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  • 1
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    Crystal structures and ligand binding of PurM proteins from Thermus thermophilus and Geobacillus kaustophilus (2016)
    Oxford University Press
    Details
    Publication Date: 2016-02-24
    Description: Crystal structures of 5-aminoimidazole ribonucleotide (AIR) synthetase, also known as PurM, from Thermus thermophilus ( Tt ) and Geobacillus kaustophilus ( Gk ) were determined. For Tt PurM, the maximum resolution was 2.2 Å and the space group was P 2 1 2 1 2 with four dimers in an asymmetric unit. For Gk PurM, the maximum resolution was 2.2 Å and the space group was P 2 1 2 1 2 with one monomer in asymmetric unit. The biological unit is dimer for both Tt PurM and Gk PurM and the dimer structures were similar to previously determined structures of PurM in general. For Tt PurM, ~50 residues at the amino terminal were disordered in the crystal structure whereas, for Gk PurM, the corresponding region covered the ATP-binding site forming an α helix in part, suggesting that the N-terminal region of PurM changes its conformation upon binding of ligands. FGAM binding site was predicted by the docking simulation followed by the MD simulation based on the SO 4 2– binding site found in the crystal structure of Tt PurM.
    Print ISSN: 0021-924X
    Electronic ISSN: 1756-2651
    Topics: Biology , Chemistry and Pharmacology
    Published by Oxford University Press on behalf of The Japanese Biochemical Society (JBS).
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  • 2
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    Structures and reaction mechanisms of the two related enzymes, PurN and PurU (2013)
    Oxford University Press
    Details
    Publication Date: 2013-12-03
    Description: The crystal structures of glycinamide ribonucleotide transformylases (PurNs) from Aquifex aeolicus ( Aa ), Geobacillus kaustophilus ( Gk ) and Symbiobacterium toebii ( St ), and of formyltetrahydrofolate hydrolase (PurU) from Thermus thermophilus ( Tt ) were determined. The monomer structures of the determined PurN and PurU were very similar to the known structure of PurN, but oligomeric states were different; Aa PurN and St PurN formed dimers, Gk PurN formed monomer and PurU formed tetramer in the crystals. PurU had a regulatory ACT domain in its N-terminal side. So far several structures of PurUs have been determined, yet, the mechanisms of the catalysis and the regulation of PurU have not been elucidated. We, therefore, modelled ligand-bound structures of PurN and PurU, and performed molecular dynamics simulations to elucidate the reaction mechanisms. The evolutionary relationship of the two enzymes is discussed based on the comparisons of the structures and the catalytic mechanisms.
    Print ISSN: 0021-924X
    Electronic ISSN: 1756-2651
    Topics: Biology , Chemistry and Pharmacology
    Published by Oxford University Press on behalf of The Japanese Biochemical Society (JBS).
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  • 3
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    Tertiary structure of bacterial selenocysteine tRNA (2013)
    Oxford University Press
    Details
    Publication Date: 2013-07-16
    Description: Selenocysteine (Sec) is translationally incorporated into proteins in response to the UGA codon. The tRNA specific to Sec (tRNA Sec ) is first ligated with serine by seryl-tRNA synthetase (SerRS). In the present study, we determined the 3.1 Å crystal structure of the tRNA Sec from the bacterium Aquifex aeolicus , in complex with the heterologous SerRS from the archaeon Methanopyrus kandleri . The bacterial tRNA Sec assumes the L-shaped structure, from which the long extra arm protrudes. Although the D-arm conformation and the extra-arm orientation are similar to those of eukaryal/archaeal tRNA Sec s, A. aeolicus tRNA Sec has unique base triples, G14:C21:U8 and C15:G20a:G48, which occupy the positions corresponding to the U8:A14 and R15:Y48 tertiary base pairs of canonical tRNAs. Methanopyrus kandleri SerRS exhibited serine ligation activity toward A. aeolicus tRNA Sec in vitro . The SerRS N-terminal domain interacts with the extra-arm stem and the outer corner of tRNA Sec . Similar interactions exist in the reported tRNA Ser and SerRS complex structure from the bacterium Thermus thermophilus . Although the catalytic C-terminal domain of M. kandleri SerRS lacks interactions with A. aeolicus tRNA Sec in the present complex structure, the conformational flexibility of SerRS is likely to allow the CCA terminal region of tRNA Sec to enter the SerRS catalytic site.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 4
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    Molecular mechanism of phenylimidazole-type GSM [Biochemistry] (2014)
    National Academy of Sciences
    Details
    Publication Date: 2014-07-23
    Description: γ-Secretase is an intramembrane-cleaving protease responsible for the generation of amyloid-β (Aβ) peptides. Recently, a series of compounds called γ-secretase modulators (GSMs) has been shown to decrease the levels of long toxic Aβ species (i.e., Aβ42), with a concomitant elevation of the production of shorter Aβ species. In this study,...
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 5
    Electronic Resource
    Electronic Resource
    Recycling of Printed Wiring Boards with Mounted Electronic Components (1997)
    Bradford : Emerald
    Circuit world 23 (1997), S. 10-15 
    Details
    ISSN: 0305-6120
    Source: Emerald Fulltext Archive Database 1994-2005
    Topics: Electrical Engineering, Measurement and Control Technology
    Notes: Recycling technology for printed wiring boards (PWBs) with mounted electroniccomponents was studied for the purpose of disassembling the boards, recovering useful materials, andreusing these materials. An automatic removal method was developed for the electronic componentson the basis of a combination of heating to above the solder melting temperature and applying impactingthe shearing forces. Most of the electronic components were recovered undamaged and the solderwas able to be recovered as particles. The solder remaining on the board was recovered by abradingthe board surface and by using a heating-impacting process. After these processes, the resinboard (a cured epoxy resin board reinforced with glass fibre)was pulverised and separatedinto a copper-rich powder (copper: 82 Wt%) and a glass fibre andresin mixture powder (glass fibre-resin powder) by gravimetric and electrostaticmethods. The recovered electronic components, solder and copper-rich powder were usedas valuable metal resources for refining. Moreover, the recovered glass fibre-resin powderwas found to be a useful filler for plastic products such as epoxy resin and ABS(acrylonitrile/butadiene/styrene copolymer) resin.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1108/03056129710370196
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    Paper (German National Licenses)
    Fulltext
  • 6
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    Analysis and attribution of trends in water levels in the Vietnamese Mekong Delta (2015)
    Wiley
    Details
    Publication Date: 2015-08-15
    Description: In the Vietnamese Mekong Delta (VMD), water levels at some stations have increased. However, the factors that cause this rise in the VMD have not been identified. We considered four factors that may have contributed to the water level rise: (1) increased runoff from upstream, (2) sea-level rise, (3) land subsidence, and (4) decrease in flood mitigation function due to construction of high dykes. We analyzed daily maximum and minimum water levels, and mean daily water levels from 24 monitoring stations from 1987 to 2006. Using daily and annual water level differences, we classified the delta into two groups; one is dominated by flows from upstream, while the other is tide-dominated. We then tested the trends of annual maximum and minimum water levels using the Mann-Kendall test, and identified the slope of the trend using the method of Sen. The areas of dyke construction were estimated using the Enhanced Vegetation Index (EVI) and Land Surface Water Index (LSWI) from the Moderate Resolution Imaging Spectroradiometer (MODIS) data. Results show (1) river inflow has little impact on rising water levels in the VMD, (2) the influence of high dykes on water level rise could not be quantified in this study, (3) both maximum and minimum water levels significantly increased in the tide-dominated area. Trend of annual minimum water level can be considered as the sum sea-level rise and land subsidence. Therefore, we attribute 6.05 mm year −1 (80%) to land subsidence and 1.42 mm year −1 (20%) to sea level rise, indicating inundations have been severe in the VMD, caused primarily by land subsidence. This article is protected by copyright. All rights reserved.
    Print ISSN: 0885-6087
    Electronic ISSN: 1099-1085
    Topics: Architecture, Civil Engineering, Surveying , Geography
    Published by Wiley
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  • 7
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    Global efforts in structural genomics (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-10-06
    Description: A worldwide initiative in structural genomics aims to capitalize on the recent successes of the genome projects. Substantial new investments in structural genomics in the past 2 years indicate the high level of support for these international efforts. Already, enormous progress has been made on high-throughput methodologies and technologies that will speed up macromolecular structure determinations. Recent international meetings have resulted in the formation of an International Structural Genomics Organization to formulate policy and foster cooperation between the public and private efforts.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stevens, R C -- Yokoyama, S -- Wilson, I A -- P50 GM62411/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2001 Oct 5;294(5540):89-92.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Joint Center for Structural Genomics, Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11588249" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Computational Biology ; Congresses as Topic ; Costs and Cost Analysis ; Crystallography, X-Ray ; Databases, Factual ; *Genomics ; Guidelines as Topic ; Humans ; Information Management ; Information Services ; International Cooperation ; Internet ; Nuclear Magnetic Resonance, Biomolecular ; Patents as Topic ; Private Sector ; *Protein Conformation ; Protein Folding ; Proteins/*chemistry ; *Proteome ; Public Sector ; Publishing ; Technology Transfer
    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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  • 8
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    Role of the ENTH domain in phosphatidylinositol-4,5-bisphosphate binding and endocytosis (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-02-13
    Description: Endocytic proteins such as epsin, AP180, and Hip1R (Sla2p) share a conserved modular region termed the epsin NH2-terminal homology (ENTH) domain, which plays a crucial role in clathrin-mediated endocytosis through an unknown target. Here, we demonstrate a strong affinity of the ENTH domain for phosphatidylinositol-4,5-bisphosphate [PtdIns(4,5)P2]. With nuclear magnetic resonance analysis of the epsin ENTH domain, we determined that a cleft formed with positively charged residues contributed to phosphoinositide binding. Overexpression of a mutant, epsin Lys76 --〉 Ala76, with an ENTH domain defective in phosphoinositide binding, blocked epidermal growth factor internalization in COS-7 cells. Thus, interaction between the ENTH domain and PtdIns(4,5)P2 is essential for endocytosis mediated by clathrin-coated pits.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Itoh, T -- Koshiba, S -- Kigawa, T -- Kikuchi, A -- Yokoyama, S -- Takenawa, T -- New York, N.Y. -- Science. 2001 Feb 9;291(5506):1047-51.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11161217" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptor Proteins, Vesicular Transport ; Amino Acid Motifs ; Amino Acid Substitution ; Animals ; COS Cells ; Carrier Proteins/*chemistry/*metabolism ; Cercopithecus aethiops ; Clathrin/metabolism ; Coated Pits, Cell-Membrane/metabolism ; DNA-Binding Proteins/metabolism ; *Endocytosis ; Epidermal Growth Factor/metabolism ; Inositol Phosphates/metabolism ; Liposomes/metabolism ; Models, Molecular ; Neuropeptides/*chemistry/*metabolism ; Nuclear Magnetic Resonance, Biomolecular ; Phosphatidylinositol 4,5-Diphosphate/*metabolism ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Recombinant Fusion Proteins/chemistry/metabolism ; Transcription Factors/metabolism ; *Vesicular Transport Proteins ; Zinc Fingers
    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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  • 9
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    Enzyme structure with two catalytic sites for double-sieve selection of substrate (1998)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1998-05-09
    Description: High-fidelity transfers of genetic information in the central dogma can be achieved by a reaction called editing. The crystal structure of an enzyme with editing activity in translation is presented here at 2.5 angstroms resolution. The enzyme, isoleucyl-transfer RNA synthetase, activates not only the cognate substrate L-isoleucine but also the minimally distinct L-valine in the first, aminoacylation step. Then, in a second, "editing" step, the synthetase itself rapidly hydrolyzes only the valylated products. For this two-step substrate selection, a "double-sieve" mechanism has already been proposed. The present crystal structures of the synthetase in complexes with L-isoleucine and L-valine demonstrate that the first sieve is on the aminoacylation domain containing the Rossmann fold, whereas the second, editing sieve exists on a globular beta-barrel domain that protrudes from the aminoacylation domain.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nureki, O -- Vassylyev, D G -- Tateno, M -- Shimada, A -- Nakama, T -- Fukai, S -- Konno, M -- Hendrickson, T L -- Schimmel, P -- Yokoyama, S -- GM15539/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1998 Apr 24;280(5363):578-82.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9554847" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Monophosphate ; Binding Sites ; Crystallography, X-Ray ; Escherichia coli/enzymology ; Hydrogen Bonding ; Hydrolysis ; Isoleucine/*metabolism ; Isoleucine-tRNA Ligase/*chemistry/metabolism ; Models, Chemical ; Models, Molecular ; Molecular Sequence Data ; Mutagenesis ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; RNA, Transfer, Ile/metabolism ; Substrate Specificity ; Thermus thermophilus/enzymology ; Transfer RNA Aminoacylation ; Valine/*metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 10
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    Molecular computation by DNA hairpin formation (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2000-05-20
    Description: Hairpin formation by single-stranded DNA molecules was exploited in a DNA-based computation in order to explore the feasibility of autonomous molecular computing. An instance of the satisfiability problem, a famous hard combinatorial problem, was solved by using molecular biology techniques. The satisfiability of a given Boolean formula was examined autonomously, on the basis of hairpin formation by the molecules that represent the formula. This computation algorithm can test several clauses in the given formula simultaneously, which could reduce the number of laboratory steps required for computation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sakamoto, K -- Gouzu, H -- Komiya, K -- Kiga, D -- Yokoyama, S -- Yokomori, T -- Hagiya, M -- New York, N.Y. -- Science. 2000 May 19;288(5469):1223-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10817993" target="_blank"〉PubMed〈/a〉
    Keywords: Algorithms ; Biotinylation ; Computational Biology/*methods ; DNA Ligases/chemistry ; DNA, Single-Stranded/*chemistry ; DNA-Directed DNA Polymerase/chemistry ; Electrophoresis, Agar Gel ; *Nucleic Acid Conformation ; Nucleic Acid Denaturation ; Polymerase Chain Reaction ; Temperature ; Templates, Genetic
    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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