli galactose chemoreceptor protein (1988)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1988-12-02
    Description: D-galactose-binding (or chemoreceptor) protein of Escherichia coli serves as an initial component for both chemotaxis towards galactose and glucose and high-affinity active transport of the two sugars. Well-refined x-ray structures of the liganded forms of the wild-type and a mutant protein isolated from a strain defective in chemotaxis but fully competent in transport have provided a molecular view of the sugar-binding site and of a site for interacting with the Trg transmembrane signal transducer. The geometry of the sugar-binding site, located in the cleft between the two lobes of the bilobate protein, is novel in that it is designed for tight binding and sequestering of either the alpha or beta anomer of the D-stereoisomer of the 4-epimers galactose and glucose. Binding specificity and affinity are conferred primarily by polar planar side-chain residues that form intricate networks of cooperative and bidentate hydrogen bonds with the sugar substrates, and secondarily by aromatic residues that sandwich the pyranose ring. Each of the pairs of anomeric hydroxyls and epimeric hydroxyls is recognized by a distinct Asp residue. The site for interaction with the transducer is about 18 A from the sugar-binding site. Mutation of Gly74 to Asp at this site, concomitant with considerable changes in the local ordered water structures, contributes to the lack of productive interaction with the transmembrane signal transducer.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Vyas, N K -- Vyas, M N -- Quiocho, F A -- New York, N.Y. -- Science. 1988 Dec 2;242(4883):1290-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3057628" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/*ultrastructure ; Binding Sites ; *Calcium-Binding Proteins ; Carrier Proteins/*ultrastructure ; *Chemotaxis ; Computer Simulation ; DNA Mutational Analysis ; Escherichia coli ; Galactose/metabolism ; Glucose/metabolism ; Hydrogen Bonding ; Models, Molecular ; *Monosaccharide Transport Proteins ; *Periplasmic Binding Proteins ; Protein Conformation ; Structure-Activity Relationship ; X-Ray Diffraction
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  • 13
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    Real-time tRNA transit on single translating ribosomes at codon resolution (2010)
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    Publication Date: 2010-04-16
    Description: Translation by the ribosome occurs by a complex mechanism involving the coordinated interaction of multiple nucleic acid and protein ligands. Here we use zero-mode waveguides (ZMWs) and sophisticated detection instrumentation to allow real-time observation of translation at physiologically relevant micromolar ligand concentrations. Translation at each codon is monitored by stable binding of transfer RNAs (tRNAs)-labelled with distinct fluorophores-to translating ribosomes, which allows direct detection of the identity of tRNA molecules bound to the ribosome and therefore the underlying messenger RNA (mRNA) sequence. We observe the transit of tRNAs on single translating ribosomes and determine the number of tRNA molecules simultaneously bound to the ribosome, at each codon of an mRNA molecule. Our results show that ribosomes are only briefly occupied by two tRNA molecules and that release of deacylated tRNA from the exit (E) site is uncoupled from binding of aminoacyl-tRNA site (A-site) tRNA and occurs rapidly after translocation. The methods outlined here have broad application to the study of mRNA sequences, and the mechanism and regulation of translation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4466108/" 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/PMC4466108/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Uemura, Sotaro -- Aitken, Colin Echeverria -- Korlach, Jonas -- Flusberg, Benjamin A -- Turner, Stephen W -- Puglisi, Joseph D -- GM51266/GM/NIGMS NIH HHS/ -- R01 GM051266/GM/NIGMS NIH HHS/ -- England -- Nature. 2010 Apr 15;464(7291):1012-7. doi: 10.1038/nature08925.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305-5126, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20393556" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Codon/*genetics ; Escherichia coli ; Fluorescence ; Kinetics ; Ligands ; Luminescent Measurements ; Optical Tweezers ; Protein Biosynthesis/genetics/*physiology ; RNA, Transfer/genetics/*metabolism ; Ribosomes/chemistry/genetics/*metabolism ; Time Factors
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  • 14
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    Ribosome dynamics and tRNA movement by time-resolved electron cryomicroscopy (2010)
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    Publication Date: 2010-07-16
    Description: The translocation step of protein synthesis entails large-scale rearrangements of the ribosome-transfer RNA (tRNA) complex. Here we have followed tRNA movement through the ribosome during translocation by time-resolved single-particle electron cryomicroscopy (cryo-EM). Unbiased computational sorting of cryo-EM images yielded 50 distinct three-dimensional reconstructions, showing the tRNAs in classical, hybrid and various novel intermediate states that provide trajectories and kinetic information about tRNA movement through the ribosome. The structures indicate how tRNA movement is coupled with global and local conformational changes of the ribosome, in particular of the head and body of the small ribosomal subunit, and show that dynamic interactions between tRNAs and ribosomal residues confine the path of the tRNAs through the ribosome. The temperature dependence of ribosome dynamics reveals a surprisingly flat energy landscape of conformational variations at physiological temperature. The ribosome functions as a Brownian machine that couples spontaneous conformational changes driven by thermal energy to directed movement.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fischer, Niels -- Konevega, Andrey L -- Wintermeyer, Wolfgang -- Rodnina, Marina V -- Stark, Holger -- England -- Nature. 2010 Jul 15;466(7304):329-33. doi: 10.1038/nature09206.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉3D Electron Cryomicroscopy Group, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Gottingen, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20631791" target="_blank"〉PubMed〈/a〉
    Keywords: Cryoelectron Microscopy ; Escherichia coli ; Kinetics ; Models, Molecular ; Molecular Conformation ; *Movement ; *Protein Biosynthesis ; RNA, Transfer/genetics/*metabolism ; Ribosome Subunits, Large, Bacterial/chemistry/metabolism ; Ribosome Subunits, Small, Bacterial/chemistry/metabolism ; Ribosomes/chemistry/*metabolism ; Temperature ; Thermodynamics ; Time Factors
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  • 15
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    Crystal structure of the anti-viral APOBEC3G catalytic domain and functional implications (2008)
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    Publication Date: 2008-10-14
    Description: The APOBEC family members are involved in diverse biological functions. APOBEC3G restricts the replication of human immunodeficiency virus (HIV), hepatitis B virus and retroelements by cytidine deamination on single-stranded DNA or by RNA binding. Here we report the high-resolution crystal structure of the carboxy-terminal deaminase domain of APOBEC3G (APOBEC3G-CD2) purified from Escherichia coli. The APOBEC3G-CD2 structure has a five-stranded beta-sheet core that is common to all known deaminase structures and closely resembles the structure of another APOBEC protein, APOBEC2 (ref. 5). A comparison of APOBEC3G-CD2 with other deaminase structures shows a structural conservation of the active-site loops that are directly involved in substrate binding. In the X-ray structure, these APOBEC3G active-site loops form a continuous 'substrate groove' around the active centre. The orientation of this putative substrate groove differs markedly (by 90 degrees) from the groove predicted by the NMR structure. We have introduced mutations around the groove, and have identified residues involved in substrate specificity, single-stranded DNA binding and deaminase activity. These results provide a basis for understanding the underlying mechanisms of substrate specificity for the APOBEC family.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2714533/" 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/PMC2714533/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Holden, Lauren G -- Prochnow, Courtney -- Chang, Y Paul -- Bransteitter, Ronda -- Chelico, Linda -- Sen, Udayaditya -- Stevens, Raymond C -- Goodman, Myron F -- Chen, Xiaojiang S -- R01 AI055926/AI/NIAID NIH HHS/ -- R01 AI055926-05/AI/NIAID NIH HHS/ -- England -- Nature. 2008 Nov 6;456(7218):121-4. doi: 10.1038/nature07357. Epub 2008 Oct 12.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Molecular and Computational Biology, University of Southern California, Los Angeles, California 90089, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18849968" target="_blank"〉PubMed〈/a〉
    Keywords: Antiviral Agents ; *Catalytic Domain ; Crystallography, X-Ray ; Cytidine Deaminase/*chemistry/genetics/isolation & purification/*metabolism ; DNA, Single-Stranded/metabolism ; Escherichia coli ; Humans ; Models, Molecular ; Muscle Proteins/chemistry ; Mutant Proteins/chemistry/genetics/metabolism ; Mutation ; Nuclear Magnetic Resonance, Biomolecular ; Protein Structure, Secondary ; Structural Homology, Protein ; Structure-Activity Relationship ; Substrate Specificity
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    Synthetic biology: The yin and yang of nature (2009)
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    Publication Date: 2009-01-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gore, Jeff -- van Oudenaarden, Alexander -- K99 GM085279/GM/NIGMS NIH HHS/ -- R00 GM085279/GM/NIGMS NIH HHS/ -- England -- Nature. 2009 Jan 15;457(7227):271-2. doi: 10.1038/457271a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19148089" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biological Clocks/*physiology ; Circadian Rhythm/*physiology ; Escherichia coli ; *Feedback, Physiological ; Gene Expression Regulation/*genetics ; Genes, Synthetic/*genetics ; Genetic Engineering ; *Models, Biological
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  • 17
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    SSB protein diffusion on single-stranded DNA stimulates RecA filament formation (2009)
    Nature Publishing Group (NPG)
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    Publication Date: 2009-10-13
    Description: Single-stranded DNA generated in the cell during DNA metabolism is stabilized and protected by binding of ssDNA-binding (SSB) proteins. Escherichia coli SSB, a representative homotetrameric SSB, binds to ssDNA by wrapping the DNA using its four subunits. However, such a tightly wrapped, high-affinity protein-DNA complex still needs to be removed or repositioned quickly for unhindered action of other proteins. Here we show, using single-molecule two- and three-colour fluorescence resonance energy transfer, that tetrameric SSB can spontaneously migrate along ssDNA. Diffusional migration of SSB helps in the local displacement of SSB by an elongating RecA filament. SSB diffusion also melts short DNA hairpins transiently and stimulates RecA filament elongation on DNA with secondary structure. This observation of diffusional movement of a protein on ssDNA introduces a new model for how an SSB protein can be redistributed, while remaining tightly bound to ssDNA during recombination and repair processes.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2782680/" 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/PMC2782680/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Roy, Rahul -- Kozlov, Alexander G -- Lohman, Timothy M -- Ha, Taekjip -- R01 GM030498/GM/NIGMS NIH HHS/ -- R01 GM030498-28/GM/NIGMS NIH HHS/ -- R01 GM065367/GM/NIGMS NIH HHS/ -- R01 GM065367-08/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2009 Oct 22;461(7267):1092-7. doi: 10.1038/nature08442. Epub 2009 Oct 11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Biophysics and Computational Biology, University of Illinois, Urbana-Champaign, Illinois 61801, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19820696" target="_blank"〉PubMed〈/a〉
    Keywords: DNA, Single-Stranded/chemistry/*metabolism ; DNA-Binding Proteins/*metabolism ; *Diffusion ; Escherichia coli ; Escherichia coli Proteins/*metabolism ; Fluorescence Resonance Energy Transfer ; *Movement ; Nucleic Acid Conformation ; Rec A Recombinases/*chemistry/*metabolism
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    Structural basis for translational fidelity ensured by transfer RNA lysidine synthetase (2009)
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    Publication Date: 2009-10-23
    Description: Maturation of precursor transfer RNA (pre-tRNA) includes excision of the 5' leader and 3' trailer sequences, removal of introns and addition of the CCA terminus. Nucleotide modifications are incorporated at different stages of tRNA processing, after the RNA molecule adopts the proper conformation. In bacteria, tRNA(Ile2) lysidine synthetase (TilS) modifies cytidine into lysidine (L; 2-lysyl-cytidine) at the first anticodon of tRNA(Ile2) (refs 4-9). This modification switches tRNA(Ile2) from a methionine-specific to an isoleucine-specific tRNA. However, the aminoacylation of tRNA(Ile2) by methionyl-tRNA synthetase (MetRS), before the modification by TilS, might lead to the misincorporation of methionine in response to isoleucine codons. The mechanism used by bacteria to avoid this pitfall is unknown. Here we show that the TilS enzyme specifically recognizes and modifies tRNA(Ile2) in its precursor form, thereby avoiding translation errors. We identified the lysidine modification in pre-tRNA(Ile2) isolated from RNase-E-deficient Escherichia coli and did not detect mature tRNA(Ile2) lacking this modification. Our kinetic analyses revealed that TilS can modify both types of RNA molecule with comparable efficiencies. X-ray crystallography and mutational analyses revealed that TilS specifically recognizes the entire L-shape structure in pre-tRNA(Ile2) through extensive interactions coupled with sequential domain movements. Our results demonstrate how TilS prevents the recognition of tRNA(Ile2) by MetRS and achieves high specificity for its substrate. These two key points form the basis for maintaining the fidelity of isoleucine codon translation in bacteria. Our findings also provide a rationale for the necessity of incorporating specific modifications at the precursor level during tRNA biogenesis.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nakanishi, Kotaro -- Bonnefond, Luc -- Kimura, Satoshi -- Suzuki, Tsutomu -- Ishitani, Ryuichiro -- Nureki, Osamu -- England -- Nature. 2009 Oct 22;461(7267):1144-8. doi: 10.1038/nature08474.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Kanagawa 225-8501, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19847269" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acyl-tRNA Synthetases/*chemistry/genetics/*metabolism ; Apoproteins/genetics/metabolism ; Bacillus subtilis ; Bacterial Proteins/*chemistry/genetics/*metabolism ; Base Sequence ; Catalytic Domain ; Crystallography, X-Ray ; Escherichia coli ; Geobacillus ; Kinetics ; Lysine/analogs & derivatives/metabolism ; Mass Spectrometry ; Models, Molecular ; Molecular Sequence Data ; *Protein Biosynthesis ; Pyrimidine Nucleosides/metabolism ; RNA, Transfer, Ile/genetics/metabolism ; Substrate Specificity
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    An unusual carbon-carbon bond cleavage reaction during phosphinothricin biosynthesis (2009)
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    Publication Date: 2009-06-12
    Description: Natural products containing phosphorus-carbon bonds have found widespread use in medicine and agriculture. One such compound, phosphinothricin tripeptide, contains the unusual amino acid phosphinothricin attached to two alanine residues. Synthetic phosphinothricin (glufosinate) is a component of two top-selling herbicides (Basta and Liberty), and is widely used with resistant transgenic crops including corn, cotton and canola. Recent genetic and biochemical studies showed that during phosphinothricin tripeptide biosynthesis 2-hydroxyethylphosphonate (HEP) is converted to hydroxymethylphosphonate (HMP). Here we report the in vitro reconstitution of this unprecedented C(sp(3))-C(sp(3)) bond cleavage reaction and X-ray crystal structures of the enzyme. The protein is a mononuclear non-haem iron(ii)-dependent dioxygenase that converts HEP to HMP and formate. In contrast to most other members of this family, the oxidative consumption of HEP does not require additional cofactors or the input of exogenous electrons. The current study expands the scope of reactions catalysed by the 2-His-1-carboxylate mononuclear non-haem iron family of enzymes.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2874955/" 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/PMC2874955/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cicchillo, Robert M -- Zhang, Houjin -- Blodgett, Joshua A V -- Whitteck, John T -- Li, Gongyong -- Nair, Satish K -- van der Donk, Wilfred A -- Metcalf, William W -- P01 GM077596/GM/NIGMS NIH HHS/ -- P01 GM077596-03/GM/NIGMS NIH HHS/ -- R01 GM059334/GM/NIGMS NIH HHS/ -- R01 GM059334-09/GM/NIGMS NIH HHS/ -- R01 GM59334/GM/NIGMS NIH HHS/ -- England -- Nature. 2009 Jun 11;459(7248):871-4. doi: 10.1038/nature07972.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19516340" target="_blank"〉PubMed〈/a〉
    Keywords: Aminobutyrates/*chemistry/*metabolism ; Biocatalysis ; Crystallography, X-Ray ; Dioxygenases/chemistry/genetics/*metabolism ; Escherichia coli ; Formates/metabolism ; Magnetic Resonance Spectroscopy ; Mass Spectrometry ; Models, Biological ; Models, Molecular ; Molecular Conformation ; Organophosphonates/metabolism
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    Molecular biology: Slip sliding on DNA (2009)
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    Publication Date: 2009-10-23
    Description: 〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2819181/" 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/PMC2819181/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉George, Nicholas P -- Keck, James L -- R01 GM068061/GM/NIGMS NIH HHS/ -- R01 GM068061-07/GM/NIGMS NIH HHS/ -- R01 GM068061-07S1/GM/NIGMS NIH HHS/ -- England -- Nature. 2009 Oct 22;461(7267):1067-8. doi: 10.1038/4611067a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19847254" target="_blank"〉PubMed〈/a〉
    Keywords: DNA, Single-Stranded/chemistry/*metabolism ; DNA-Binding Proteins/*metabolism ; *Diffusion ; Escherichia coli ; Escherichia coli Proteins/*metabolism ; Fluorescence Resonance Energy Transfer ; *Movement ; Nucleic Acid Conformation ; Rec A Recombinases/*chemistry/*metabolism
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  • 21
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    Protein synthesis: Translocation in slow motion (2010)
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    Publication Date: 2010-07-16
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ehrenberg, Mans -- England -- Nature. 2010 Jul 15;466(7304):325-6. doi: 10.1038/466325a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20631789" target="_blank"〉PubMed〈/a〉
    Keywords: Cryoelectron Microscopy ; Escherichia coli ; Kinetics ; *Movement ; *Protein Biosynthesis ; RNA, Transfer/genetics/*metabolism ; Ribosomes/chemistry/*metabolism ; Temperature ; Thermodynamics
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  • 22
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    Single-molecule dynamics of gating in a neurotransmitter transporter homologue (2010)
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    Publication Date: 2010-05-14
    Description: Neurotransmitter:Na(+) symporters (NSS) remove neurotransmitters from the synapse in a reuptake process that is driven by the Na(+) gradient. Drugs that interfere with this reuptake mechanism, such as cocaine and antidepressants, profoundly influence behaviour and mood. To probe the nature of the conformational changes that are associated with substrate binding and transport, we have developed a single-molecule fluorescence imaging assay and combined it with functional and computational studies of the prokaryotic NSS homologue LeuT. Here we show molecular details of the modulation of intracellular gating of LeuT by substrates and inhibitors, as well as by mutations that alter binding, transport or both. Our direct observations of single-molecule transitions, reflecting structural dynamics of the intracellular region of the transporter that might be masked by ensemble averaging or suppressed under crystallographic conditions, are interpreted in the context of an allosteric mechanism that couples ion and substrate binding to transport.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2940119/" 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/PMC2940119/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhao, Yongfang -- Terry, Daniel -- Shi, Lei -- Weinstein, Harel -- Blanchard, Scott C -- Javitch, Jonathan A -- DA022413/DA/NIDA NIH HHS/ -- DA023694/DA/NIDA NIH HHS/ -- DA12408/DA/NIDA NIH HHS/ -- DA17293/DA/NIDA NIH HHS/ -- K05 DA022413/DA/NIDA NIH HHS/ -- K99 DA023694/DA/NIDA NIH HHS/ -- K99 DA023694-02/DA/NIDA NIH HHS/ -- R01 DA017293/DA/NIDA NIH HHS/ -- England -- Nature. 2010 May 13;465(7295):188-93. doi: 10.1038/nature09057.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Molecular Recognition, Columbia University College of Physicians and Surgeons, 630 W. 168th, New York, New York 10032, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20463731" target="_blank"〉PubMed〈/a〉
    Keywords: Alanine/metabolism ; Allosteric Regulation ; Aquifoliaceae/*chemistry ; Bacterial Proteins/*chemistry/genetics/*metabolism ; Crystallography, X-Ray ; Cysteine/chemistry/metabolism ; Escherichia coli ; Fluorescence Resonance Energy Transfer ; Leucine/metabolism ; Models, Molecular ; Molecular Dynamics Simulation ; Plasma Membrane Neurotransmitter Transport ; Proteins/*chemistry/genetics/*metabolism ; Protein Conformation ; Sodium/metabolism
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  • 23
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    Low-resolution real-space envelopes: an approach to the ab initio macromolecular phase problem (1991)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1991-04-05
    Description: An ab initio approach to the phase problem in macromolecular x-ray crystallography is described. A random gas of hard-sphere point scatterers is allowed to condense under the constraint of the solvent fraction and the restraint of the observed Fourier amplitude data. Two applications to real macromolecular examples are discussed. This method produces an approximate outline of the bulk solvent regions and thus yields a low-resolution picture of the unit cell that can be extended to higher resolutions in special cases, such as through the use of molecular replacement or of noncrystallographic symmetry-based phase extension.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Subbiah, S -- GM-41455/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1991 Apr 5;252(5002):128-33.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Beckman Laboratories for Structural Biology, Department of Cell Biology, Stanford University School of Medicine, CA 94305.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2011749" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/ultrastructure ; Coliphages ; *Crystallography ; Escherichia coli ; Pancreatic Elastase/*ultrastructure ; *Protein Conformation ; Repressor Proteins/*ultrastructure ; Viral Proteins/ultrastructure ; *X-Ray Diffraction
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    RNA-protein interactions in 30S ribosomal subunits: folding and function of 16S rRNA (1989)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1989-05-19
    Description: Chemical probing methods have been used to "footprint" 16S ribosomal RNA (rRNA) at each step during the in vitro assembly of twenty 30S subunit ribosomal proteins. These experiments yield information about the location of each protein relative to the structure of 16S rRNA and provide the basis for derivation of a detailed model for the three-dimensional folding of 16S rRNA. Several lines of evidence suggest that protein-dependent conformational changes in 16S rRNA play an important part in the cooperativity of ribosome assembly and in fine-tuning of the conformation and dynamics of 16S rRNA in the 30S subunit.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stern, S -- Powers, T -- Changchien, L M -- Noller, H F -- GM-17129/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1989 May 19;244(4906):783-90.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Thimann Laboratories, University of California, Santa Cruz 95064.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2658053" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Escherichia coli ; Models, Molecular ; Molecular Sequence Data ; Molecular Structure ; Nucleic Acid Conformation ; RNA, Ribosomal/*metabolism ; RNA, Ribosomal, 16S/*metabolism ; Ribosomal Proteins/*metabolism ; Ribosomes/physiology
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 25
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    Role of beta gamma subunits of G proteins in targeting the beta-adrenergic receptor kinase to membrane-bound receptors (1992)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1992-08-28
    Description: The rate and extent of the agonist-dependent phosphorylation of beta 2-adrenergic receptors and rhodopsin by beta-adrenergic receptor kinase (beta ARK) are markedly enhanced on addition of G protein beta gamma subunits. With a model peptide substrate it was demonstrated that direct activation of the kinase could not account for this effect. G protein beta gamma subunits were shown to interact directly with the COOH-terminal region of beta ARK, and formation of this beta ARK-beta gamma complex resulted in receptor-facilitated membrane localization of the enzyme. The beta gamma subunits of transducin were less effective at both enhancing the rate of receptor phosphorylation and binding to the COOH-terminus of beta ARK, suggesting that the enzyme preferentially binds specific beta gamma complexes. The beta gamma-mediated membrane localization of beta ARK serves to intimately link receptor activation to beta ARK-mediated desensitization.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pitcher, J A -- Inglese, J -- Higgins, J B -- Arriza, J L -- Casey, P J -- Kim, C -- Benovic, J L -- Kwatra, M M -- Caron, M G -- Lefkowitz, R J -- 4R37-HL16039/HL/NHLBI NIH HHS/ -- GM 44944/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1992 Aug 28;257(5074):1264-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Research Institute, Department of Medicine, Duke University Medical Center, Durham, NC 27710.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1325672" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Cattle ; *Cyclic AMP-Dependent Protein Kinases ; Dose-Response Relationship, Drug ; Escherichia coli ; GTP-Binding Proteins/*physiology ; Gene Expression Regulation/drug effects ; In Vitro Techniques ; Molecular Sequence Data ; Phosphorylation ; Protein Kinases/*pharmacology ; Protein Processing, Post-Translational ; Receptors, Adrenergic, beta/*drug effects/*metabolism ; Recombinant Fusion Proteins ; Rhodopsin/metabolism ; Time Factors ; Virulence Factors, Bordetella/pharmacology ; beta-Adrenergic Receptor Kinases
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Asymmetry in the structure of the ABC transporter-binding protein complex BtuCD-BtuF (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-08-04
    Description: BtuCD is an adenosine triphosphate-binding cassette (ABC) transporter that translocates vitamin B12 from the periplasmic binding protein BtuF into the cytoplasm of Escherichia coli. The 2.6 angstrom crystal structure of a complex BtuCD-F reveals substantial conformational changes as compared with the previously reported structures of BtuCD and BtuF. The lobes of BtuF are spread apart, and B12 is displaced from the binding pocket. The transmembrane BtuC subunits reveal two distinct conformations, and the translocation pathway is closed to both sides of the membrane. Electron paramagnetic resonance spectra of spin-labeled cysteine mutants reconstituted in proteoliposomes are consistent with the conformation of BtuCD-F that was observed in the crystal structure. A comparison with BtuCD and the homologous HI1470/71 protein suggests that the structure of BtuCD-F may reflect a posttranslocation intermediate.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hvorup, Rikki N -- Goetz, Birke A -- Niederer, Martina -- Hollenstein, Kaspar -- Perozo, Eduardo -- Locher, Kaspar P -- New York, N.Y. -- Science. 2007 Sep 7;317(5843):1387-90. Epub 2007 Aug 2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Molecular Biology and Biophysics, ETH Zurich, HPK D14.3, 8093 Zurich, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17673622" target="_blank"〉PubMed〈/a〉
    Keywords: ATP-Binding Cassette Transporters/*chemistry ; Amino Acid Sequence ; Crystallography, X-Ray ; Electron Spin Resonance Spectroscopy ; Escherichia coli ; Escherichia coli Proteins/*chemistry ; Models, Molecular ; Molecular Sequence Data ; Periplasmic Binding Proteins/*chemistry ; Protein Binding ; Protein Conformation ; Recombinant Fusion Proteins/chemistry
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    Archaeal type III RuBisCOs function in a pathway for AMP metabolism (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-02-17
    Description: The type III ribulose-1,5-bisphosphate carboxylase-oxygenase (RuBisCO) present in the archaeon Thermococcus kodakaraensis was found to participate in adenosine 5'-monophosphate (AMP) metabolism, a role that is distinct from that of classical RuBisCOs of the Calvin-Benson-Bassham cycle. Genes annotated as thymidine phosphorylase (deoA) and eucaryal translation initiation factor 2B (e2b2) were found to encode AMP phosphorylase and ribose-1,5-bisphosphate isomerase, respectively. These enzymes supplied the RuBisCO substrate, ribulose-1,5-bisphosphate, from AMP and phosphate. Archaea with type III RuBisCOs all harbor both DeoA and the corresponding E2b2 homologs. In this pathway, adenine was released from AMP and the phosphoribose moiety entered central-carbon metabolism.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sato, Takaaki -- Atomi, Haruyuki -- Imanaka, Tadayuki -- New York, N.Y. -- Science. 2007 Feb 16;315(5814):1003-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17303759" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Monophosphate/*metabolism ; Archaea/enzymology/genetics/metabolism ; Archaeal Proteins/*metabolism ; Escherichia coli ; Metabolic Networks and Pathways ; Methionine/metabolism ; Pentosephosphates/metabolism ; Recombinant Proteins ; Ribulose-Bisphosphate Carboxylase/classification/*metabolism ; Thermococcus/*enzymology/genetics ; Thymidine Phosphorylase/genetics
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    Structures of the bacterial ribosome in classical and hybrid states of tRNA binding (2011)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2011-05-21
    Description: During protein synthesis, the ribosome controls the movement of tRNA and mRNA by means of large-scale structural rearrangements. We describe structures of the intact bacterial ribosome from Escherichia coli that reveal how the ribosome binds tRNA in two functionally distinct states, determined to a resolution of ~3.2 angstroms by means of x-ray crystallography. One state positions tRNA in the peptidyl-tRNA binding site. The second, a fully rotated state, is stabilized by ribosome recycling factor and binds tRNA in a highly bent conformation in a hybrid peptidyl/exit site. The structures help to explain how the ratchet-like motion of the two ribosomal subunits contributes to the mechanisms of translocation, termination, and ribosome recycling.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3176341/" 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/PMC3176341/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dunkle, Jack A -- Wang, Leyi -- Feldman, Michael B -- Pulk, Arto -- Chen, Vincent B -- Kapral, Gary J -- Noeske, Jonas -- Richardson, Jane S -- Blanchard, Scott C -- Cate, Jamie H Doudna -- CA92584/CA/NCI NIH HHS/ -- GM074127-04S1/GM/NIGMS NIH HHS/ -- GM07739/GM/NIGMS NIH HHS/ -- GM079238/GM/NIGMS NIH HHS/ -- GM088674/GM/NIGMS NIH HHS/ -- GM65050/GM/NIGMS NIH HHS/ -- P01 CA092584/CA/NCI NIH HHS/ -- P01 GM063210/GM/NIGMS NIH HHS/ -- P01-GM63210/GM/NIGMS NIH HHS/ -- R01 GM065050/GM/NIGMS NIH HHS/ -- R01 GM065050-11/GM/NIGMS NIH HHS/ -- R01 GM074127/GM/NIGMS NIH HHS/ -- R01 GM079238/GM/NIGMS NIH HHS/ -- R01 GM088674/GM/NIGMS NIH HHS/ -- RR-15301/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 2011 May 20;332(6032):981-4. doi: 10.1126/science.1202692.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21596992" target="_blank"〉PubMed〈/a〉
    Keywords: Anticodon/chemistry/metabolism ; Crystallography, X-Ray ; Escherichia coli ; Escherichia coli Proteins/metabolism ; Models, Molecular ; Nucleic Acid Conformation ; Protein Biosynthesis ; RNA, Bacterial/chemistry/*metabolism ; RNA, Messenger/chemistry/metabolism ; RNA, Ribosomal, 16S/chemistry/metabolism ; RNA, Ribosomal, 23S/chemistry/metabolism ; RNA, Transfer, Amino Acyl/chemistry/metabolism ; RNA, Transfer, Phe/chemistry/*metabolism ; Ribosomal Proteins/metabolism ; Ribosome Subunits, Large, Bacterial/*chemistry/*metabolism/ultrastructure ; Ribosome Subunits, Small, Bacterial/*chemistry/*metabolism/ultrastructure
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    Expanding the fluorine chemistry of living systems using engineered polyketide synthase pathways (2013)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2013-09-07
    Description: Organofluorines represent a rapidly expanding proportion of molecules that are used in pharmaceuticals, diagnostics, agrochemicals, and materials. Despite the prevalence of fluorine in synthetic compounds, the known biological scope is limited to a single pathway that produces fluoroacetate. Here, we demonstrate that this pathway can be exploited as a source of fluorinated building blocks for introduction of fluorine into natural-product scaffolds. Specifically, we have constructed pathways involving two polyketide synthase systems, and we show that fluoroacetate can be used to incorporate fluorine into the polyketide backbone in vitro. We further show that fluorine can be inserted site-selectively and introduced into polyketide products in vivo. These results highlight the prospects for the production of complex fluorinated natural products using synthetic biology.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4057101/" 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/PMC4057101/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Walker, Mark C -- Thuronyi, Benjamin W -- Charkoudian, Louise K -- Lowry, Brian -- Khosla, Chaitan -- Chang, Michelle C Y -- 1 DP2 OD008696/OD/NIH HHS/ -- 1 T32 GMO66698/PHS HHS/ -- 1S10RR023679-01/RR/NCRR NIH HHS/ -- F32 CA137994/CA/NCI NIH HHS/ -- R01 GM087934/GM/NIGMS NIH HHS/ -- S10 RR16634-01/RR/NCRR NIH HHS/ -- T32 GM066698/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2013 Sep 6;341(6150):1089-94. doi: 10.1126/science.1242345.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720-1460, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24009388" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/chemistry/genetics/metabolism ; Base Sequence ; Biological Products/chemistry/*metabolism ; Burkholderia/enzymology ; Coenzyme A Ligases/chemistry/genetics/metabolism ; Escherichia coli ; Fluoroacetates/chemistry/*metabolism ; Metabolic Networks and Pathways ; Molecular Sequence Data ; Polyketide Synthases/chemistry/genetics/*metabolism ; Polyketides/chemistry/*metabolism ; Protein Engineering ; Protein Structure, Tertiary ; Streptomyces coelicolor/enzymology
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    Nucleotide control of interdomain interactions in the conformational reaction cycle of SecA (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-09-21
    Description: The SecA adenosine triphosphatase (ATPase) mediates extrusion of the amino termini of secreted proteins from the eubacterial cytosol based on cycles of reversible binding to the SecYEG translocon. We have determined the crystal structure of SecA with and without magnesium-adenosine diphosphate bound to the high-affinity ATPase site at 3.0 and 2.7 angstrom resolution, respectively. Candidate sites for preprotein binding are located on a surface containing the SecA epitopes exposed to the periplasm upon binding to SecYEG and are thus positioned to deliver preprotein to SecYEG. Comparisons with structurally related ATPases, including superfamily I and II ATP-dependent helicases, suggest that the interaction geometry of the tandem motor domains in SecA is modulated by nucleotide binding, which is shown by fluorescence anisotropy experiments to reverse an endothermic domain-dissociation reaction hypothesized to gate binding to SecYEG.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hunt, John F -- Weinkauf, Sevil -- Henry, Lisa -- Fak, John J -- McNicholas, Paul -- Oliver, Donald B -- Deisenhofer, Johann -- New York, N.Y. -- Science. 2002 Sep 20;297(5589):2018-26.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Sciences, 702A Fairchild Center, MC2434, Columbia University, New York, NY 10027, USA. hunt@sid.bio.columbia.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12242434" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Diphosphate/chemistry/*metabolism ; Adenosine Triphosphatases/*chemistry/*metabolism ; Adenosine Triphosphate/chemistry/*metabolism ; Amino Acid Motifs ; Amino Acid Sequence ; Bacillus subtilis/*enzymology ; Bacterial Proteins/*chemistry/metabolism ; Binding Sites ; Crystallization ; Crystallography, X-Ray ; DNA Helicases/chemistry ; DNA, Bacterial/chemistry/metabolism ; DNA, Single-Stranded/chemistry/metabolism ; Dimerization ; Escherichia coli ; Escherichia coli Proteins/*chemistry/*metabolism ; Eukaryotic Initiation Factor-4A ; Fluorescence Polarization ; Fourier Analysis ; Hydrogen Bonding ; Ligands ; Membrane Transport Proteins/*chemistry/*metabolism ; Models, Molecular ; Molecular Sequence Data ; Peptide Initiation Factors/chemistry ; Peptides/chemistry ; Protein Binding ; Protein Conformation ; Protein Folding ; Protein Precursors/metabolism ; Protein Structure, Secondary ; *Protein Structure, Tertiary ; Temperature
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    Catalysis of ribosomal translocation by sparsomycin (2003)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2003-05-17
    Description: During protein synthesis, transfer RNAs (tRNAs) are translocated from the aminoacyl to peptidyl to exit sites of the ribosome, coupled to the movement of messenger RNA (mRNA), in a reaction catalyzed by elongation factor G (EF-G) and guanosine triphosphate (GTP). Here, we show that the peptidyl transferase inhibitor sparsomycin triggers accurate translocation in vitro in the absence of EF-G and GTP. Our results provide evidence that translocation is a function inherent to the ribosome and that the energy to drive this process is stored in the tRNA-mRNA-ribosome complex after peptide-bond formation. These findings directly implicate the peptidyl transferase center of the 50S subunit in the mechanism of translocation, a process involving large-scale movement of tRNA and mRNA in the 30S subunit, some 70 angstroms away.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fredrick, Kurt -- Noller, Harry F -- GM17129/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2003 May 16;300(5622):1159-62.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Molecular Biology of RNA, Sinsheimer Laboratories, University of California, Santa Cruz, CA 95064, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12750524" target="_blank"〉PubMed〈/a〉
    Keywords: Acylation ; Anti-Bacterial Agents/pharmacology ; Catalysis ; Codon ; Enzyme Inhibitors/pharmacology ; Escherichia coli ; Escherichia coli Proteins/drug effects/metabolism ; Peptide Elongation Factor G/metabolism ; Peptidyl Transferases/antagonists & inhibitors ; Protein Biosynthesis ; RNA, Bacterial/drug effects/metabolism ; RNA, Messenger/drug effects/*metabolism ; RNA, Transfer/drug effects/*metabolism ; Ribosomes/drug effects/*metabolism ; Sparsomycin/*pharmacology
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    Activation of a phytopathogenic bacterial effector protein by a eukaryotic cyclophilin (2005)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2005-03-05
    Description: Innate immunity in higher plants invokes a sophisticated surveillance system capable of recognizing bacterial effector proteins. In Arabidopsis, resistance to infection by strains of Pseudomonas syringae expressing the effector AvrRpt2 requires the plant resistance protein RPS2. AvrRpt2 was identified as a putative cysteine protease that results in the elimination of the Arabidopsis protein RIN4. RIN4 cleavage serves as a signal to activate RPS2-mediated resistance. AvrRpt2 is delivered into the plant cell, where it is activated by a eukaryotic factor that we identify as cyclophilin. This activation of AvrRpt2 is necessary for protease activity. Active AvrRpt2 can then directly cleave RIN4.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Coaker, Gitta -- Falick, Arnold -- Staskawicz, Brian -- R01-FM069680-01/PHS HHS/ -- New York, N.Y. -- Science. 2005 Apr 22;308(5721):548-50. Epub 2005 Mar 3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15746386" target="_blank"〉PubMed〈/a〉
    Keywords: Arabidopsis/*immunology/*metabolism/microbiology ; Arabidopsis Proteins/genetics/*metabolism ; Bacterial Proteins/chemistry/*metabolism ; Carrier Proteins/genetics/*metabolism ; Cyclophilins/*metabolism ; Cyclosporine/pharmacology ; Cysteine Endopeptidases/metabolism ; Enzyme Activation ; Escherichia coli ; Mass Spectrometry ; Mutation ; Peptide Mapping ; Plant Diseases ; Pseudomonas syringae/*metabolism/pathogenicity ; Recombinant Fusion Proteins/metabolism ; Saccharomyces cerevisiae/genetics/metabolism ; Sirolimus/pharmacology
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    NMR structure of Mistic, a membrane-integrating protein for membrane protein expression (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-02-26
    Description: Although structure determination of soluble proteins has become routine, our understanding of membrane proteins has been limited by experimental bottlenecks in obtaining both sufficient yields of protein and ordered crystals. Mistic is an unusual Bacillus subtilis integral membrane protein that folds autonomously into the membrane, bypassing the cellular translocon machinery. Using paramagnetic probes, we determined by nuclear magnetic resonance (NMR) spectroscopy that the protein forms a helical bundle with a surprisingly polar lipid-facing surface. Additional experiments suggest that Mistic can be used for high-level production of other membrane proteins in their native conformations, including many eukaryotic proteins that have previously been intractable to bacterial expression.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Roosild, Tarmo P -- Greenwald, Jason -- Vega, Mark -- Castronovo, Samantha -- Riek, Roland -- Choe, Senyon -- GM056653/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2005 Feb 25;307(5713):1317-21.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Structural Biology Laboratory, Salk Institute, San Diego, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15731457" target="_blank"〉PubMed〈/a〉
    Keywords: Bacillus subtilis/*chemistry ; Bacterial Proteins/*chemistry/*metabolism ; Cell Membrane/chemistry ; Crystallography, X-Ray ; Electron Spin Resonance Spectroscopy ; Escherichia coli ; Hydrogen Bonding ; Lipid Bilayers ; Membrane Proteins/*chemistry/*metabolism ; Micelles ; Models, Molecular ; Molecular Sequence Data ; Molecular Weight ; Mutation ; Nuclear Magnetic Resonance, Biomolecular ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Receptors, Transforming Growth Factor beta/chemistry/metabolism ; Recombinant Proteins/chemistry/metabolism
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    The structure of a retinal-forming carotenoid oxygenase (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-04-12
    Description: Enzymes that produce retinal and related apocarotenoids constitute a sequence- and thus structure-related family, a member of which was analyzed by x-ray diffraction. This member is an oxygenase and contains an Fe2+-4-His arrangement at the axis of a seven-bladed beta-propeller chain fold covered by a dome formed by six large loops. The Fe2+ is accessible through a long nonpolar tunnel that holds a carotenoid derivative in one of the crystals. On binding, three consecutive double bonds of this carotenoid changed from a straight all-trans to a cranked cis-trans-cis conformation. The remaining trans bond is located at the dioxygen-ligated Fe2+ and cleaved by oxygen.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kloer, Daniel P -- Ruch, Sandra -- Al-Babili, Salim -- Beyer, Peter -- Schulz, Georg E -- R01 EY020551/EY/NEI NIH HHS/ -- New York, N.Y. -- Science. 2005 Apr 8;308(5719):267-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institut fur Organische Chemie und Biochemie, Albert-Ludwigs-Universitat, Albertstrasse 21, 79104 Freiburg im Breisgau, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15821095" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Cloning, Molecular ; Crystallography, X-Ray ; Escherichia coli ; Humans ; Molecular Sequence Data ; Oxygenases/*chemistry ; Protein Conformation ; Recombinant Proteins ; Retinaldehyde/*chemistry ; Synechocystis/*enzymology/genetics
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    Outer membrane active transport: structure of the BtuB:TonB complex (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-06-03
    Description: In Gram-negative bacteria, the import of essential micronutrients across the outer membrane requires a transporter, an electrochemical gradient of protons across the inner membrane, and an inner membrane protein complex (ExbB, ExbD, TonB) that couples the proton-motive force to the outer membrane transporter. The inner membrane protein TonB binds directly to a conserved region, called the Ton-box, of the transporter. We solved the structure of the cobalamin transporter BtuB in complex with the C-terminal domain of TonB. In contrast to its conformations in the absence of TonB, the Ton-box forms a beta strand that is recruited to the existing beta sheet of TonB, which is consistent with a mechanical pulling model of transport.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shultis, David D -- Purdy, Michael D -- Banchs, Christian N -- Wiener, Michael C -- DK59999/DK/NIDDK NIH HHS/ -- GM00Z055/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2006 Jun 2;312(5778):1396-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16741124" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Outer Membrane Proteins/*chemistry/metabolism ; Biological Transport, Active ; Crystallography, X-Ray ; Escherichia coli ; Escherichia coli Proteins/*chemistry/metabolism ; Magnetic Resonance Spectroscopy ; Membrane Proteins/*chemistry/metabolism ; Membrane Transport Proteins/*chemistry/metabolism ; Models, Molecular ; Protein Binding ; Protein Conformation ; Protein Structure, Secondary
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    GTP hydrolysis in protein synthesis: two for Tu? (1993)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1993-02-26
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schimmel, P -- New York, N.Y. -- Science. 1993 Feb 26;259(5099):1264-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, Massachusetts Institute of Technology, Cambridge 02139.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8446896" target="_blank"〉PubMed〈/a〉
    Keywords: Energy Metabolism ; Escherichia coli ; Guanosine Triphosphate/*metabolism ; In Vitro Techniques ; *Peptide Chain Elongation, Translational ; Peptide Elongation Factor Tu/*metabolism ; Ribosomes/*metabolism
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Dynamic pathways of -1 translational frameshifting (2014)
    Nature Publishing Group (NPG)
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    Publication Date: 2014-06-12
    Description: Spontaneous changes in the reading frame of translation are rare (frequency of 10(-3) to 10(-4) per codon), but can be induced by specific features in the messenger RNA (mRNA). In the presence of mRNA secondary structures, a heptanucleotide 'slippery sequence' usually defined by the motif X XXY YYZ, and (in some prokaryotic cases) mRNA sequences that base pair with the 3' end of the 16S ribosomal rRNA (internal Shine-Dalgarno sequences), there is an increased probability that a specific programmed change of frame occurs, wherein the ribosome shifts one nucleotide backwards into an overlapping reading frame (-1 frame) and continues by translating a new sequence of amino acids. Despite extensive biochemical and genetic studies, there is no clear mechanistic description for frameshifting. Here we apply single-molecule fluorescence to track the compositional and conformational dynamics of individual ribosomes at each codon during translation of a frameshift-inducing mRNA from the dnaX gene in Escherichia coli. Ribosomes that frameshift into the -1 frame are characterized by a tenfold longer pause in elongation compared to non-frameshifted ribosomes, which translate through unperturbed. During the pause, interactions of the ribosome with the mRNA stimulatory elements uncouple EF-G catalysed translocation from normal ribosomal subunit reverse-rotation, leaving the ribosome in a non-canonical intersubunit rotated state with an exposed codon in the aminoacyl-tRNA site (A site). tRNA(Lys) sampling and accommodation to the empty A site and EF-G action either leads to the slippage of the tRNAs into the -1 frame or maintains the ribosome into the 0 frame. Our results provide a general mechanistic and conformational framework for -1 frameshifting, highlighting multiple kinetic branchpoints during elongation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4472451/" 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/PMC4472451/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chen, Jin -- Petrov, Alexey -- Johansson, Magnus -- Tsai, Albert -- O'Leary, Sean E -- Puglisi, Joseph D -- GM099687/GM/NIGMS NIH HHS/ -- GM51266/GM/NIGMS NIH HHS/ -- R01 GM051266/GM/NIGMS NIH HHS/ -- R01 GM099687/GM/NIGMS NIH HHS/ -- England -- Nature. 2014 Aug 21;512(7514):328-32. doi: 10.1038/nature13428. Epub 2014 Jun 11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Department of Applied Physics, Stanford University, Stanford, California 94305-4090, USA [2] Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305-5126, USA. ; Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305-5126, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24919156" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/genetics ; Codon/genetics ; DNA Polymerase III/genetics ; Escherichia coli ; *Frameshifting, Ribosomal ; Kinetics ; *Peptide Chain Elongation, Translational ; Peptide Elongation Factor G/metabolism ; RNA, Messenger/genetics ; RNA, Transfer, Amino Acyl/metabolism ; Reading Frames/genetics ; Ribosome Subunits/chemistry/metabolism ; Ribosomes/chemistry/*metabolism ; Rotation ; Time Factors
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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    CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III (2011)
    Nature Publishing Group (NPG)
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    Publication Date: 2011-04-02
    Description: CRISPR/Cas systems constitute a widespread class of immunity systems that protect bacteria and archaea against phages and plasmids, and commonly use repeat/spacer-derived short crRNAs to silence foreign nucleic acids in a sequence-specific manner. Although the maturation of crRNAs represents a key event in CRISPR activation, the responsible endoribonucleases (CasE, Cas6, Csy4) are missing in many CRISPR/Cas subtypes. Here, differential RNA sequencing of the human pathogen Streptococcus pyogenes uncovered tracrRNA, a trans-encoded small RNA with 24-nucleotide complementarity to the repeat regions of crRNA precursor transcripts. We show that tracrRNA directs the maturation of crRNAs by the activities of the widely conserved endogenous RNase III and the CRISPR-associated Csn1 protein; all these components are essential to protect S. pyogenes against prophage-derived DNA. Our study reveals a novel pathway of small guide RNA maturation and the first example of a host factor (RNase III) required for bacterial RNA-mediated immunity against invaders.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3070239/" 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/PMC3070239/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Deltcheva, Elitza -- Chylinski, Krzysztof -- Sharma, Cynthia M -- Gonzales, Karine -- Chao, Yanjie -- Pirzada, Zaid A -- Eckert, Maria R -- Vogel, Jorg -- Charpentier, Emmanuelle -- P 17238/Austrian Science Fund FWF/Austria -- England -- Nature. 2011 Mar 31;471(7340):602-7. doi: 10.1038/nature09886.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Laboratory for Molecular Infection Medicine Sweden, Umea, Sweden.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21455174" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/chemistry/genetics/immunology/metabolism ; Conserved Sequence ; DNA, Viral/genetics/metabolism ; Escherichia coli ; Models, Biological ; Prophages/genetics ; RNA Precursors/genetics/metabolism ; RNA Processing, Post-Transcriptional ; RNA, Bacterial/biosynthesis/*genetics/immunology/*metabolism ; RNA, Guide/*genetics ; Ribonuclease III/*metabolism ; Streptococcus pyogenes/*genetics/*immunology/metabolism/virology
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    Adenylylation control by intra- or intermolecular active-site obstruction in Fic proteins (2012)
    Nature Publishing Group (NPG)
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    Publication Date: 2012-01-24
    Description: Fic proteins that are defined by the ubiquitous FIC (filamentation induced by cyclic AMP) domain are known to catalyse adenylylation (also called AMPylation); that is, the transfer of AMP onto a target protein. In mammalian cells, adenylylation of small GTPases through Fic proteins injected by pathogenic bacteria can cause collapse of the actin cytoskeleton and cell death. It is unknown how this potentially deleterious adenylylation activity is regulated in the widespread Fic proteins that are found in all domains of life and that are thought to have critical roles in intrinsic signalling processes. Here we show that FIC-domain-mediated adenylylation is controlled by a conserved mechanism of ATP-binding-site obstruction that involves an inhibitory alpha-helix (alpha(inh)) with a conserved (S/T)XXXE(G/N) motif, and that in this mechanism the invariable glutamate competes with ATP gamma-phosphate binding. Consistent with this, FIC-domain-mediated growth arrest of bacteria by the VbhT toxin of Bartonella schoenbuchensis is intermolecularly repressed by the VbhA antitoxin through tight binding of its alpha(inh) to the FIC domain of VbhT, as shown by structure and function analysis. Furthermore, structural comparisons with other bacterial Fic proteins, such as Fic of Neisseria meningitidis and of Shewanella oneidensis, show that alpha(inh) frequently constitutes an amino-terminal or carboxy-terminal extension to the FIC domain, respectively, partially obstructing the ATP binding site in an intramolecular manner. After mutation of the inhibitory motif in various Fic proteins, including the human homologue FICD (also known as HYPE), adenylylation activity is considerably boosted, consistent with the anticipated relief of inhibition. Structural homology modelling of all annotated Fic proteins indicates that inhibition by alpha(inh) is universal and conserved through evolution, as the inhibitory motif is present in approximately 90% of all putatively adenylylation-active FIC domains, including examples from all domains of life and from viruses. Future studies should reveal how intrinsic or extrinsic factors modulate adenylylation activity by weakening the interaction of alpha(inh) with the FIC active site.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Engel, Philipp -- Goepfert, Arnaud -- Stanger, Frederic V -- Harms, Alexander -- Schmidt, Alexander -- Schirmer, Tilman -- Dehio, Christoph -- England -- Nature. 2012 Jan 22;482(7383):107-10. doi: 10.1038/nature10729.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Focal Area Infection Biology, Biozentrum, University of Basel, CH-4056 Basel, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22266942" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; Bacterial Proteins/*chemistry/*metabolism ; Bartonella ; Carrier Proteins/chemistry/metabolism ; Catalysis ; Catalytic Domain ; Cyclic AMP/*metabolism ; Escherichia coli ; Escherichia coli Proteins/chemistry/metabolism ; Glutamic Acid/metabolism ; Humans ; Membrane Proteins/chemistry/metabolism ; Microbial Viability ; Models, Molecular ; Molecular Weight ; Neisseria meningitidis ; Protein Structure, Tertiary ; Shewanella
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    Non-adaptive origins of interactome complexity (2011)
    Nature Publishing Group (NPG)
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    Publication Date: 2011-05-20
    Description: The boundaries between prokaryotes, unicellular eukaryotes and multicellular eukaryotes are accompanied by orders-of-magnitude reductions in effective population size, with concurrent amplifications of the effects of random genetic drift and mutation. The resultant decline in the efficiency of selection seems to be sufficient to influence a wide range of attributes at the genomic level in a non-adaptive manner. A key remaining question concerns the extent to which variation in the power of random genetic drift is capable of influencing phylogenetic diversity at the subcellular and cellular levels. Should this be the case, population size would have to be considered as a potential determinant of the mechanistic pathways underlying long-term phenotypic evolution. Here we demonstrate a phylogenetically broad inverse relation between the power of drift and the structural integrity of protein subunits. This leads to the hypothesis that the accumulation of mildly deleterious mutations in populations of small size induces secondary selection for protein-protein interactions that stabilize key gene functions. By this means, the complex protein architectures and interactions essential to the genesis of phenotypic diversity may initially emerge by non-adaptive mechanisms.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3121905/" 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/PMC3121905/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fernandez, Ariel -- Lynch, Michael -- R01 GM036827/GM/NIGMS NIH HHS/ -- R01 GM036827-17S1/GM/NIGMS NIH HHS/ -- R01GM036827/GM/NIGMS NIH HHS/ -- R01GM072614/GM/NIGMS NIH HHS/ -- England -- Nature. 2011 May 18;474(7352):502-5. doi: 10.1038/nature09992.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Computer Science, The University of Chicago, Chicago, Illinois 60637, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21593762" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Caenorhabditis elegans ; Computational Biology ; Escherichia coli ; *Evolution, Molecular ; *Genetic Drift ; Hemoglobins/chemistry/metabolism ; Humans ; Hydrogen Bonding ; Metabolic Networks and Pathways/genetics/*physiology ; Models, Genetic ; Models, Molecular ; Phenotype ; Phylogeny ; Population Density ; Protein Binding ; Protein Conformation ; Proteins/chemistry/genetics/*metabolism ; Selection, Genetic ; Solubility ; Species Specificity ; Superoxide Dismutase/chemistry/metabolism ; Water/chemistry
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    N-linked glycosylation of folded proteins by the bacterial oligosaccharyltransferase (2006)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2006-11-18
    Description: N-linked protein glycosylation is found in all domains of life. In eukaryotes, it is the most abundant protein modification of secretory and membrane proteins, and the process is coupled to protein translocation and folding. We found that in bacteria, N-glycosylation can occur independently of the protein translocation machinery. In an in vitro assay, bacterial oligosaccharyltransferase glycosylated a folded endogenous substrate protein with high efficiency and folded bovine ribonuclease A with low efficiency. Unfolding the eukaryotic substrate greatly increased glycosylation. We propose that in the bacterial system, glycosylation sites are located in flexible parts of folded proteins, whereas the eukaryotic cotranslational glycosylation evolved to a mechanism presenting the substrate in a flexible form before folding.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kowarik, Michael -- Numao, Shin -- Feldman, Mario F -- Schulz, Benjamin L -- Callewaert, Nico -- Kiermaier, Eva -- Catrein, Ina -- Aebi, Markus -- New York, N.Y. -- Science. 2006 Nov 17;314(5802):1148-50.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Microbiology, Department of Biology, Eidgenossische Technische Hochschule (ETH) Zurich, 8093 Zurich, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17110579" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Bacterial Proteins/*metabolism ; Campylobacter jejuni ; Cattle ; Escherichia coli ; Glycoproteins/*metabolism ; Glycosylation ; Hexosyltransferases/metabolism ; Membrane Proteins/metabolism ; Molecular Sequence Data ; *Protein Folding ; Protein Transport ; Recombinant Proteins/metabolism
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    Common genetic variants modulate pathogen-sensing responses in human dendritic cells (2014)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2014-03-08
    Description: Little is known about how human genetic variation affects the responses to environmental stimuli in the context of complex diseases. Experimental and computational approaches were applied to determine the effects of genetic variation on the induction of pathogen-responsive genes in human dendritic cells. We identified 121 common genetic variants associated in cis with variation in expression responses to Escherichia coli lipopolysaccharide, influenza, or interferon-beta (IFN-beta). We localized and validated causal variants to binding sites of pathogen-activated STAT (signal transducer and activator of transcription) and IRF (IFN-regulatory factor) transcription factors. We also identified a common variant in IRF7 that is associated in trans with type I IFN induction in response to influenza infection. Our results reveal common alleles that explain interindividual variation in pathogen sensing and provide functional annotation for genetic variants that alter susceptibility to inflammatory diseases.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4124741/" 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/PMC4124741/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lee, Mark N -- Ye, Chun -- Villani, Alexandra-Chloe -- Raj, Towfique -- Li, Weibo -- Eisenhaure, Thomas M -- Imboywa, Selina H -- Chipendo, Portia I -- Ran, F Ann -- Slowikowski, Kamil -- Ward, Lucas D -- Raddassi, Khadir -- McCabe, Cristin -- Lee, Michelle H -- Frohlich, Irene Y -- Hafler, David A -- Kellis, Manolis -- Raychaudhuri, Soumya -- Zhang, Feng -- Stranger, Barbara E -- Benoist, Christophe O -- De Jager, Philip L -- Regev, Aviv -- Hacohen, Nir -- DP1 CA174427/CA/NCI NIH HHS/ -- DP1 MH100706/DP/NCCDPHP CDC HHS/ -- DP1 MH100706/MH/NIMH NIH HHS/ -- DP2 OD002230/OD/NIH HHS/ -- F32 AG043267/AG/NIA NIH HHS/ -- P30 DK043351/DK/NIDDK NIH HHS/ -- P50 HG006193/HG/NHGRI NIH HHS/ -- R01 AI091568/AI/NIAID NIH HHS/ -- R01 AR063759/AR/NIAMS NIH HHS/ -- R01 DK097768/DK/NIDDK NIH HHS/ -- R01 HG004037/HG/NHGRI NIH HHS/ -- RC2 GM093080/GM/NIGMS NIH HHS/ -- T32 GM007753/GM/NIGMS NIH HHS/ -- T32 HG002295/HG/NHGRI NIH HHS/ -- U19 AI082630/AI/NIAID NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2014 Mar 7;343(6175):1246980. doi: 10.1126/science.1246980.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24604203" target="_blank"〉PubMed〈/a〉
    Keywords: Adult ; Autoimmune Diseases/genetics ; Communicable Diseases/genetics ; Dendritic Cells/drug effects/*immunology ; Escherichia coli ; Female ; *Gene-Environment Interaction ; Genetic Loci ; Genome-Wide Association Study ; HEK293 Cells ; Host-Pathogen Interactions/*genetics ; Humans ; Influenza A virus ; Interferon Regulatory Factor-7/*genetics ; Interferon-beta/pharmacology ; Lipopolysaccharides/immunology ; Male ; Middle Aged ; Polymorphism, Single Nucleotide ; Quantitative Trait Loci ; STAT Transcription Factors/*genetics ; Transcriptome ; Young Adult
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    Control of cell fate by a deubiquitinating enzyme encoded by the fat facets gene (1995)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1995-12-15
    Description: Ubiquitin is a highly conserved polypeptide found in all eukaryotes. The major function of ubiquitin is to target proteins for complete or partial degradation by a multisubunit protein complex called the proteasome. Here, the Drosophila fat facets gene, which is required for the appropriate determination of particular cells in the fly eye, was shown to encode a ubiquitin-specific protease (Ubp), an enzyme that cleaves ubiquitin from ubiquitin-protein conjugates. The Fat facets protein (FAF) acts as a regulatory Ubp that prevents degradation of its substrate by the proteasome. Flies bearing fat facets gene mutations were used to show that a Ubp is cell type--and substrate-specific and a regulator of cell fate decisions in a multicellular organism.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Huang, Y -- Baker, R T -- Fischer-Vize, J A -- New York, N.Y. -- Science. 1995 Dec 15;270(5243):1828-31.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Zoology, University of Texas, Austin 78712, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8525378" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Base Sequence ; *Cell Differentiation/genetics ; Cysteine/metabolism ; Drosophila/embryology/enzymology/genetics ; Endopeptidases/genetics/*metabolism ; Escherichia coli ; Eye/embryology ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; Oligodeoxyribonucleotides ; Recombinant Fusion Proteins/genetics/metabolism ; Ubiquitins/*metabolism ; beta-Galactosidase/genetics
    Print ISSN: 0036-8075
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    Site-directed hydroxyl radical probing of the rRNA neighborhood of ribosomal protein S5 (1996)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1996-06-14
    Description: Cysteine residues were introduced into three different positions distributed on the surface of ribosomal protein S5, to serve as targets for derivatization with an Fe(II)-ethyl-enediaminetetraacetic acid linker. Hydroxyl radicals generated locally from the tethered Fe(II) in intermediate ribonucleoprotein particles or in 30S ribosomal subunits reconstituted from derivatized S5 caused cleavage of the RNA, resulting in characteristically different cleavage patterns for the three different tethering positions. These findings provide constraints for the three-dimensional folding of 16S ribosomal RNA (rRNA) and for the orientation of S5 in the 30S subunit, and they further suggest that antibiotic resistance and accuracy mutations in S5 may involve perturbation of 16S rRNA.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Heilek, G M -- Noller, H F -- New York, N.Y. -- Science. 1996 Jun 14;272(5268):1659-62.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Molecular Biology of RNA, Sinsheimer Laboratories, University of California, Santa Cruz 95064, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8658142" target="_blank"〉PubMed〈/a〉
    Keywords: Anti-Bacterial Agents/pharmacology ; Cloning, Molecular ; Cysteine/chemistry ; Edetic Acid/analogs & derivatives ; Escherichia coli ; Ferrous Compounds/chemistry ; Hydroxyl Radical/*chemistry ; Models, Molecular ; Molecular Probes ; Mutagenesis, Site-Directed ; Nucleic Acid Conformation ; Organometallic Compounds ; Protein Conformation ; RNA, Ribosomal/*chemistry ; RNA, Ribosomal, 16S/chemistry/drug effects ; Ribosomal Proteins/*chemistry/genetics ; Spectinomycin/pharmacology
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    DNA template and activator-coactivator requirements for transcriptional synergism by Drosophila bicoid (1995)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1995-12-15
    Description: The template and coactivator requirements for synergistic transcription directed by a single activator, Bicoid (BCD), bound to multiple sites have been determined. Mutagenesis studies in combination with protein binding experiments and reconstituted transcription reactions identified two independent activation domains of BCD that target different coactivator subunits (TAFII110 and TAFII60) of the basal transcription factor IID (TFIID). The presence of both coactivators is required for BCD to recruit the TATA binding protein (TBP)-TAF complex to the promoter and direct synergistic activation of transcription. Thus, contact between multiple activation domains of BCD and different targets within the TFIID complex can mediate transcriptional synergism.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sauer, F -- Hansen, S K -- Tjian, R -- New York, N.Y. -- Science. 1995 Dec 15;270(5243):1825-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California, Berkeley 94720-3204, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8525377" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Cell Line ; DNA/*metabolism ; DNA-Binding Proteins/genetics/metabolism ; Drosophila/*genetics/metabolism ; *Drosophila Proteins ; Enhancer Elements, Genetic ; Escherichia coli ; *Homeodomain Proteins ; Insect Hormones/genetics/*metabolism ; Juvenile Hormones/genetics/metabolism ; Mutagenesis ; Peptide Fragments/genetics/metabolism ; Promoter Regions, Genetic ; Protein Binding ; Recombinant Fusion Proteins/genetics/metabolism ; TATA-Box Binding Protein ; Templates, Genetic ; Trans-Activators/*metabolism ; Transcription Factor TFIID ; Transcription Factors/genetics/metabolism ; *Transcription, Genetic
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  • 46
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    Head-on collision between a DNA replication apparatus and RNA polymerase transcription complex (1995)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1995-02-24
    Description: An in vitro system reconstituted from purified proteins has been used to examine what happens when the DNA replication apparatus of bacteriophage T4 collides with an Escherichia coli RNA polymerase ternary transcription complex that is poised to move in the direction opposite to that of the moving replication fork. In the absence of a DNA helicase, the replication fork stalls for many minutes after its encounter with the RNA polymerase. However, when the T4 gene 41 DNA helicase is present, the replication fork passes the RNA polymerase after a pause of a few seconds. This brief pause is longer than the pause observed for a codirectional collision between the same two polymerases, suggesting that there is an inherent disadvantage to having replication and transcription directions oriented head to head. As for a codirectional collision, the RNA polymerase remains competent to resume faithful RNA chain elongation after the DNA replication fork passes; most strikingly, the RNA polymerase has switched from its original template strand to use the newly synthesized daughter DNA strand as the template.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Liu, B -- Alberts, B M -- GM-24020/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1995 Feb 24;267(5201):1131-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Biophysics, University of California, San Francisco 94143-0448.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7855590" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteriophage T4 ; Base Sequence ; DNA Helicases/metabolism ; *DNA Replication ; DNA, Bacterial/genetics/metabolism ; DNA, Circular/metabolism ; DNA, Viral/biosynthesis/genetics ; DNA-Directed DNA Polymerase/metabolism ; DNA-Directed RNA Polymerases/*metabolism ; Escherichia coli ; Molecular Sequence Data ; RNA, Messenger/*biosynthesis ; Replicon/*physiology ; Templates, Genetic ; *Transcription, Genetic
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  • 47
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    Identification of RANTES, MIP-1 alpha, and MIP-1 beta as the major HIV-suppressive factors produced by CD8+ T cells (1995)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1995-12-15
    Description: Evidence suggests that CD8+ T lymphocytes are involved in the control of human immunodeficiency virus (HIV) infection in vivo, either by cytolytic mechanisms or by the release of HIV-suppressive factors (HIV-SF). The chemokines RANTES, MIP-1 alpha, and MIP-1 beta were identified as the major HIV-SF produced by CD8+ T cells. Two active proteins purified from the culture supernatant of an immortalized CD8+ T cell clone revealed sequence identity with human RANTES and MIP-1 alpha. RANTES, MIP-1 alpha, and MIP-1 beta were released by both immortalized and primary CD8+ T cells. HIV-SF activity produced by these cells was completely blocked by a combination of neutralizing antibodies against RANTES, MIP-1 alpha, and MIP-1 beta. Recombinant human RANTES, MIP-1 alpha, and MIP-1 beta induced a dose-dependent inhibition of different strains of HIV-1, HIV-2, and simian immunodeficiency virus (SIV). These data may have relevance for the prevention and therapy of AIDS.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cocchi, F -- DeVico, A L -- Garzino-Demo, A -- Arya, S K -- Gallo, R C -- Lusso, P -- New York, N.Y. -- Science. 1995 Dec 15;270(5243):1811-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Tumor Cell Biology, National Cancer Institute, Bethesda, MD 20892, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8525373" target="_blank"〉PubMed〈/a〉
    Keywords: Adult ; Amino Acid Sequence ; Animals ; Antiviral Agents/*physiology ; CD8-Positive T-Lymphocytes/*immunology ; Cell Division/physiology ; Cell Line ; Cells, Cultured ; Chemokine CCL4 ; Chemokine CCL5/antagonists & inhibitors/*immunology ; Culture Media, Conditioned ; Cytokines/antagonists & inhibitors/*immunology ; Dose-Response Relationship, Immunologic ; Escherichia coli ; HIV Infections/immunology ; HIV-1/*immunology ; HIV-2/immunology ; Herpesvirus 6, Human/immunology ; Herpesvirus 7, Human/immunology ; Human T-lymphotropic virus 1/immunology ; Humans ; Immunoglobulin G/immunology ; Lymphocyte Activation ; Macaca nemestrina ; Macrophage Inflammatory Proteins ; Molecular Sequence Data ; Monokines/antagonists & inhibitors/*immunology ; Recombinant Proteins/immunology ; Simian Immunodeficiency Virus/immunology
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  • 48
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    Structural analysis of substrate binding by the molecular chaperone DnaK (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-06-14
    Description: DnaK and other members of the 70-kilodalton heat-shock protein (hsp70) family promote protein folding, interaction, and translocation, both constitutively and in response to stress, by binding to unfolded polypeptide segments. These proteins have two functional units: a substrate-binding portion binds the polypeptide, and an adenosine triphosphatase portion facilitates substrate exchange. The crystal structure of a peptide complex with the substrate-binding unit of DnaK has now been determined at 2.0 angstroms resolution. The structure consists of a beta-sandwich subdomain followed by alpha-helical segments. The peptide is bound to DnaK in an extended conformation through a channel defined by loops from the beta sandwich. An alpha-helical domain stabilizes the complex, but does not contact the peptide directly. This domain is rotated in the molecules of a second crystal lattice, which suggests a model of conformation-dependent substrate binding that features a latch mechanism for maintaining long lifetime complexes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhu, X -- Zhao, X -- Burkholder, W F -- Gragerov, A -- Ogata, C M -- Gottesman, M E -- Hendrickson, W A -- GM 34102/GM/NIGMS NIH HHS/ -- GM 37219/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1996 Jun 14;272(5268):1606-14.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Biophysics, College of Physicians and Surgeons, Columbia University, New York 10032, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8658133" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Chaperonins/chemistry/*metabolism ; Crystallography, X-Ray ; Escherichia coli ; *Escherichia coli Proteins ; HSP70 Heat-Shock Proteins/chemistry/*metabolism ; Models, Molecular ; Molecular Sequence Data ; Peptides/metabolism ; Protein Binding ; Protein Conformation ; Sequence Homology, Amino Acid
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    Crystal structure of DNA recombination protein RuvA and a model for its binding to the Holliday junction (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-10-18
    Description: The Escherichia coli DNA binding protein RuvA acts in concert with the helicase RuvB to drive branch migration of Holliday intermediates during recombination and DNA repair. The atomic structure of RuvA was determined at a resolution of 1.9 angstroms. Four monomers of RuvA are related by fourfold symmetry in a manner reminiscent of a four-petaled flower. The four DNA duplex arms of a Holliday junction can be modeled in a square planar configuration and docked into grooves on the concave surface of the protein around a central pin that may facilitate strand separation during the migration reaction. The model presented reveals how a RuvAB-junction complex may also accommodate the resolvase RuvC.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rafferty, J B -- Sedelnikova, S E -- Hargreaves, D -- Artymiuk, P J -- Baker, P J -- Sharples, G J -- Mahdi, A A -- Lloyd, R G -- Rice, D W -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 1996 Oct 18;274(5286):415-21.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Krebs Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Sheffield S10 2TN, UK. d.rice@sheffield.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8832889" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/*chemistry/metabolism ; Base Composition ; Crystallography, X-Ray ; DNA Helicases/metabolism ; DNA, Bacterial/chemistry/*metabolism ; DNA-Binding Proteins/*chemistry/metabolism ; Endodeoxyribonucleases/metabolism ; Escherichia coli ; *Escherichia coli Proteins ; Hydrogen Bonding ; Models, Molecular ; *Nucleic Acid Conformation ; Oligodeoxyribonucleotides/chemistry/metabolism ; *Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; *Recombination, Genetic
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    Enzymatic synthesis of a quorum-sensing autoinducer through use of defined substrates (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-06-14
    Description: Many bacteria, including several pathogens of plants and humans, use a pheromone called an autoinducer to regulate gene expression in a cell density-dependent manner. Agrobacterium autoinducer [AAI, N-(3-oxo-octanoyl)-L-homoserine lactone] of A. tumefaciens is synthesized by the Tral protein, which is encoded by the tumor-inducing plasmid. Purified hexahistidinyl-Tral (H6-Tral) used S-adenosylmethionine to make the homoserine lactone moiety of AAI, but did not use related compounds. H6-Tral used 3-oxo-octanoyl-acyl carrier protein to make the 3-oxo-octanoyl moiety of AAI, but did not use 3-oxo-octanoyl-coenzyme A. These results demonstrate the enzymatic synthesis of an autoinducer through the use of purified substrates.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉More, M I -- Finger, L D -- Stryker, J L -- Fuqua, C -- Eberhard, A -- Winans, S C -- GM42893/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1996 Jun 14;272(5268):1655-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Section of Microbiology, Cornell University, Ithaca, New York 14853, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8658141" target="_blank"〉PubMed〈/a〉
    Keywords: 3-Oxoacyl-(Acyl-Carrier-Protein) Synthase/antagonists & inhibitors/metabolism ; Acyl Carrier Protein/metabolism ; Agrobacterium tumefaciens/*genetics/metabolism ; Base Sequence ; Cerulenin/pharmacology ; Chromatography, Gel ; Chromatography, High Pressure Liquid ; Cloning, Molecular ; DNA Helicases/*metabolism ; DNA Primers ; Escherichia coli ; Escherichia coli Proteins ; Fatty Acids/metabolism ; *Gene Expression Regulation, Bacterial/drug effects ; Homoserine/*analogs & derivatives/biosynthesis ; Malonyl Coenzyme A/metabolism ; Molecular Sequence Data ; NADP/metabolism ; Plasmids ; S-Adenosylmethionine/metabolism
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    Context dependence of hydrogen bond free energy revealed by substitutions in an RNA hairpin (1992)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1992-04-20
    Description: Prediction and modeling of RNA structure requires knowledge of the free energy contributions of various interactions. Many unusual hydrogen bonds were recently proposed in the structure of a GCAA hairpin determined from nuclear magnetic resonance. The contributions of these hydrogen bonds to the folding stability of the hairpin formed by rGGCGCAAGCC have now been investigated through the use of functional group substitutions. These and previous results suggest a strong context dependence for the free energy of hydrogen bond formation. The results also suggest that the phylogenetic preference for GNRA (where N = A, C, G, or U and R = A or G) tetraloops may have a functional rather than thermodynamic basis.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉SantaLucia, J Jr -- Kierzek, R -- Turner, D H -- GM22939/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1992 Apr 10;256(5054):217-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of Rochester, NY 14627-0216.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1373521" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Calorimetry ; Drug Stability ; Escherichia coli ; Hydrogen Bonding ; Molecular Sequence Data ; *Nucleic Acid Conformation ; Oligodeoxyribonucleotides/*chemistry ; Phylogeny ; RNA/*chemistry ; RNA, Ribosomal, 16S/*genetics ; Thermodynamics
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    Toward a model for the interaction between elongation factor Tu and the ribosome (1993)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1993-02-26
    Description: In the elongation cycle of bacterial protein synthesis the interaction between elongation factor-Tu (EF-Tu).guanosine triphosphate (GTP), aminoacyl-transfer RNA (aa-tRNA), and messenger RNA-programmed ribosomes is associated with the hydrolysis of GTP. This interaction determines the selection of the proper aa-tRNA for incorporation into the polypeptide. In the canonical scheme, one molecule of GTP is hydrolyzed in the EF-Tu-dependent binding of aa-tRNA to the ribosome, and a second molecule is hydrolyzed in the elongation factor-G (EF-G)-mediated translocation of the polypeptide from the ribosomal A site to the P site. Substitution of Asp138 with Asn in EF-Tu changed the substrate specificity from GTP to xanthosine triphosphate and demonstrated that the EF-Tu-mediated reactions involved the hydrolysis of two nucleotide triphosphates for each Phe incorporated. This stoichiometry of two is associated with the binding of the correct aa-tRNA to the ribosome.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Weijland, A -- Parmeggiani, A -- New York, N.Y. -- Science. 1993 Feb 26;259(5099):1311-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉SDI n. 61840 du Centre National de la Recherche Scientifique, Laboratoire de Biochimie, Ecole Polytechnique, Palaiseau, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8446899" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/metabolism ; Base Sequence ; Escherichia coli ; GTP Phosphohydrolase-Linked Elongation Factors/metabolism ; GTP-Binding Proteins/metabolism ; Guanosine Triphosphate/*metabolism ; Models, Biological ; Molecular Sequence Data ; *Peptide Chain Elongation, Translational ; Peptide Elongation Factor Tu/*metabolism ; RNA, Transfer, Amino Acyl/metabolism ; Ribosomes/*metabolism
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  • 53
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    A covalent enzyme-substrate intermediate with saccharide distortion in a mutant T4 lysozyme (1993)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1993-12-24
    Description: The glycosyl-enzyme intermediate in lysozyme action has long been considered to be an oxocarbonium ion, although precedent from other glycosidases and theoretical considerations suggest it should be a covalent enzyme-substrate adduct. The mutation of threonine 26 to glutamic acid in the active site cleft of phage T4 lysozyme (T4L) produced an enzyme that cleaved the cell wall of Escherichia coli but left the product covalently bound to the enzyme. The crystalline complex was nonisomorphous with wild-type T4L, and analysis of its structure showed a covalent linkage between the product and the newly introduced glutamic acid 26. The covalently linked sugar ring was substantially distorted, suggesting that distortion of the substrate toward the transition state is important for catalysis, as originally proposed by Phillips. It is also postulated that the adduct formed by the mutant is an intermediate, consistent with a double displacement mechanism of action in which the glycosidic linkage is cleaved with retention of configuration as originally proposed by Koshland. The peptide part of the cell wall fragment displays extensive hydrogen-bonding interactions with the carboxyl-terminal domain of the enzyme, consistent with previous studies of mutations in T4L.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kuroki, R -- Weaver, L H -- Matthews, B W -- GM21967/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1993 Dec 24;262(5142):2030-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Molecular Biology, Howard Hughes Medical Institute, University of Oregon, Eugene 97403.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8266098" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Bacteriophage T4/*enzymology ; Binding Sites ; Carbohydrate Conformation ; Carbohydrate Sequence ; Cell Wall/*metabolism ; Chickens ; Disaccharides/*metabolism ; Egg White ; Escherichia coli ; Molecular Sequence Data ; Muramidase/*metabolism ; Mutation ; Oligopeptides/*metabolism ; Peptidoglycan
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    Biochemistry. Tinkering with acellular division (2008)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2008-05-10
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lutkenhaus, Joe -- R37GM09764/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2008 May 9;320(5877):755-6. doi: 10.1126/science.1158463.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, KS 66160, USA. jlutkenh@kumc.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18467579" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/physiology ; Cell Cycle Proteins/physiology ; *Cell-Free System ; Cytokinesis/*physiology ; Cytoskeletal Proteins/physiology ; Escherichia coli ; Escherichia coli Proteins/physiology
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    RNA Pol II accumulates at promoters of growth genes during developmental arrest (2009)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2009-03-03
    Description: When Caenorhabditis elegans larvae hatch from the egg case in the absence of food, their development is arrested (L1 arrest), and they show increased stress resistance until food becomes available. To study nutritional control of larval development, we analyzed growth and gene expression profiles during L1 arrest and recovery. Larvae that were fed responded relatively slowly to starvation compared with the rapid response of arrested larvae to feeding. Chromatin immunoprecipitation of RNA polymerase II (Pol II) followed by deep sequencing showed that during L1 arrest, Pol II continued transcribing starvation-response genes, but the enzyme accumulated on the promoters of growth and development genes. In response to feeding, promoter accumulation decreased, and elongation and messenger RNA levels increased. Therefore, accumulation of Pol II at promoters anticipates nutritionally controlled gene expression during C. elegans development.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Baugh, L Ryan -- Demodena, John -- Sternberg, Paul W -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2009 Apr 3;324(5923):92-4. doi: 10.1126/science.1169628. Epub 2009 Feb 26.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute and Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19251593" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Caenorhabditis elegans/*genetics/*growth & development/metabolism ; Chromatin Immunoprecipitation ; Cluster Analysis ; Escherichia coli ; Food ; Gene Expression Profiling ; *Gene Expression Regulation, Developmental ; Genes, Helminth ; Nutritional Physiological Phenomena ; Oligonucleotide Array Sequence Analysis ; Principal Component Analysis ; *Promoter Regions, Genetic ; RNA Polymerase II/*metabolism ; RNA, Helminth/genetics/metabolism ; RNA, Messenger/genetics/metabolism ; Signal Transduction ; Starvation ; Transcription, Genetic ; Up-Regulation
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    Endotoxin-induced structural transformations in liquid crystalline droplets (2011)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2011-05-21
    Description: The ordering of liquid crystals (LCs) is known to be influenced by surfaces and contaminants. Here, we report that picogram per milliliter concentrations of endotoxin in water trigger ordering transitions in micrometer-size LC droplets. The ordering transitions, which occur at surface concentrations of endotoxin that are less than 10(-5) Langmuir, are not due to adsorbate-induced changes in the interfacial energy of the LC. The sensitivity of the LC to endotoxin was measured to change by six orders of magnitude with the geometry of the LC (droplet versus slab), supporting the hypothesis that interactions of endotoxin with topological defects in the LC mediate the response of the droplets. The LC ordering transitions depend strongly on glycophospholipid structure and provide new designs for responsive soft matter.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3448959/" 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/PMC3448959/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lin, I-Hsin -- Miller, Daniel S -- Bertics, Paul J -- Murphy, Christopher J -- de Pablo, Juan J -- Abbott, Nicholas L -- CA105730/CA/NCI NIH HHS/ -- CA108467/CA/NCI NIH HHS/ -- R01 CA108467/CA/NCI NIH HHS/ -- R21 AI092004/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2011 Jun 10;332(6035):1297-300. doi: 10.1126/science.1195639. Epub 2011 May 19.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison, WI 53706-1607, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21596951" target="_blank"〉PubMed〈/a〉
    Keywords: Crystallization ; Endotoxins/*chemistry ; Escherichia coli ; Lipid A/chemistry ; Liquid Crystals/*chemistry ; Molecular Structure ; Surface Properties ; Water/*chemistry
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    C9orf72 repeat expansions cause neurodegeneration in Drosophila through arginine-rich proteins (2014)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2014-08-12
    Description: An expanded GGGGCC repeat in C9orf72 is the most common genetic cause of frontotemporal dementia and amyotrophic lateral sclerosis. A fundamental question is whether toxicity is driven by the repeat RNA itself and/or by dipeptide repeat proteins generated by repeat-associated, non-ATG translation. To address this question, we developed in vitro and in vivo models to dissect repeat RNA and dipeptide repeat protein toxicity. Expression of pure repeats, but not stop codon-interrupted "RNA-only" repeats in Drosophila caused adult-onset neurodegeneration. Thus, expanded repeats promoted neurodegeneration through dipeptide repeat proteins. Expression of individual dipeptide repeat proteins with a non-GGGGCC RNA sequence revealed that both poly-(glycine-arginine) and poly-(proline-arginine) proteins caused neurodegeneration. These findings are consistent with a dual toxicity mechanism, whereby both arginine-rich proteins and repeat RNA contribute to C9orf72-mediated neurodegeneration.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mizielinska, Sarah -- Gronke, Sebastian -- Niccoli, Teresa -- Ridler, Charlotte E -- Clayton, Emma L -- Devoy, Anny -- Moens, Thomas -- Norona, Frances E -- Woollacott, Ione O C -- Pietrzyk, Julian -- Cleverley, Karen -- Nicoll, Andrew J -- Pickering-Brown, Stuart -- Dols, Jacqueline -- Cabecinha, Melissa -- Hendrich, Oliver -- Fratta, Pietro -- Fisher, Elizabeth M C -- Partridge, Linda -- Isaacs, Adrian M -- 089701/Wellcome Trust/United Kingdom -- 098565/Wellcome Trust/United Kingdom -- G0701441/Medical Research Council/United Kingdom -- G1000287/Medical Research Council/United Kingdom -- MR/J004022/1/Medical Research Council/United Kingdom -- Wellcome Trust/United Kingdom -- Medical Research Council/United Kingdom -- New York, N.Y. -- Science. 2014 Sep 5;345(6201):1192-4. doi: 10.1126/science.1256800. Epub 2014 Aug 7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Neurodegenerative Disease, UCL Institute of Neurology, London WC1N 3BG, UK. ; Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany. ; Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany. Department of Genetics, Evolution and Environment, Institute of Healthy Ageing, University College London, London WC1E 6BT, UK. ; Department of Neurodegenerative Disease, UCL Institute of Neurology, London WC1N 3BG, UK. Department of Genetics, Evolution and Environment, Institute of Healthy Ageing, University College London, London WC1E 6BT, UK. ; Department of Neurodegenerative Disease, UCL Institute of Neurology, London WC1N 3BG, UK. MRC Prion Unit, UCL Institute of Neurology, London WC1N 3BG, UK. ; Institute of Brain, Behaviour and Mental Health, Faculty of Human and Medical Sciences, University of Manchester, Manchester M13 9PT, UK. ; Department of Genetics, Evolution and Environment, Institute of Healthy Ageing, University College London, London WC1E 6BT, UK. ; Department of Neurodegenerative Disease, UCL Institute of Neurology, London WC1N 3BG, UK. MRC Centre for Neuromuscular Disease, UCL Institute of Neurology, London WC1N 3BG, UK. ; Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany. Department of Genetics, Evolution and Environment, Institute of Healthy Ageing, University College London, London WC1E 6BT, UK. a.isaacs@prion.ucl.ac.uk l.partridge@ucl.ac.uk. ; Department of Neurodegenerative Disease, UCL Institute of Neurology, London WC1N 3BG, UK. a.isaacs@prion.ucl.ac.uk l.partridge@ucl.ac.uk.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25103406" target="_blank"〉PubMed〈/a〉
    Keywords: Amyotrophic Lateral Sclerosis/*genetics/pathology ; Animals ; Cell Line, Tumor ; DNA Repeat Expansion/*genetics ; Dipeptides/metabolism ; Disease Models, Animal ; Drosophila melanogaster/*genetics ; Escherichia coli ; Frontotemporal Dementia/*genetics/pathology ; Humans ; Neurons/metabolism/pathology ; Proteins/*genetics
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    Mechanism of the C5 stereoinversion reaction in the biosynthesis of carbapenem antibiotics (2014)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2014-03-08
    Description: The bicyclic beta-lactam/2-pyrrolidine precursor to all carbapenem antibiotics is biosynthesized by attachment of a carboxymethylene unit to C5 of L-proline followed by beta-lactam ring closure. Carbapenem synthase (CarC), an Fe(II) and 2-(oxo)glutarate (Fe/2OG)-dependent oxygenase, then inverts the C5 configuration. Here we report the structure of CarC in complex with its substrate and biophysical dissection of its reaction to reveal the stereoinversion mechanism. An Fe(IV)-oxo intermediate abstracts the hydrogen (H*) from C5, and tyrosine 165, a residue not visualized in the published structures of CarC lacking bound substrate, donates H* to the opposite face of the resultant radical. The reaction oxidizes the Fe(II) cofactor to Fe(III), limiting wild-type CarC to one turnover, but substitution of the H*-donating tyrosine disables stereoinversion and confers to CarC the capacity for catalytic substrate oxidation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4160820/" 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/PMC4160820/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chang, Wei-chen -- Guo, Yisong -- Wang, Chen -- Butch, Susan E -- Rosenzweig, Amy C -- Boal, Amie K -- Krebs, Carsten -- Bollinger, J Martin Jr -- GM 058518/GM/NIGMS NIH HHS/ -- GM 069657/GM/NIGMS NIH HHS/ -- GM 100011/GM/NIGMS NIH HHS/ -- R01 GM069657/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2014 Mar 7;343(6175):1140-4. doi: 10.1126/science.1248000.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24604200" target="_blank"〉PubMed〈/a〉
    Keywords: Carbapenems/*biosynthesis/*chemistry ; Catalysis ; Crystallography, X-Ray ; Enzymes/*chemistry/genetics ; Escherichia coli ; Hydrogen/chemistry ; Oxidation-Reduction ; Pectobacterium carotovorum/*enzymology ; Stereoisomerism ; Tyrosine/chemistry
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    ARTIFICIAL PHOTOSYNTHESIS. More efficient together (2015)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2015-11-14
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhang, Tian -- New York, N.Y. -- Science. 2015 Nov 13;350(6262):738-9. doi: 10.1126/science.aad6452.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2970 Horsholm, Denmark. zhang@biosustain.dtu.dk.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26564832" target="_blank"〉PubMed〈/a〉
    Keywords: Carbon Dioxide/chemistry ; *Chemistry Techniques, Synthetic ; Chemistry, Bioinorganic ; Escherichia coli ; Methanosarcina ; *Photosynthesis ; *Solar Energy
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    Operon structure and cotranslational subunit association direct protein assembly in bacteria (2015)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2015-09-26
    Description: Assembly of protein complexes is considered a posttranslational process involving random collision of subunits. We show that within the Escherichia coli cytosol, bacterial luciferase subunits LuxA and LuxB assemble into complexes close to the site of subunit synthesis. Assembly efficiency decreases markedly if subunits are synthesized on separate messenger RNAs from genes integrated at distant chromosomal sites. Subunit assembly initiates cotranslationally on nascent LuxB in vivo. The ribosome-associated chaperone trigger factor delays the onset of cotranslational interactions until the LuxB dimer interface is fully exposed. Protein assembly is thus directly coupled to the translation process and involves spatially confined, actively chaperoned cotranslational subunit interactions. Bacterial gene organization into operons therefore reflects a fundamental cotranslational mechanism for spatial and temporal regulation that is vital to effective assembly of protein complexes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shieh, Yu-Wei -- Minguez, Pablo -- Bork, Peer -- Auburger, Josef J -- Guilbride, D Lys -- Kramer, Gunter -- Bukau, Bernd -- New York, N.Y. -- Science. 2015 Nov 6;350(6261):678-80. doi: 10.1126/science.aac8171. Epub 2015 Sep 24.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Molecular Biology of the University of Heidelberg (ZMBH) and German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, Heidelberg D-69120, Germany. ; European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany. ; European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany. Max-Delbruck-Centre for Molecular Medicine, Robert-Rossle-Strasse 10, 13125 Berlin, Germany. ; Center for Molecular Biology of the University of Heidelberg (ZMBH) and German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, Heidelberg D-69120, Germany. Malaria Research Foundation, Post Office Box 10420, Aspen, CO 81612, USA. ; Center for Molecular Biology of the University of Heidelberg (ZMBH) and German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, Heidelberg D-69120, Germany. bukau@zmbh.uni-heidelberg.de g.kramer@zmbh.uni-heidelberg.de.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26405228" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteria/*genetics/*metabolism ; Bacterial Proteins/chemistry/genetics/metabolism ; Escherichia coli ; *Gene Order ; Genes, Bacterial ; Green Fluorescent Proteins/chemistry/genetics/metabolism ; Luciferases, Bacterial/chemistry/*genetics/*metabolism ; Luminescent Proteins/chemistry/genetics/metabolism ; Molecular Chaperones/metabolism ; *Operon ; Protein Biosynthesis ; Protein Structure, Secondary ; Protein Subunits/chemistry/deficiency/genetics/metabolism ; RNA, Messenger/metabolism ; Recombinant Fusion Proteins/chemistry/genetics/metabolism ; Ribosomes/metabolism ; Vibrio/enzymology
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    Conformational changes in 16S ribosomal RNA induced by 30S ribosomal subunit proteins from Escherichia coli (1978)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1978-12-01
    Description: Laser light scattering has been used to evaluate conformational differences between free 16S RNA and several specific protein-16S RNA complexes. Proteins that interact strongly with the 16S RNA early in subunit assembly stabilize the RNA chain against unfolding in 1 mM Mg2+ and actually promote the formation of a more compact teriary structure in 20 mM Mg2+. A vital function of these proteins may therfore consist in altering the configuration of the RNA so that further assembly reactions can take place.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bogdanov, A A -- Zimmermann, R A -- Wang, C C -- Ford, N C Jr -- New York, N.Y. -- Science. 1978 Dec 1;202(4371):999-1001.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/362531" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins ; Diffusion ; Escherichia coli ; Nucleic Acid Conformation ; Protein Binding ; RNA, Bacterial ; *RNA, Ribosomal ; Ribonucleoproteins ; *Ribosomal Proteins ; Ribosomes/*ultrastructure
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    Expression of a bacterial gene in mammalian cells (1980)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1980-09-19
    Description: Transfection of cultured monkey kidney cells with recombinant DNA constructed with a cloned Escherichia coli gene that codes for xanthine-guanine phosphoribosyltransferase and several different SV40 DNA-based vectors, results in the synthesis of readily measurable quantities of the bacterial enzyme. Moreover, the physiological defect in purine nucleotide synthesis characteristic of human Lesch-Nyhan cells can be overcome by the introduction of the bacterial gene into these cells.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mulligan, R C -- Berg, P -- New York, N.Y. -- Science. 1980 Sep 19;209(4463):1422-7.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/6251549" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cells, Cultured ; Cloning, Molecular/methods ; DNA, Bacterial/*genetics ; *DNA, Recombinant ; Escherichia coli ; *Genes ; Haplorhini ; Humans ; Hypoxanthine Phosphoribosyltransferase/genetics ; Lesch-Nyhan Syndrome/*genetics ; Pentosyltransferases/*genetics ; Simian virus 40/genetics ; Transduction, Genetic ; Transformation, Genetic
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    Isolation of mutants of an animal virus in bacteria (1980)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1980-09-19
    Description: Mutants of animal viruses can be isolated in bacteria by recombinant DNA methods. Since no viral functions are required for propagation of recombinants in bacteria, viral mutants with lethal changes in cis- or trans-acting elements can be isolated, as well as partially or conditionally defective mutants. In the cases of viruses with small DNA genomes, such as the tumorigenic simian virus 40 (SV40), the entire viral DNA can be inserted into the bacterial plasmid pBR322 and cloned in Escherichia coli. Recombinant plasmids with a single copy of SV40 DNA cause morphological transformation of mouse cells in culture with the same efficiency as SV40 DNA isolated from virus-infected monkey cells, but the recombinant DNA is noninfectious and replicates poorly in permissive cells. However, SV40 DNA excised from the plasmid replicates as well as authentic viral DNA and is fully infectious. SV40 mutants with small deletions or base substitutions have been isolated by in vitro site-specific or random local mutagenesis of recombinant DNA followed by cloning in E. coli. Many of the mutants thus isolated are defective in specific viral functions.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Peden, K W -- Pipas, J M -- Pearson-White, S -- Nathans, D -- New York, N.Y. -- Science. 1980 Sep 19;209(4463):1392-6.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/6251547" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antigens, Neoplasm/*genetics ; Antigens, Viral/genetics ; Cell Transformation, Viral ; Cells, Cultured ; Chromosome Deletion ; DNA, Recombinant ; DNA, Viral/*genetics ; Escherichia coli ; *Mutation ; Simian virus 40/*genetics ; Viral Proteins/*genetics ; Virus Replication
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    Rabies virus glycoprotein analogs: biosynthesis in Escherichia coli (1983)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1983-02-11
    Description: The surface of rabies virus is composed of an approximately 60,000 dalton glycoprotein, in which most of the antigenic and immunogenic determinants of the virus reside. We have constructed plasmids for the direct expression in Escherichia coli of the mature full length rabies glycoprotein gene and also for the expression of a glycoprotein gene which has been truncated to exclude the coding region for a hydrophobic, possibly transmembrane, domain of the protein. Escherichia coli harboring the plasmids synthesize analog proteins which conform by several biochemical and antigenic criteria to rabies glycoprotein.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yelverton, E -- Norton, S -- Obijeski, J F -- Goeddel, D V -- New York, N.Y. -- Science. 1983 Feb 11;219(4585):614-20.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/6297004" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Cloning, Molecular ; Escherichia coli ; Genes, Viral ; Genetic Vectors ; Glycoproteins/*genetics/immunology ; Plasmids ; Rabies virus/*genetics/immunology ; Viral Proteins/immunology
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    Sedimentation field flow fractionation of DNA's (1984)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1984-07-27
    Description: Sedimentation field flow fractionation (SFFF) is a method for purifying and providing mass or size distribution information on samples containing particulates or soluble macromolecules. Since SFFF separations are based on simple physical phenomena related to first principles, molecular weight (or particle sizes) can be determined without calibration standards. SFFF is a gentle technique suited for fractionating biomolecules. Studies with the fragile lambda DNA (molecular weight, 33 X 10(6] and smaller supercoiled plasmids have shown that these materials are not altered during SFFF separation; molecular weights and conformation remain unchanged, and biological activity is not reduced. Recoveries of nucleic acids approach 100 percent. Typically, components with about 20 percent difference in mass can be separated essentially to baseline if required. Fractionation time is usually independent of molecular weight, and separations often can be carried out within an hour.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schallinger, L E -- Yau, W W -- Kirkland, J J -- New York, N.Y. -- Science. 1984 Jul 27;225(4660):434-7.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/6377495" target="_blank"〉PubMed〈/a〉
    Keywords: Chemical Fractionation ; DNA/*isolation & purification ; DNA, Bacterial/isolation & purification ; DNA, Recombinant/isolation & purification ; DNA, Superhelical/isolation & purification ; Escherichia coli ; Molecular Conformation ; Molecular Weight ; Particle Size
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    Differential breakdown of phylogenetically diverse ribosomal RNA's inserted via liposomes into mammalian cells (1982)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1982-07-02
    Description: Liposomes were used to deliver ribosomal RNA's from the different organisms into cultivated mouse plasmacytoma cells. Ribosomal RNA from Escherichia coli was degraded intracellularly within 1 hour, whereas mouse and yeast ribosomal RNA's were degraded more slowly. This indicates that cells can discriminated between different ribosomal RNA's.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lavelle, D -- Ostro, M J -- Giacomoni, D -- GM 27935/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1982 Jul 2;217(4554):59-61.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/6178157" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Line ; Escherichia coli ; Kinetics ; *Liposomes ; Mice ; Molecular Weight ; Neoplasms, Experimental/metabolism ; Plasmacytoma/*metabolism ; RNA, Bacterial/metabolism ; RNA, Ribosomal/*metabolism ; Saccharomyces cerevisiae ; Species Specificity
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    Endotoxin-stimulated opioid peptide secretion: two secretory pools and feedback control in vivo (1982)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1982-08-27
    Description: Small doses of endotoxin evoked a dramatic biphasic response of opioid peptide secretion into blood in sheep. The first phase began within minutes and coincided with a brief hypertensive response to endotoxin well before the appearance of fever or hypotension. The ratio of beta-endorphin to beta-lipotropin fell abruptly at the onset of the second phase of release, suggesting early depletion of a pool rich in beta-endorphin and subsequent emergence of a pool rich in unprocessed precursor. The concentration of cerebrospinal fluid opioids increased tenfold during the second phase. Naloxone administration augmented endotoxin-induced opioid secretion in both early and late phases, suggesting a short-loop feedback regulation of stress-induced endorphin secretion.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Carr, D B -- Bergland, R -- Hamilton, A -- Blume, H -- Kasting, N -- Arnold, M -- Martin, J B -- Rosenblatt, M -- AM 07028-06/AM/NIADDK NIH HHS/ -- AM 26252/AM/NIADDK NIH HHS/ -- New York, N.Y. -- Science. 1982 Aug 27;217(4562):845-8.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/6285473" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Blood Pressure/drug effects ; Endorphins/blood/cerebrospinal fluid/*secretion ; Endotoxins/*pharmacology ; Escherichia coli ; Feedback ; Kinetics ; Naloxone/pharmacology ; Peptide Fragments/blood/cerebrospinal fluid ; Sheep ; beta-Endorphin
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    Binding of cis- and trans-dichlorodiammineplatinum(II) to DNA: evidence for unwinding and shortening of the double helix (1979)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1979-03-09
    Description: The antitumor drug cis-dichlorodiammineplatinum(II) (cis-DDP) and the inactive trans isomer bind and produce cooperative changes in closed and nicked circular duplex DNA's. Covalent binding of both platinum complexes to the closed circular DNA alters the degree of supercoiling, presumably by disrupting and unwinding the double helix. Electron micrographs show the platinated DNA's to be shortened by up to 50 percent of their original length. At similar ratios of bound platinum per nucleotide, the electrophoretic mobilities of the DNA's in gels containing the dye ethidium bromide are the same for both isomers. The only detectable difference in the binding of the two platinum isomers is an increase in the electrophoretic mobility in nondye gels of closed circular DNA having small amounts of bound cis-DDP that is not apparent for the trans complex.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cohen, G L -- Bauer, W R -- Barton, J K -- Lippard, S J -- New York, N.Y. -- Science. 1979 Mar 9;203(4384):1014-6.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/370979" target="_blank"〉PubMed〈/a〉
    Keywords: Cisplatin/*metabolism/pharmacology ; DNA/*metabolism ; DNA, Circular/metabolism ; DNA, Superhelical/metabolism ; Electrophoresis ; Escherichia coli ; Isomerism ; Nucleic Acid Conformation/drug effects ; Plasmids
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    Effect of interferon-alpha 1 from E. coli on some cell functions (1980)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1980-09-19
    Description: Interferon-alpha 1 from Escherichia coli transformed with a hybrid plasmid containing a human leukocyte complementary DNA insert, induces resistance to virus in appropriate target cells. It also shares the following properties with natural leukocyte interferon (IFN). (i) It enhances natural killing activity of human lymphocytes, (ii) it enhances antibody-dependent cell-mediated cytotoxicity, (iii) it suppresses antigen- and mitogen-induced leukocyte migration inhibition, (iv) it inhibits growth of IFN-sensitive Burkitt lymphoma cells. Since these activities are exhibited by a cloned protein species, they are due to IFN itself and not to other human proteins.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Masucci, M G -- Szigeti, R -- Klein, E -- Klein, G -- Gruest, J -- Montagnier, L -- Taira, H -- Hall, A -- Nagata, S -- Weissmann, C -- New York, N.Y. -- Science. 1980 Sep 19;209(4463):1431-5.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/6158096" target="_blank"〉PubMed〈/a〉
    Keywords: Antibody-Dependent Cell Cytotoxicity/drug effects ; Cell Division/drug effects ; Cell Migration Inhibition ; Cloning, Molecular ; *DNA, Recombinant ; Escherichia coli ; Humans ; Hypersensitivity, Delayed/immunology ; Immunity, Cellular/drug effects ; Interferons/genetics/*pharmacology ; Structure-Activity Relationship
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    Cytotaxins after the sedimentation behavior of human granulocytes (1979)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1979-08-31
    Description: Human granulocytes from the peripheral blood of healthy donors were subjected to transient gravity sedimentation analysis in Ficoll density gradient columns (37 degrees C) containing different concentrations of Escherichia coli endotoxin-activated serum and medium 199. A dramatic serum concentration-dependent dispersion of the cells based on changes in sedimentation velocity was observed as a function of time, using a new optical scanning instrument. The phenomenon was virtually abolished in the presence of cytochalasin B, a known inhibitor of cellular chemotaxis. The width (second statistical moment) of the sedimenting cell distribution increased in a sigmoid fashion as a function of time regardless of cytotaxin concentration. This indicates that a slow and nonlinear response of the granulocytes to the cytotaxins occurs. This new kinetic method should be useful in examining an alternate manifestation of the chemoresponsiveness of phagocytic cells and of cell interactions in general.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Catsimpoolas, N -- Kurtz, S R -- Skrabut, E M -- Griffith, A L -- Valeri, C R -- New York, N.Y. -- Science. 1979 Aug 31;205(4409):936-7.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/382355" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Toxins/pharmacology ; Centrifugation, Density Gradient/methods ; Cytochalasin B/*pharmacology ; Endotoxins/*pharmacology ; Escherichia coli ; Granulocytes/cytology/*drug effects ; Humans
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    Characterization by tandem mass spectrometry of structural modifications in proteins (1987)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1987-08-28
    Description: Tandem mass spectrometry can be used to solve a number of protein structural problems that are not amenable to conventional methods for amino acid sequencing. Typical problems that use this approach involve characterization of peptides with blocked amino termini or peptides that have been otherwise posttranslationally processed, such as, by phosphorylation or sulfation. The structure and homogeneity of synthetic peptides can also be evaluated. Since peptides can be selectively characterized in the presence of other peptides or contaminants, the need for extensive purification is reduced or eliminated.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Biemann, K -- Scoble, H A -- GM05472/GM/NIGMS NIH HHS/ -- RR00317/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 1987 Aug 28;237(4818):992-8.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3303336" target="_blank"〉PubMed〈/a〉
    Keywords: *Amino Acid Sequence ; Amino Acyl-tRNA Synthetases ; Escherichia coli ; Humans ; *Mass Spectrometry ; Phosphorylation ; Protein Processing, Post-Translational ; Proteins ; Saccharomyces cerevisiae
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    Molecular cloning and expression of a human B-cell growth factor gene in Escherichia coli (1987)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1987-03-20
    Description: A human B-cell growth factor (BCGF) (12 kilodaltons) supports the clonal proliferation of B lymphocytes. A clone was isolated that contained the proper structural sequence to encode biologically active, 12-kilodalton BCGF in Escherichia coli and to hybridize to a specific messenger RNA, identified by in vitro translation in Xenopus laevis oocytes. A relatively hydrophobic region of 18 amino acids was found at the amino terminal of the 124-amino acid-long polypeptide. The carboxyl terminal is composed of at least 32 amino acids that are derived from nucleotide sequences bearing significant homology to the Alu repeat family.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sharma, S -- Mehta, S -- Morgan, J -- Maizel, A -- 16672/PHS HHS/ -- CA38499/CA/NCI NIH HHS/ -- CA39798/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 1987 Mar 20;235(4795):1489-92.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3547651" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; B-Lymphocytes/*physiology ; Base Sequence ; Cloning, Molecular ; DNA/genetics ; Escherichia coli ; Gene Expression Regulation ; Growth Substances/*genetics ; Interleukin-4 ; Lymphokines/*genetics ; Repetitive Sequences, Nucleic Acid ; Sequence Homology, Nucleic Acid
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  • 73
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    Activation of adenovirus promoters by the adenovirus E1A protein in cell-free extracts (1987)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1987-08-28
    Description: The primary product of the adenovirus E1A gene is a protein that is sufficient for controlling host-cell proliferation and immortalizing primary rodent cells. The mechanism by which the protein induces these cellular effects is poorly understood, but might be linked to its ability to regulate RNA transcription from a number of viral and cellular genes. The mechanism of E1A's transcriptional-activation (trans-activation) was studied here by monitoring the protein's effect on specific adenovirus promoters in two types of transcriptional systems in vitro. One of these systems consisted of extracts from transformed cells constitutively expressing E1A, and the other consisted of extracts of HeLa cells supplemented with a plasmid-encoded E1A protein purified from Escherichia coli. The results show that the E1A protein specifically stimulates transcription from adenovirus promoters; thus, the induction of cellular transcription factors is not necessary to explain the stimulation of transcription by E1A.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Spangler, R -- Bruner, M -- Dalie, B -- Harter, M L -- CA 28414/CA/NCI NIH HHS/ -- CA00978/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 1987 Aug 28;237(4818):1044-6.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2956686" target="_blank"〉PubMed〈/a〉
    Keywords: Adenoviridae/*genetics ; Adenovirus Early Proteins ; Cell-Free System ; Escherichia coli ; HeLa Cells ; Humans ; Oncogene Proteins, Viral/*pharmacology ; Promoter Regions, Genetic/*drug effects ; Virus Activation/drug effects
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    Passive immunization against cachectin/tumor necrosis factor protects mice from lethal effect of endotoxin (1985)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1985-08-30
    Description: A highly specific polyclonal rabbit antiserum directed against murine cachectin/tumor necrosis factor (TNF) was prepared. When BALB/c mice were passively immunized with the antiserum or with purified immune globulin, they were protected against the lethal effect of the endotoxin lipopolysaccharide produced by Escherichia coli. The prophylactic effect was dose-dependent and was most effective when the antiserum was administered prior to the injection of the endotoxin. Antiserum to cachectin/TNF did not mitigate the febrile response of endotoxin-treated animals, and very high doses of endotoxin could overcome the protective effect. The median lethal dose of endotoxin in mice pretreated with 50 microliters of the specific antiserum was approximately 2.5 times greater the median lethal dose for controls given nonimmune serum. The data suggest that cachectin/TNF is one of the principal mediators of the lethal effect of endotoxin.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Beutler, B -- Milsark, I W -- Cerami, A C -- AM01314/AM/NIADDK NIH HHS/ -- New York, N.Y. -- Science. 1985 Aug 30;229(4716):869-71.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3895437" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Endotoxins/*toxicity ; Escherichia coli ; Female ; Glycoproteins/immunology/*physiology ; Immune Sera ; Immunization, Passive ; Lethal Dose 50 ; Lipopolysaccharides/*toxicity ; Mice ; Mice, Inbred BALB C ; Proteins/immunology/*physiology ; Tumor Necrosis Factor-alpha
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    Enzymatic amplification of beta-globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia (1985)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1985-12-20
    Description: Two new methods were used to establish a rapid and highly sensitive prenatal diagnostic test for sickle cell anemia. The first involves the primer-mediated enzymatic amplification of specific beta-globin target sequences in genomic DNA, resulting in the exponential increase (220,000 times) of target DNA copies. In the second technique, the presence of the beta A and beta S alleles is determined by restriction endonuclease digestion of an end-labeled oligonucleotide probe hybridized in solution to the amplified beta-globin sequences. The beta-globin genotype can be determined in less than 1 day on samples containing significantly less than 1 microgram of genomic DNA.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Saiki, R K -- Scharf, S -- Faloona, F -- Mullis, K B -- Horn, G T -- Erlich, H A -- Arnheim, N -- New York, N.Y. -- Science. 1985 Dec 20;230(4732):1350-4.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2999980" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Anemia, Sickle Cell/*diagnosis/genetics ; Base Sequence ; Clinical Laboratory Techniques ; DNA Restriction Enzymes ; DNA-Directed DNA Polymerase ; Escherichia coli ; *Gene Amplification ; Globins/*genetics ; Humans ; Nucleic Acid Hybridization ; Polymorphism, Genetic
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    Abnormal proteins serve as eukaryotic stress signals and trigger the activation of heat shock genes (1986)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1986-04-25
    Description: Heat shock protein (hsp) genes, a group of ubiquitous genes, are activated by various metabolic stresses. The suggestion that denaturation of intracellular proteins may be produced by the metabolic stresses and then signal the activation of the hsp genes was examined by co-injection of purified proteins and hsp genes into frog oocytes. Activation of hsp genes was observed if the proteins were denatured prior to injection but not if they were introduced in their native form. Furthermore, the activation of hsp genes by abnormal proteins and by heat shock appears to occur by a common mechanism. A model for the transcriptional regulation of the genes is based on competition for degradation between abnormal intracellular proteins and a labile regulatory factor.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ananthan, J -- Goldberg, A L -- Voellmy, R -- GM31125/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1986 Apr 25;232(4749):522-4.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3083508" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Drosophila melanogaster ; Escherichia coli ; *Gene Expression Regulation/drug effects ; Genes ; Globins/pharmacology ; Heat-Shock Proteins/*genetics/physiology ; Hot Temperature ; Oocytes/metabolism ; Proteins/pharmacology/*physiology ; Xenopus laevis
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    Pertussis toxin inhibition of B cell and macrophage responses to bacterial lipopolysaccharide (1986)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1986-11-07
    Description: Lipopolysaccharide, a component of the outer membrane of Gram-negative bacteria, activates B lymphocytes and macrophages. Pertussis toxin, which inactivates several members of the G protein family of signaling components, including Gi and transducin, was found to inhibit the lipopolysaccharide-induced responses of the WEHI-231 B lymphoma cell line and the P388D1 macrophage cell line. These results, combined with the demonstration that lipopolysaccharide inhibits adenylate cyclase activity in P388D1 cells, strongly argues that lipopolysaccharide activation of cells is mediated by a Gi-like receptor-effector coupling protein.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jakway, J P -- DeFranco, A L -- AI-20038/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 1986 Nov 7;234(4777):743-6.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3095921" target="_blank"〉PubMed〈/a〉
    Keywords: *Adenylate Cyclase Toxin ; Antibodies, Anti-Idiotypic/immunology ; B-Lymphocytes/*physiology ; Cell Line ; Dose-Response Relationship, Drug ; Escherichia coli ; GTP-Binding Proteins/*physiology ; Immunoglobulin M/immunology ; Interleukin-1/metabolism ; Lipopolysaccharides/*antagonists & inhibitors/immunology ; Lymphocyte Activation/drug effects ; Macrophage Activation/drug effects ; Macrophages/*physiology ; *Pertussis Toxin ; Virulence Factors, Bordetella/*pharmacology
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    Natural abundances of carbon isotopes in acetate from a coastal marine sediment (1987)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1987-04-03
    Description: Measurements of the natural abundances of carbon isotopes were made in acetate samples isolated from the anoxic marine sediment of Cape Lookout Bight, North Carolina. The typical value of the total acetate carbon isotope ratio (delta 13C) was -16.1 +/- 0.2 per mil. The methyl and carboxyl groups were determined to be -26.4 +/- 0.3 and -6.0 +/- 0.3 per mil, respectively, for one sample. The isotopic composition of the acetate is thought to have resulted from isotopic discriminations that occurred during the cycling of that molecule. Measurements of this type, which have not been made previously in the natural environment, may provide information about the dominant microbial pathways in anoxic sediments as well as the processes that influence the carbon isotopic composition of biogenic methane from many sources.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Blair, N E -- Martens, C S -- Des Marais, D J -- OCE82-08666/CE/NCIPC CDC HHS/ -- New York, N.Y. -- Science. 1987 Apr 3;236:66-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Marine, Earth, and Atmospheric Sciences, North Carolina State University, Raleigh 27695, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11539717" target="_blank"〉PubMed〈/a〉
    Keywords: Acetates/analysis/*chemistry/metabolism ; Acetobacter ; Carbon/*analysis/chemistry/metabolism ; Carbon Isotopes ; Clostridium ; *Environmental Microbiology ; Escherichia coli ; Geologic Sediments/*chemistry ; Marine Biology ; Methane/analysis/chemistry/metabolism ; North Carolina
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  • 79
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    Structure of the GDP domain of EF-Tu and location of the amino acids homologous to ras oncogene proteins (1985)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1985-10-04
    Description: A 2.7 angstrom resolution x-ray diffraction analysis of a trypsin-modified form of the Escherichia coli elongation factor Tu reveals that the GDP-binding domain has a structure similar to that of other nucleotide-binding proteins. The GDP ligand is located at the COOH-terminal end of the beta sheet and is linked to the protein via a Mg2+ ion salt bridge. The location of the guanine ring is unusual; the purine ring is located on the outer edge of the domain, not deep within a hydrophobic pocket. The amino acids from Pro10 to Arg44 and from Gly59 to Glu190 have been assigned to the electron density with computer graphic techniques, and the resulting model is consistent with all known biochemical data. An analysis of the structure reveals that four regions of the amino acid sequence that are homologous with the family of ras oncogene proteins, termed p21, are located in the vicinity of the GDP-binding site, and most of the invariant amino acids shared by the proteins interact directly with the GDP ligand.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jurnak, F -- GM 26895/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1985 Oct 4;230(4721):32-6.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3898365" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Amino Acids/*analysis ; Binding Sites ; Chemistry, Physical ; Computers ; Escherichia coli ; Fourier Analysis ; Guanine Nucleotides/*analysis ; Guanosine Diphosphate/*analysis ; Magnesium/metabolism ; *Oncogenes ; Peptide Elongation Factor Tu ; Peptide Elongation Factors/*analysis ; Physicochemical Phenomena ; Protein Conformation ; Trypsin/metabolism ; X-Ray Diffraction
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  • 80
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    A model for the tertiary structure of p21, the product of the ras oncogene (1985)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1985-10-04
    Description: A model was developed for the structure of p21, the protein with a molecular weight of 21,000 that is produced by the ras genes. This model predicts that p21 consists of a central core of beta-sheet structure, connected by loops and alpha helices. Four of these loops comprise the guanine nucleotide binding site. The phosphoryl binding region is made up of amino acid sequences from 10 to 16 and from 57 to 63 of p21. The latter sequence may contain a site for magnesium binding. Amino acids defining guanine specificity are Asn-116 and Asp-119, and sequences around amino acid 145 may contribute to guanine binding. The model makes it possible to visualize how oncogenic mutations of p21 affect interaction with guanine nucleotides.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉McCormick, F -- Clark, B F -- la Cour, T F -- Kjeldgaard, M -- Norskov-Lauritsen, L -- Nyborg, J -- New York, N.Y. -- Science. 1985 Oct 4;230(4721):78-82.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3898366" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acids/analysis ; Animals ; *Aspartate Carbamoyltransferase ; Base Sequence ; Binding Sites ; *Carbamoyl-Phosphate Synthase (Glutamine-Hydrolyzing) ; Cattle ; *Dihydroorotase ; Escherichia coli ; Guanine Nucleotides/metabolism ; Humans ; Macromolecular Substances ; Magnesium/metabolism ; Membrane Proteins/analysis ; Models, Chemical ; *Multienzyme Complexes ; Mutation ; *Oncogenes ; Peptide Elongation Factor Tu ; Peptide Elongation Factors/analysis ; Protein Conformation ; Proteins/*analysis ; RNA, Transfer, Amino Acyl/metabolism ; Saccharomyces cerevisiae ; Transducin
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    Intercontinental spread of a new antibiotic resistance gene on an epidemic plasmid (1985)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1985-10-04
    Description: Bacteria of different genera isolated at nine medical centers in different parts of the United States and at one center in Venezuela during the first decade of gentamicin usage carried the gentamicin resistance gene 2"-aminoglycoside nucleotidyltransferase on the same transferable plasmid. Such widespread dissemination of a newly observed resistance gene on one plasmid suggests that a new resistance gene may emerge once on a single plasmid, which then carries it to other centers and other plasmids. The resistance gene might, therefore, be contained if detected early.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉O'Brien, T F -- Pla, M P -- Mayer, K H -- Kishi, H -- Gilleece, E -- Syvanen, M -- Hopkins, J D -- AI 19250/AI/NIAID NIH HHS/ -- GM 21842/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1985 Oct 4;230(4721):87-8.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2994226" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteria/drug effects/*genetics ; Conjugation, Genetic ; Drug Resistance, Microbial ; Electrophoresis, Agar Gel ; Escherichia coli ; *Genes, Bacterial ; Gentamicins/*therapeutic use ; Humans ; Intestines/microbiology ; Nucleotidyltransferases/genetics ; *Plasmids
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    In vivo half-life of a protein is a function of its amino-terminal residue (1986)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1986-10-10
    Description: When a chimeric gene encoding a ubiquitin-beta-galactosidase fusion protein is expressed in the yeast Saccharomyces cerevisiae, ubiquitin is cleaved off the nascent fusion protein, yielding a deubiquitinated beta-galactosidase (beta gal). With one exception, this cleavage takes place regardless of the nature of the amino acid residue of beta gal at the ubiquitin-beta gal junction, thereby making it possible to expose different residues at the amino-termini of the otherwise identical beta gal proteins. The beta gal proteins thus designed have strikingly different half-lives in vivo, from more than 20 hours to less than 3 minutes, depending on the nature of the amino acid at the amino-terminus of beta gal. The set of individual amino acids can thus be ordered with respect to the half-lives that they confer on beta gal when present at its amino-terminus (the "N-end rule"). The currently known amino-terminal residues in long-lived, noncompartmentalized intracellular proteins from both prokaryotes and eukaryotes belong exclusively to the stabilizing class as predicted by the N-end rule. The function of the previously described posttranslational addition of single amino acids to protein amino-termini may also be accounted for by the N-end rule. Thus the recognition of an amino-terminal residue in a protein may mediate both the metabolic stability of the protein and the potential for regulation of its stability.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bachmair, A -- Finley, D -- Varshavsky, A -- GM31530/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1986 Oct 10;234(4773):179-86.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3018930" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acids/*metabolism ; Escherichia coli ; Half-Life ; Methionine/metabolism ; Models, Biological ; Protein Processing, Post-Translational ; Proteins/*metabolism ; Recombinant Proteins/metabolism ; Saccharomyces cerevisiae ; Ubiquitins/metabolism ; beta-Galactosidase/metabolism
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  • 83
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    Functional role of aspartic acid-27 in dihydrofolate reductase revealed by mutagenesis (1986)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1986-03-07
    Description: The crystal structures and enzymic properties of two mutant dihydrofolate reductases (Escherichia coli) were studied in order to clarify the functional role of an invariant carboxylic acid (aspartic acid at position 27) at the substrate binding site. One mutation, constructed by oligonucleotide-directed mutagenesis, replaces Asp27 with asparagine; the other is a primary-site revertant to Ser27. The only structural perturbations involve two internally bound water molecules. Both mutants have low but readily measurable activity, which increases rapidly with decreasing pH. The mutant enzymes were also characterized with respect to relative folate: dihydrofolate activities and kinetic deuterium isotope effects. It is concluded that Asp27 participates in protonation of the substrate but not in electrostatic stabilization of a positively charged, protonated transition state.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Howell, E E -- Villafranca, J E -- Warren, M S -- Oatley, S J -- Kraut, J -- F32 GM09375/GM/NIGMS NIH HHS/ -- GM10928/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1986 Mar 7;231(4742):1123-8.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3511529" target="_blank"〉PubMed〈/a〉
    Keywords: *Aspartic Acid ; Crystallography ; Deuterium ; Escherichia coli ; Kinetics ; Methotrexate/metabolism ; Mutation ; Protein Binding ; Structure-Activity Relationship ; *Tetrahydrofolate Dehydrogenase
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    In vivo determination of the pyridine nucleotide reduction charge by carbon-13 nuclear magnetic resonance spectroscopy (1983)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1983-10-07
    Description: An intracellular coenzyme has been observed by carbon-13 nuclear magnetic resonance spectroscopy. The pyridine nucleotides in Escherichia coli were specifically labeled with carbon-13 from the biosynthetic precursor, nicotinic acid. The intracellular redox status and metabolic transformations of the pyridine nucleotides were examined under a variety of conditions. A highly reduced nicotinamide adenine dinucleotide pool was observed under anaerobic conditions only in cells that were cultured aerobically on glycerol.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Unkefer, C J -- Blazer, R M -- London, R E -- F32 HL06262/HL/NHLBI NIH HHS/ -- New York, N.Y. -- Science. 1983 Oct 7;222(4619):62-5.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/6353573" target="_blank"〉PubMed〈/a〉
    Keywords: Aerobiosis ; Anaerobiosis ; Escherichia coli ; Magnetic Resonance Spectroscopy/*methods ; NAD/*metabolism ; NADP/*metabolism ; Oxidation-Reduction
    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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    Generating controlled reducing environments in aerobic recombinant Escherichia coli fermentations: Effects on cell growth, oxygen uptake, heat shock protein expression, and in vivo CAT activity (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 59 (1998), S. 248-259 
    Details
    ISSN: 0006-3592
    Keywords: Escherichia coli ; Chloramphenicol Acetyltransferase (CAT) ; Culture Redox Potential (CRP) ; Dithiothreitol (DTT) ; reducing agents ; molecular chaperones ; proteases ; heat shock ; stress response ; protein folding ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: The independent control of culture redox potential (CRP) by the regulated addition of a reducing agent, dithiothreitol (DTT) was demonstrated in aerated recombinant Escherichia coli fermentations. Moderate levels of DTT addition resulted in minimal changes to specific oxygen uptake, growth rate, and dissolved oxygen. Excessive levels of DTT addition were toxic to the cells resulting in cessation of growth. Chloramphenicol acetyltransferase (CAT) activity (nmoles/μg total protein min.) decreased in batch fermentation experiments with respect to increasing levels of DTT addition. To further investigate the mechanisms affecting CAT activity, experiments were performed to assay heat shock protein expression and specific CAT activity (nmoles/μg CAT min.). Expression of such molecular chaperones as GroEL and DnaK were found to increase after addition of DTT. Additionally, sigma factor 32 (σ32) and several proteases were seen to increase dramatically during addition of DTT. Specific CAT activity (nmoles/μg CAT min.) varied greatly as DTT was added, however, a minimum in activity was found at the highest level of DTT addition in E. coli strains RR1 [pBR329] and JM105 [pROEX-CAT]. In conjunction, cellular stress was found to reach a maximum at the same levels of DTT. Although DTT addition has the potential for directly affecting intracellular protein folding, the effects felt from the increased stress within the cell are likely the dominant effector. That the effects of DTT were measured within the cytoplasm of the cell suggests that the periplasmic redox potential was also altered. The changes in specific CAT activity, molecular chaperones, and other heat shock proteins, in the presence of minimal growth rate and oxygen uptake alterations, suggest that the ex vivo control of redox potential provides a new process for affecting the yield and conformation of heterologous proteins in aerated E. coli fermentations. © 1998 John Wiley & Sons, Inc. Biotechnol Bioeng 59: 248-259, 1998.
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    Modulation of the phosphate-starvation response in Escherichia coli by genetic manipulation of the polyphosphate pathways (1996)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 51 (1996), S. 434-438 
    Details
    ISSN: 0006-3592
    Keywords: polyphosphate ; Escherichia coli ; phosphate starvation ; gene expression ; heterologous ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: The effect of intracellular polyphosphate on the phosphate-starvation response in Escherichia coli was studied by genetically manipulating the intracellular polyphosphate levels and by performing phosphate shifts on the genetically engineered strains. Strains that produced large quantities of polyphosphate and were able to degrade it induced the phosphate-starvation response to a lesser extent than wild-type strains, whereas strains that were unable to degrade a large intracellular polyphosphate pool induced the phosphate-starvation response to a greater extent than wild-type strains. These results have important implications for expression of heterologous genes under control of the phoA promoter. © 1996 John Wiley & Sons, Inc.
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    A novel technique for the measurement of disruption in high-pressure homogenization: Studies on E. coli containing recombinant inclusion bodies (1991)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 38 (1991), S. 363-370 
    Details
    ISSN: 0006-3592
    Keywords: homogenization, high-pressure ; cell disruption ; inclusion bodies ; size distribution ; centrifuge, analytical ; Escherichia coli ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: The high-pressure homogenization of Escherichia coli, strain JM101, containing inclusion bodies of recombinant porcine somatotropin was investigated. A novel technique employing an analytical disc centrifuge was used to monitor the disruption. This a direct technique which measures cell disintegration rather than soluble protein release. The technique is particularly suited to measurements where the disruption approaches 100%. The disk centrifuge provides a size distribution of the homogenate, and furnishes evidence for the preferential disruption of larger cells. For E. coli containing inclusion bodies, and increase in the cell feed concentration from 145 g/L (wet weight) to 330 g/L resulted is poorer homogenization. Poorer disruption was also obtained by lowering the feed temperature from 20°C to 5°C. Only slight variations in performance were obtained by increasing the feed pH from 7.5 to 9.0 or by storing the feed at 4°C for 24 h prior to disruption. Comparison with uninduced E. coli strain JM101, showed that the disruption obtained is higher for bacteria containing a recombinant inclusion body.
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    URL: http://dx.doi.org/10.1002/bit.260380406
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    Acetic acid formation in escherichia coli fermentation (1992)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 39 (1992), S. 663-671 
    Details
    ISSN: 0006-3592
    Keywords: Escherichia coli ; acetic acid ; methionine ; yeast extract ; continuous fermentation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Acetic acid formation in Escherichia coli fermentation has been studied in continuous cultures. Experimental results suggest that the limited capacity of the oxidative metabolism (perhaps the limited capacity of TCA cycle) may be responsible for acetic acid formation. At low growth rates, both anabolic and catabolic requirements may be satisfied by the oxidative metabolism. However, at high growth rates these two demands may exceed the capacity of the oxidative metabolism alone. It is proposed that under these circumstances, E. coli reorganizes the oxidative metabolism to first meet the anabolic requisition and then supply the necessary amount of energy using both the remaining capacity of the oxidative metabolism and acetic acid formation metabolism. Escherichia coli selects acetic acid synthesis as the aerobic energy source because it generates the second largest amount of ATP and NADH2. According to our proposition, acetic acid formation could be reduced by decreasing the anabolic requirement, i.e., reducing glucose uptake, or by increasing the capacity of the oxidative metabolism. These two approaches were experimentally confirmed by observing reduced acetic acid formation by reducing the glucose uptake with a yeast extract addition and enhancing the capacity of oxidative metabolism with a methionine addition.
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    Rapid protein release from Escherichia coli by chemical permeabilization under fermentation conditions (1992)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 39 (1992), S. 732-740 
    Details
    ISSN: 0006-3592
    Keywords: cell disruption ; chemical permeabilization ; Escherichia coli ; fermentation ; protein recovery ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Overall protein release greater than 75% in less than 1 h can be attained by exposing exponentially growing Escherichia coli cells to 0.4 M guanidine plus 0.5% Triton X-100 at 37°C in medium. Cell growth stops immediately upon addition of the chemicals, but the cells are not lysed. Guanidine concentrations lower than 0.2 M, in conjunction with 0.5% Triton X-100, do not release significant intracellular protein, nor do they inhibit cell growth. Under these conditions, the cells undergo an adaptation that confers resistance to protein release by further treatment with guanidine and Triton X-100. Cells treated with 0.2 M guanidine plus 0.5% Triton X-100 display intermediate behavior. Protein release is approximately 35%, and growth is temporarily interrupted by an extended lag phase. Subsequent resumption of cell growth results in resistant cells and no additional protein release. This resistance is shown to be reversible and is most likely due to physiological adaptation rather than genetic mutation.
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    Synthesis and lysis of formate by immobilized cells of Escherichia coli (1992)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 39 (1992), S. 775-780 
    Details
    ISSN: 0006-3592
    Keywords: formate ; Escherichia coli ; formate hydrogenlyase ; cell immobilization ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Formate hydrogenlyase (FHL) activity was induced in a strain of Escherichia coli S13 during anaerobic growth in yeast extract-tryptone medium containing 100 mM formate. The cells obtained at the optimum growth phase were immobilized in 2.5% (w/v) agar gel when 50-60% of the whole cell FHL activity was retained. The immobilized FHL system had good storage stability and recycling efficiency. In the lysis of formate, an increase of formate concentration to 1.18M increased QH2 (initial) value of the immobilized cell, and subsequently cells, hydrogen evolution, in general, ceased after 6 to 8 of incubation, resulting in incomplete lysis of formate. Presence of small amount of glucose (28 mM) was more or less quantitatively lysed with concomitant disappearence of glucose from the medium. Synthesis of formate from hydrogen and bicarbonate solution by the immobilized cells was also characterized. Presence of glucose (10 mM) in 50 mM bicarbonate solution stimulated formate synthesis by immobilized cells. The pH optimum range, Km, and specific activity of the immobilized cells for the lysis of formate were 6.8-7.2 0.4M, and 66 mL/g cell-h, respectively. The cells could fix hydrogen to the extent of 24.4% (w/w) of its own wet cell mass in a 72-h reaction cycle. Potentiality of the immobilized FHL system for biotechnological exploitation was discussed.
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    Relieving effects of glycine and methionine from acetic acid inhibition in Escherichia coli fermentation (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 41 (1993), S. 316-324 
    Details
    ISSN: 0006-3592
    Keywords: Escherichia coli ; acetic acid ; inhibition ; glycine ; methionine ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Among amino acids screened for their potential to relieve wild and recombinant Escherichia coli from the negative effects of acetic acid, glycine, and methionine showed a sparing effect. In the presence of 2 g/L of acetic acid, addition of 0.5 g/L of glycine or methionine resulted in either a complete recovery or a further enhancement in the specific growth rate, while the enhancement was significant but not fully complete in the presence of 4 g/L of acetic acid. The addition of 0.5 g/L of methionine alleviated the negative effect of acetic acid on recombinant E. Coli growth to produce more β-lactamase, which was encoded by plasmid pUC18. In continuous fermentation the methionine effect on recombinant. E. coli metabolism depended on dilution rate; at high dilution rates, above 0.4 h-1, the methionine addition enhanced β-lactamase production and reduced acetic acid formation, while at low dilution rates, below 0.3 h -1, the effect was reversed. In def-batch fermentation with wild-type E. Coli, cell growth rate and cell yield from glucose were enhanced with methionine addition, while the acetic acid concentration reached over 4 g/L. © 1993 John Wiley & Sons, Inc.
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    In situ fermentation monitoring with recombinant firefly luciferase (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 42 (1993), S. 30-36 
    Details
    ISSN: 0006-3592
    Keywords: Escherichia coli ; fiber optic ; firefly luciferase ; on-line ; viability ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: A novel method is described for the on-line determination of viable cell number. It has been tested in fermentations of Escherichia coli. The cells are transfected with the gene for firefly luciferase and fed low levels of luciferin in the medium. The reaction requires ATP, so the nonviable cells cannot produce light. Thus, light production is linear with viable cell density from innoculation through most of exponential growth. The light emitted by these cells is then conducted from the reaction vessel to the light detection equipment by an optical fiber. With the equipment described below, as few as a 106 cells/mL, or an OD600 of 0.004, are easily detectable and concentrations greater than 1010 cells/mL are well within range. The data are collected by a computer, so adaptation to on-line control applications is straightforward. During lag phase, this method is much more accurate then optical density measurements. At the end of exponential growth, rapid changes in light production mark carbon source depletion and the onset of cell lysis. A simple model accounts for the luciferin used during the fermentation and corrects the light detected to the proper cell density. © 1993 John Wiley & Sons, Inc.
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    Biochemical production capabilities of escherichia coli (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 42 (1993), S. 59-73 
    Details
    ISSN: 0006-3592
    Keywords: Escherichia coli ; amino acids ; nucleotides ; biosynthesis ; linear optimization ; metabolic fluxes ; metabolic engineering ; stoichiometry ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Microbial metabolism provides at mechanism for the conversion of substrates into useful biochemicals. Utilization of microbes in industrial processes requires a modification of their natural metabolism in order to increase the efficiency of the desired conversion. Redirection of metabolic fluxes forms the basis of the newly defined field of metabolic engineering. In this study we use a flux balance based approach to study the biosynthesis of the 20 amino acids and 4 nucleotides as biochemical products. These amino acids and nucleotides are primary products of biosynthesis as well as important industrial products and precursors for the production of other biochemicals. The biosynthetic reactions of the bacterium Escherichia coli have been formulated into a metabolic network, and growth has been defined as a balanced drain on the metabolite pools corresponding to the cellular composition. Theoretical limits on the conversion of glucose, glycerol, and acetate substrates to biomass as well as the biochemical products have been computed. The substrate that results in the maximal carbon conversion to a particular product is identified. Criteria have been developed to identify metabolic constraints in the optimal solutions. The constraints of stoichiometry, energy, and redox have been determined in the conversions of glucose, glycerol, and acetate substrates into the biochemicals. Flux distributions corresponding to the maximal production of the biochemicals are presented. The goals of metabolic engineering are the optimal redirection of fluxes from generating biomass toward producing the desired biochemical. Optimal biomass generation is shown to decrease in a piecewise linear manner with increasing product formation. In some cases, synergy is observed between biochemical production and growth, leading to an increased overall carbon conversion. Balanced growth and product formation are important in a bioprocess, particularly for nonsecreted products. © 1993 John Wiley & Sons, Inc.
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    Use of glucose starvation to limit growth and induce protein production in Escherichia coli (1992)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 40 (1992), S. 271-279 
    Details
    ISSN: 0006-3592
    Keywords: carbon starvation ; Escherichia coli ; growth control ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: The use of glucose starvation to uncouple the production of recombinant β-galactosidase from cell growth in Escherichia coli was investigated. A lacZ operon fusion to the carbon starvation-inducible cst-1 locus was used to control β-galactosidase synthesis. β-Galactosidase induction was observed only under aerobic starvation conditions, and its expression continued for 6 h following the onset of glucose starvation. The cessation of β-galactosidase expression closely correlated with the exhaustion of acetate, an overflow metabolite of glucose, from the culture medium. Our results suggest the primary role of acetate in cst-1-controlled protein expression is that of an energy source. Using this information, we metered acetate to a glucose-starved culture and produced a metabolically sluggish state, where growth was limited to a low linear rate and production of recombiant β-galactosidase occurred continuously throughout the experiment. The cst-1 controlled β-galactosidase synthesis was also induced at low dilution rates in a glucose-limited chemostat, suggesting possible applications to high-density cell systems such as glucose-limited recycle reactors. This work demonstrates that by using an appropriate promoter system and nutrient limitation, growth can be restrained while recombinant protein production is induced and maintained.
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    Defined media optimization for growth of recombinant Escherichia coli X90 (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 41 (1993), S. 221-230 
    Details
    ISSN: 0006-3592
    Keywords: Escherichia coli ; medium optimization ; chemostat ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: An optimized, defined minimal medium was developed to support balanced growth of Escherichia coli X90 harboring a recombinant plasmid. Foreign protein expression was repressed in these studies. A pulse injection technique was used to identify the growth responses to nutrients in a chemostat. Once the nutrients essential for growth had been identified, the yield coefficients for individual medium components. These yield coefficients were used to develop an optimized, glucose-limited defined minimal medium that supports balanced cell growth in chemostat culture. The biomass and substrate concentrations follow the Monod chemostat model. The maximum specific growth rate determined in a washout experiment is 0.87 h-1 for this strain in the optimized medium. the glucose yield factor is 0.42 g DCW/g glucose and the maintenance coefficient is zero in the glucose-limited chemostat culture. © 1993 John Wiley & Sons, Inc.
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    Structured model of genetic control via the lac promoter in Escherichia coli (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 43 (1994), S. 399-410 
    Details
    ISSN: 0006-3592
    Keywords: lac-based promoters ; Escherichia coli ; genetic control ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: A model that describes induction of protein synthesis from lac-based promoters has been developed and incorporated into the single-cell model of Escherichia coli with transcriptional and translational modifications. Unlike previous models of lac-based promoters, this model allows a priori prediction of the intracellular parameters controlling transcription from lac-based promoters with only the extracellular levels of substrate and inducer as inputs. Because of the structural detail of the model, it is possible to simulate different genetic constructions for comparison, such as Laclq strains versus wild-type cells, or including lacl on a multicopy plasmid. Expression from lac to tac promoters is predicted to yield 5% and 30% of the total cellular protein, respectively, with a pBR322-type plasmid. The model predicts the experimental observation that the Laclq strain is not as fully induced as the wild-type strains, even at higher inducer concentrations. Additionally, the model predicts the right order of magnitude of protein production from lac and tac promoters when mechanisms for attenuation of transcription at lower translational efficiency are considered. Finally, the model predicts that for high copy number systems ribosomes become limiting in the synthesis of plasmid-encoded proteins. © 1994 John Wiley & Sons, Inc.
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    Overproduction of glycogen in Escherichia coli blocked in the acetate pathway improves cell growth (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 44 (1994), S. 132-139 
    Details
    ISSN: 0006-3592
    Keywords: glycogen ; Escherichia coli ; cell growth ; acetate ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Excessive production of acetate is a problem frequently encountered in aerobic high-cell-density fermentations of Escherichia coli. Here, we have examined genetic alterations resulting in glycogen overproduction as a possible means to direct the flux of carbon away from the acetate pool. Glycogen overaccumulation was achieved either by using a regulatory glgQ mutation or by transforming cells with a plasmid containing the glycogen biosynthesis genes glgC (encoding ADPG pyrophosphorylase) and glgA (encoding glycogen synthase) under their native promoter. Both strategies resulted in an approximately five-fold increase in glycogen levels but had no significant effect on acetate excretion. The glgC and glgA genes were then placed under the control of the isopropyl---D-thiogalactopyranoside (IPTG) inducible tac promoter, and this construct was used to stimulate glycogen production in a mutant defective in acetate biosynthesis due to deletion of the ack (acetate kinase) and pta (phosphotransacetylase) genes. If glycogen overproduction in the ack pta strain was induced during the late log phase, biomass production increased by 15 to 20% relative to uninduced controls. Glycogen overaccumulation had a significant influence on carbon partitioning: The output of carbon dioxide peaked earlier than in the control strain, and the levels of an unusual fermentation byproduct, pyruvate, were reduced. Exogenous pyruvate was metabolized more rapidly, suggesting higher activity of gluconeogenesis or the tricarboxylic acid (TCA) cycle as a result of glycogen overproduction. Potential mechanisms of the observed metabolic alterations are discussed. Our results suggest that ack pta mutants over producing glycogen may be a suitable starting point for constructing E. coli strains with improved characteristics in high-cell-density fermentations. © 1994 John Wiley & Sons, Inc.
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    Predictions for oxygen supply control to enhance population stability of engineered production strains (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 43 (1994), S. 275-285 
    Details
    ISSN: 0006-3592
    Keywords: Escherichia coli ; amino acids ; linear optimization ; metabolic fluxes ; metabolic engineering ; culture stability ; oxygen ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: The simultaneous growth and product formation in a microbial culture is an important feature of several laboratory, industrial, and environmental bioprocesses. Metabolic burden associated with product formation in these bioprocesses may lead to growth advantage of a nonproducing mutant leading to a loss of the producing population over time. A simple population dynamics model demonstrates the extreme sensitivity of population stability to the engineered productivity of a strain. Here we use flux balance analysis to estimate the effects of the metabolic burden associated with product secretion on optimal growth rates. Comparing the optimal growth rates of the producing and nonproducing strains under a given processing condition allows us to predict the population stability. In order to increase stability of an engineered strain, we determine processing conditions that simultaneously maximize the growth rate of the producing population while minimizing the growth rate of a nonproducing population. Using valine, tryptophan, and lysine production as specific examples, we demonstrate that although an appropriate choice of oxygenation may increase culture longevity more than twofold, total production as governed by economic criterion can be increased by several orders of magnitude. Choice of optimal nutrient and oxygen supply rates to enhance stability is important both for strain screening as well as for culture of engineered strains. Appropriate design of the culture environment can thus be used to enhance the productivity of bioprocesses that use engineered production strains. © 1994 John Wiley & Sons, Inc.
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    Ribosomal protein limitations in Escherichia coli under conditions of high translational activity (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 43 (1994), S. 388-398 
    Details
    ISSN: 0006-3592
    Keywords: ribosome synthesis ; Escherichia coli ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Details of the mechanism for ribosome synthesis have been incorporated in the single-cell Escherichia coli model, which enable us to predict the amount of protein synthesizing machinery under different environmental conditions. The predictions agree quite well with available experimental data. The model predicts that ribosomal protein limitations are important when the translational apparatus is in high demand. Ribosomal RNA synthesis is induced by an increase in translational activity, which, in turn, stimulates ribosomal protein synthesis. However, as the demand increases still more, the ribosomal protein mRNA must compete with the plasmid mRNA for ribosomes, and the efficiency of translation of ribosomal proteins is reduced. © 1994 John Wiley & Sons, Inc.
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    Recovery of bacteria from growth media by starch-dependent floc formation (1991)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 38 (1991), S. 314-318 
    Details
    ISSN: 0006-3592
    Keywords: Escherichia coli ; maltoporin ; harvesting bacteria ; bacterial surfaces ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Addition of starch to suspensions of Escherichia coli K-12 resulted in the formation of bacterial flocs. The flocculation was dependent on the high expression of a receptor for starch (maltoporin) on the surface of the bacterium. Factors influencing floc formation were investigated and optimal conditions for flocculation based on cell density, starch concentration, time, and pH established. As quantitated by a sedimentation assay, over 80% of bacteria in a culture could be removed by settling without centrifugation in 3 h under optimal conditions. Floc formation was evident with bacteria containing wild-type maltoporin but was faster and occurred to a greater extent with strains expressing a high-affinity allele (lamB1400) of the starch receptor. Bacteria could be harvested by floc formation directly in growth medium under defined conditions of maltoporin expression and medium composition. These results demonstrate the effectiveness of starch-dependent aggregation in the harvesting of cells, using an inexpensive, biologically acceptable agent to induce flocculation.
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    URL: http://dx.doi.org/10.1002/bit.260380313
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