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  • Cloning, Molecular
  • Kinetics
  • American Association for the Advancement of Science (AAAS)  (1,864)
  • Elsevier  (396)
  • American Association for the Advancement of Science
  • American Association of Petroleum Geologists (AAPG)
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  • 1
    Publication Date: 2016-01-30
    Description: In several human pathogens, thyX-encoded flavin-dependent thymidylate synthase (FDTS) catalyzes the last step in the biosynthesis of thymidylate, one of the four DNA nucleotides. ThyX is absent in humans, rendering FDTS an attractive antibiotic target; however, the lack of mechanistic understanding prohibits mechanism-based drug design. Here, we report trapping and characterization of two consecutive intermediates, which together with previous crystal structures indicate that the enzyme's reduced flavin relays a methylene from the folate carrier to the nucleotide acceptor. Furthermore, these results corroborate an unprecedented activation of the nucleotide that involves no covalent modification but only electrostatic polarization by the enzyme's active site. These findings indicate a mechanism that is very different from thymidylate biosynthesis in humans, underscoring the promise of FDTS as an antibiotic target.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4744818/" 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/PMC4744818/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mishanina, Tatiana V -- Yu, Liping -- Karunaratne, Kalani -- Mondal, Dibyendu -- Corcoran, John M -- Choi, Michael A -- Kohen, Amnon -- R01 GM110775/GM/NIGMS NIH HHS/ -- T32 GM008365/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2016 Jan 29;351(6272):507-10. doi: 10.1126/science.aad0300.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of Iowa, Iowa City, IA 52242, USA. amnon-kohen@uiowa.edu. ; Nuclear Magnetic Resonance (NMR) Core Facility and Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA. ; Department of Chemistry, University of Iowa, Iowa City, IA 52242, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26823429" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/*chemistry ; Catalysis ; Catalytic Domain ; *DNA Methylation ; Flavins/chemistry ; Folic Acid/chemistry ; Folic Acid Transporters/chemistry ; Humans ; Kinetics ; Thermotoga maritima/enzymology ; Thymidine Monophosphate/*biosynthesis/chemistry ; Thymidylate Synthase/*chemistry
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  • 2
    Publication Date: 2015-09-01
    Description: Cycloadditions, such as the [4+2] Diels-Alder reaction to form six-membered rings, are among the most powerful and widely used methods in synthetic chemistry. The analogous [2+2] alkene cycloaddition to synthesize cyclobutanes is kinetically accessible by photochemical methods, but the substrate scope and functional group tolerance are limited. Here, we report iron-catalyzed intermolecular [2+2] cycloaddition of unactivated alkenes and cross cycloaddition of alkenes and dienes as regio- and stereoselective routes to cyclobutanes. Through rational ligand design, development of this base metal-catalyzed method expands the chemical space accessible from abundant hydrocarbon feedstocks.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hoyt, Jordan M -- Schmidt, Valerie A -- Tondreau, Aaron M -- Chirik, Paul J -- F32 GM109594/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2015 Aug 28;349(6251):960-3. doi: 10.1126/science.aac7440.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Princeton University, Princeton, NJ 08544, USA. ; Department of Chemistry, Princeton University, Princeton, NJ 08544, USA. pchirik@princeton.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26315433" target="_blank"〉PubMed〈/a〉
    Keywords: Alkenes/*chemistry ; Catalysis ; Cycloaddition Reaction ; Cyclobutanes/*chemical synthesis/*chemistry ; Dimerization ; Iron/*chemistry ; Kinetics ; Ligands ; Molecular Structure ; Stereoisomerism
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  • 3
    Publication Date: 2015-03-21
    Description: Base-pairing interactions between nucleic acids mediate target recognition in many biological processes. We developed a super-resolution imaging and modeling platform that enabled the in vivo determination of base pairing-mediated target recognition kinetics. We examined a stress-induced bacterial small RNA, SgrS, which induces the degradation of target messenger RNAs (mRNAs). SgrS binds to a primary target mRNA in a reversible and dynamic fashion, and formation of SgrS-mRNA complexes is rate-limiting, dictating the overall regulation efficiency in vivo. Examination of a secondary target indicated that differences in the target search kinetics contribute to setting the regulation priority among different target mRNAs. This super-resolution imaging and analysis approach provides a conceptual framework that can be generalized to other small RNA systems and other target search processes.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4410144/" 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/PMC4410144/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fei, Jingyi -- Singh, Digvijay -- Zhang, Qiucen -- Park, Seongjin -- Balasubramanian, Divya -- Golding, Ido -- Vanderpool, Carin K -- Ha, Taekjip -- GM 112659/GM/NIGMS NIH HHS/ -- GM065367/GM/NIGMS NIH HHS/ -- GM082837/GM/NIGMS NIH HHS/ -- GM092830/GM/NIGMS NIH HHS/ -- R01 GM065367/GM/NIGMS NIH HHS/ -- R01 GM082837/GM/NIGMS NIH HHS/ -- R01 GM092830/GM/NIGMS NIH HHS/ -- R01 GM112659/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2015 Mar 20;347(6228):1371-4. doi: 10.1126/science.1258849.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for the Physics of Living Cells, Department of Physics, University of Illinois, Urbana, IL, USA. ; Center for Biophysics and Computational Biology, University of Illinois, Urbana, IL, USA. ; Department of Microbiology, University of Illinois, Urbana, IL, USA. ; Center for the Physics of Living Cells, Department of Physics, University of Illinois, Urbana, IL, USA. Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA. ; Department of Microbiology, University of Illinois, Urbana, IL, USA. tjha@illinois.edu cvanderp@life.uiuc.edu. ; Center for the Physics of Living Cells, Department of Physics, University of Illinois, Urbana, IL, USA. Center for Biophysics and Computational Biology, University of Illinois, Urbana, IL, USA. Carl R. Woese Institute for Genomic Biology, Howard Hughes Medical Institute, Urbana, IL, USA. Howard Hughes Medical Institute, Urbana, IL, USA. tjha@illinois.edu cvanderp@life.uiuc.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25792329" target="_blank"〉PubMed〈/a〉
    Keywords: *Base Pairing ; Endoribonucleases/chemistry/genetics ; Escherichia coli/genetics/metabolism ; Kinetics ; Molecular Imaging/*methods ; Mutation ; Phosphoenolpyruvate Sugar Phosphotransferase System/genetics ; *RNA Stability ; RNA, Messenger/*chemistry ; RNA, Small Untranslated/*chemistry
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  • 4
    Publication Date: 2015-09-26
    Description: Experimental, theoretical, and computational studies of small proteins suggest that interresidue contacts not present in the folded structure play little or no role in the self-assembly mechanism. Non-native contacts can, however, influence folding kinetics by introducing additional local minima that slow diffusion over the global free-energy barrier between folded and unfolded states. Here, we combine single-molecule fluorescence with all-atom molecular dynamics simulations to discover the structural origin for the slow diffusion that markedly decreases the folding rate for a designed alpha-helical protein. Our experimental determination of transition path times and our analysis of the simulations point to non-native salt bridges between helices as the source, which provides a quantitative glimpse of how specific intramolecular interactions influence protein folding rates by altering dynamics and not activation free energies.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chung, Hoi Sung -- Piana-Agostinetti, Stefano -- Shaw, David E -- Eaton, William A -- Intramural NIH HHS/ -- New York, N.Y. -- Science. 2015 Sep 25;349(6255):1504-10. doi: 10.1126/science.aab1369.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892-0520, USA. chunghoi@niddk.nih.gov stefano.piana-agostinetti@DEShawResearch.com david.shaw@DEShawResearch.com eaton@helix.nih.gov. ; D. E. Shaw Research, New York, NY 10036, USA. chunghoi@niddk.nih.gov stefano.piana-agostinetti@DEShawResearch.com david.shaw@DEShawResearch.com eaton@helix.nih.gov. ; D. E. Shaw Research, New York, NY 10036, USA. Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA. chunghoi@niddk.nih.gov stefano.piana-agostinetti@DEShawResearch.com david.shaw@DEShawResearch.com eaton@helix.nih.gov.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26404828" target="_blank"〉PubMed〈/a〉
    Keywords: Diffusion ; Entropy ; Hydrogen-Ion Concentration ; Kinetics ; *Models, Chemical ; Molecular Dynamics Simulation ; *Protein Folding ; Protein Structure, Secondary ; Proteins/*chemistry
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  • 5
    Publication Date: 2015-04-11
    Description: To address how the configuration of conjugated ubiquitins determines the recognition of substrates by the proteasome, we analyzed the degradation kinetics of substrates with chemically defined ubiquitin configurations. Contrary to the view that a tetraubiquitin chain is the minimal signal for efficient degradation, we find that distributing the ubiquitins as diubiquitin chains provides a more efficient signal. To understand how the proteasome actually discriminates among ubiquitin configurations, we developed single-molecule assays that distinguished intermediate steps of degradation kinetically. The level of ubiquitin on a substrate drives proteasome-substrate interaction, whereas the chain structure of ubiquitin affects translocation into the axial channel on the proteasome. Together these two features largely determine the susceptibility of substrates for proteasomal degradation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4450770/" 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/PMC4450770/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lu, Ying -- Lee, Byung-hoon -- King, Randall W -- Finley, Daniel -- Kirschner, Marc W -- GM43601/GM/NIGMS NIH HHS/ -- GM66492/GM/NIGMS NIH HHS/ -- R01 GM039023/GM/NIGMS NIH HHS/ -- R01 GM066492/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2015 Apr 10;348(6231):1250834. doi: 10.1126/science.1250834.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA. ; Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA. ; Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA. marc@hms.harvard.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25859050" target="_blank"〉PubMed〈/a〉
    Keywords: Cyclin B/metabolism ; Geminin/metabolism ; Humans ; Kinetics ; Proteasome Endopeptidase Complex/chemistry/*metabolism ; Protein Binding ; Protein Transport ; *Proteolysis ; Securin/metabolism ; Stochastic Processes ; Ubiquitin/chemistry/*metabolism ; Ubiquitinated Proteins/chemistry/*metabolism ; Ubiquitination
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  • 6
    Publication Date: 2015-04-11
    Description: Biological processes require specific enzymatic reactions, paradoxically involving short recognition sequences. As an example, cell-cycle timing depends on a sequence of ubiquitylation events mediated by the anaphase-promoting complex (APC) based on short redundant motifs. To understand the origin of specificity, we designed single-molecule fluorescence assays that capture transient ubiquitylation reactions. We find that the APC-mediated ubiquitylation involves a highly processive initial reaction on the substrate, followed by multiple encounters and reactions at a slower rate. The initial ubiquitylation greatly enhances the substrate's binding affinity in subsequent reactions, by both increasing the on-rate and decreasing the off-rate. We postulate that these cycles of positive feedback enable high specificity for substrates with short recognition motifs in a complex cellular environment.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4449139/" 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/PMC4449139/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lu, Ying -- Wang, Weiping -- Kirschner, Marc W -- 5R01GM039023-26/GM/NIGMS NIH HHS/ -- R01 GM039023/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2015 Apr 10;348(6231):1248737. doi: 10.1126/science.1248737. Epub 2015 Apr 9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA. ; Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA. marc@hms.harvard.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25859049" target="_blank"〉PubMed〈/a〉
    Keywords: Anaphase-Promoting Complex-Cyclosome/antagonists & ; inhibitors/chemistry/*metabolism ; Cell Cycle ; Cyclin A/metabolism ; Cyclin B/metabolism ; Feedback, Physiological ; Fluorescence ; Fluorescent Dyes ; HeLa Cells ; Humans ; Kinetics ; Protein Binding ; Protein Interaction Domains and Motifs ; SMN Complex Proteins/metabolism ; Substrate Specificity ; Ubiquitin/metabolism ; Ubiquitination
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  • 7
    Publication Date: 2015-04-25
    Description: Protein synthesis rates can affect gene expression and the folding and activity of the translation product. Interactions between the nascent polypeptide and the ribosome exit tunnel represent one mode of regulating synthesis rates. The SecM protein arrests its own translation, and release of arrest at the translocon has been proposed to occur by mechanical force. Using optical tweezers, we demonstrate that arrest of SecM-stalled ribosomes can indeed be rescued by force alone and that the force needed to release stalling can be generated in vivo by a nascent chain folding near the ribosome tunnel exit. We formulate a kinetic model describing how a protein can regulate its own synthesis by the force generated during folding, tuning ribosome activity to structure acquisition by a nascent polypeptide.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4618485/" 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/PMC4618485/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Goldman, Daniel H -- Kaiser, Christian M -- Milin, Anthony -- Righini, Maurizio -- Tinoco, Ignacio Jr -- Bustamante, Carlos -- 5K99GM086516/GM/NIGMS NIH HHS/ -- 5R01GM32543/GM/NIGMS NIH HHS/ -- GM10840/GM/NIGMS NIH HHS/ -- K99 GM086516/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2015 Apr 24;348(6233):457-60. doi: 10.1126/science.1261909. Epub 2015 Apr 23.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of California, Berkeley, CA 94720, USA. ; Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA. Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA. carlos@alice.berkeley.edu kaiser@jhu.edu. ; Department of Chemistry, University of California, Berkeley, CA 94720, USA. Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA. ; Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA. ; Department of Chemistry, University of California, Berkeley, CA 94720, USA. Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA. Department of Physics, University of California, Berkeley, CA 94720, USA. Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA. Kavli Energy Nanosciences Institute at Berkeley, Berkeley, CA 94720, USA. Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA. carlos@alice.berkeley.edu kaiser@jhu.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25908824" target="_blank"〉PubMed〈/a〉
    Keywords: Escherichia coli/*metabolism ; Escherichia coli Proteins/*biosynthesis/*chemistry ; In Vitro Techniques ; Kinetics ; Mechanical Processes ; Optical Tweezers ; *Peptide Chain Elongation, Translational ; *Protein Folding ; Ribosomes/chemistry/*metabolism ; Transcription Factors/*biosynthesis/*chemistry
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  • 8
    Publication Date: 2015-04-25
    Description: In cells, biosynthetic machinery coordinates protein synthesis and folding to optimize efficiency and minimize off-pathway outcomes. However, it has been difficult to delineate experimentally the mechanisms responsible. Using fluorescence resonance energy transfer, we studied cotranslational folding of the first nucleotide-binding domain from the cystic fibrosis transmembrane conductance regulator. During synthesis, folding occurred discretely via sequential compaction of N-terminal, alpha-helical, and alpha/beta-core subdomains. Moreover, the timing of these events was critical; premature alpha-subdomain folding prevented subsequent core formation. This process was facilitated by modulating intrinsic folding propensity in three distinct ways: delaying alpha-subdomain compaction, facilitating beta-strand intercalation, and optimizing translation kinetics via codon usage. Thus, de novo folding is translationally tuned by an integrated cellular response that shapes the cotranslational folding landscape at critical stages of synthesis.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kim, Soo Jung -- Yoon, Jae Seok -- Shishido, Hideki -- Yang, Zhongying -- Rooney, LeeAnn A -- Barral, Jose M -- Skach, William R -- P30CA069533/CA/NCI NIH HHS/ -- P30EYE010572/PHS HHS/ -- R01DK51818/DK/NIDDK NIH HHS/ -- R01GM53457/GM/NIGMS NIH HHS/ -- S10OD012246/OD/NIH HHS/ -- S10RR025571/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 2015 Apr 24;348(6233):444-8. doi: 10.1126/science.aaa3974.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Biology, Oregon Health and Science University (OHSU), Portland, OR 97239, USA. ; Department of Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, TX 77550-0620, USA. Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77550-0620, USA. ; Department of Biochemistry and Molecular Biology, Oregon Health and Science University (OHSU), Portland, OR 97239, USA. Cystic Fibrosis Foundation Therapeutics, Bethesda, MD 20814, USA. skachw@ohsu.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25908822" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Codon/chemistry/*metabolism ; Cystic Fibrosis Transmembrane Conductance ; Regulator/*biosynthesis/*chemistry/genetics ; Fluorescence Resonance Energy Transfer ; Humans ; Kinetics ; Molecular Sequence Data ; *Peptide Chain Elongation, Translational ; *Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Ribosomes/chemistry/metabolism
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  • 9
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2014-03-29
    Description: The existence of BRCA1 was proven in 1990 by mapping predisposition to young-onset breast cancer in families to chromosome 17q21. Knowing that such a gene existed and approximately where it lay triggered efforts by public and private groups to clone and sequence it. The press baptized the competition "the race" and reported on it in detail for the next 4 years. BRCA1 was positionally cloned in September 1994. Twenty years later, I reflect on "the race" and its consequences for breast cancer prevention and treatment.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉King, Mary-Claire -- R01 CA157744/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2014 Mar 28;343(6178):1462-5. doi: 10.1126/science.1251900.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Medicine and Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24675952" target="_blank"〉PubMed〈/a〉
    Keywords: BRCA1 Protein/*genetics/history ; Breast Neoplasms/*genetics/history ; Chromosome Mapping ; Chromosomes, Human, Pair 17/*genetics ; Cloning, Molecular ; Female ; Genetic Linkage ; History, 20th Century ; Humans
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  • 10
    Publication Date: 2014-05-09
    Description: The regenerative power of tissues and organs in biology has no analog in synthetic materials. Although self-healing of microscopic defects has been demonstrated, the regrowth of material lost through catastrophic damage requires a regenerative-like approach. We demonstrate a vascular synthetic system that restores mechanical performance in response to large-scale damage. Gap-filling scaffolds are created through a two-stage polymer chemistry that initially forms a shape-conforming dynamic gel but later polymerizes to a solid structural polymer with robust mechanical properties. Through the control of reaction kinetics and vascular delivery rate, we filled impacted regions that exceed 35 mm in diameter within 20 min and restored mechanical function within 3 hours. After restoration of impact damage, 62% of the total absorbed energy was recovered in comparison with that in initial impact tests.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉White, S R -- Moore, J S -- Sottos, N R -- Krull, B P -- Santa Cruz, W A -- Gergely, R C R -- New York, N.Y. -- Science. 2014 May 9;344(6184):620-3. doi: 10.1126/science.1251135.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Aerospace Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24812399" target="_blank"〉PubMed〈/a〉
    Keywords: Gels/chemistry ; Kinetics ; Mechanical Processes ; Models, Chemical ; *Polymerization ; Polymers/*chemistry ; *Regeneration
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  • 11
    Publication Date: 2014-03-29
    Description: The cloning of the breast cancer susceptibility genes BRCA1 and BRCA2 nearly two decades ago helped set in motion an avalanche of research exploring how genomic information can be optimally applied to identify and clinically care for individuals with a high risk of developing cancer. Genetic testing for mutations in BRCA1, BRCA2, and other breast cancer susceptibility genes has since proved to be a valuable tool for determining eligibility for enhanced screening and prevention strategies, as well as for identifying patients most likely to benefit from a targeted therapy. Here, we discuss the landscape of inherited mutations and sequence variants in BRCA1 and BRCA2, the complexities of determining disease risk when the pathogenicity of sequence variants is uncertain, and current strategies for clinical management of women who carry BRCA1/2 mutations.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4074902/" 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/PMC4074902/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Couch, Fergus J -- Nathanson, Katherine L -- Offit, Kenneth -- 3P30CA008748-47/CA/NCI NIH HHS/ -- CA016520/CA/NCI NIH HHS/ -- CA116167/CA/NCI NIH HHS/ -- CA116201/CA/NCI NIH HHS/ -- CA128978/CA/NCI NIH HHS/ -- CA135509/CA/NCI NIH HHS/ -- P50 CA116201/CA/NCI NIH HHS/ -- R01 CA128978/CA/NCI NIH HHS/ -- R01 CA135509/CA/NCI NIH HHS/ -- U01 CA116167/CA/NCI NIH HHS/ -- U01 CA164947/CA/NCI NIH HHS/ -- U01CA164947/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2014 Mar 28;343(6178):1466-70. doi: 10.1126/science.1251827.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Experimental Pathology and Laboratory Medicine, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24675953" target="_blank"〉PubMed〈/a〉
    Keywords: BRCA1 Protein/*genetics ; BRCA2 Protein/*genetics ; Breast Neoplasms/*drug therapy/genetics/prevention & control ; Cloning, Molecular ; Female ; *Genetic Predisposition to Disease ; Humans ; Models, Genetic ; Mutation ; *Precision Medicine
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  • 12
    Publication Date: 2014-08-16
    Description: The assembly of artificial cells capable of executing synthetic DNA programs has been an important goal for basic research and biotechnology. We assembled two-dimensional DNA compartments fabricated in silicon as artificial cells capable of metabolism, programmable protein synthesis, and communication. Metabolism is maintained by continuous diffusion of nutrients and products through a thin capillary, connecting protein synthesis in the DNA compartment with the environment. We programmed protein expression cycles, autoregulated protein levels, and a signaling expression gradient, equivalent to a morphogen, in an array of interconnected compartments at the scale of an embryo. Gene expression in the DNA compartment reveals a rich, dynamic system that is controlled by geometry, offering a means for studying biological networks outside a living cell.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Karzbrun, Eyal -- Tayar, Alexandra M -- Noireaux, Vincent -- Bar-Ziv, Roy H -- New York, N.Y. -- Science. 2014 Aug 15;345(6198):829-32. doi: 10.1126/science.1255550.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Materials and Interfaces, Weizmann Institute of Science, Rehovot 76100, Israel. ; Department of Physics, University of Minnesota, Minneapolis, MN 55455, USA. ; Department of Materials and Interfaces, Weizmann Institute of Science, Rehovot 76100, Israel. roy.bar-ziv@weizmann.ac.il.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25124443" target="_blank"〉PubMed〈/a〉
    Keywords: Artificial Cells/*metabolism/ultrastructure ; *DNA/genetics/metabolism ; Diffusion ; *Gene Expression ; Gene Expression Regulation ; Gene Regulatory Networks ; Green Fluorescent Proteins/genetics/metabolism ; Kinetics ; Microfluidic Analytical Techniques ; Oligonucleotide Array Sequence Analysis ; Proteins/*metabolism ; Silicon ; Software ; Synthetic Biology/methods ; Templates, Genetic ; Transcription, Genetic
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  • 13
    Publication Date: 2014-02-08
    Description: Although the effects of kinetics on crystal growth are well understood, the role of substrate curvature is not yet established. We studied rigid, two-dimensional colloidal crystals growing on spherical droplets to understand how the elastic stress induced by Gaussian curvature affects the growth pathway. In contrast to crystals grown on flat surfaces or compliant crystals on droplets, these crystals formed branched, ribbon-like domains with large voids and no topological defects. We show that this morphology minimizes the curvature-induced elastic energy. Our results illustrate the effects of curvature on the ubiquitous process of crystallization, with practical implications for nanoscale disorder-order transitions on curved manifolds, including the assembly of viral capsids, phase separation on vesicles, and crystallization of tetrahedra in three dimensions.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Meng, Guangnan -- Paulose, Jayson -- Nelson, David R -- Manoharan, Vinothan N -- New York, N.Y. -- Science. 2014 Feb 7;343(6171):634-7. doi: 10.1126/science.1244827.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physics, Harvard University, Cambridge, MA 02138, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24503849" target="_blank"〉PubMed〈/a〉
    Keywords: Capsid/chemistry ; Colloids/*chemistry ; Crystallization/*statistics & numerical data ; *Elasticity ; Kinetics ; Normal Distribution ; *Stress, Mechanical
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  • 14
    Publication Date: 2014-07-06
    Description: Activation of the small guanosine triphosphatase H-Ras by the exchange factor Son of Sevenless (SOS) is an important hub for signal transduction. Multiple layers of regulation, through protein and membrane interactions, govern activity of SOS. We characterized the specific activity of individual SOS molecules catalyzing nucleotide exchange in H-Ras. Single-molecule kinetic traces revealed that SOS samples a broad distribution of turnover rates through stochastic fluctuations between distinct, long-lived (more than 100 seconds), functional states. The expected allosteric activation of SOS by Ras-guanosine triphosphate (GTP) was conspicuously absent in the mean rate. However, fluctuations into highly active states were modulated by Ras-GTP. This reveals a mechanism in which functional output may be determined by the dynamical spectrum of rates sampled by a small number of enzymes, rather than the ensemble average.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4255705/" 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/PMC4255705/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Iversen, Lars -- Tu, Hsiung-Lin -- Lin, Wan-Chen -- Christensen, Sune M -- Abel, Steven M -- Iwig, Jeff -- Wu, Hung-Jen -- Gureasko, Jodi -- Rhodes, Christopher -- Petit, Rebecca S -- Hansen, Scott D -- Thill, Peter -- Yu, Cheng-Han -- Stamou, Dimitrios -- Chakraborty, Arup K -- Kuriyan, John -- Groves, Jay T -- P01 AI091580/AI/NIAID NIH HHS/ -- R01 AI104789/AI/NIAID NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2014 Jul 4;345(6192):50-4. doi: 10.1126/science.1250373.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA. ; Department of Chemical Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA. ; Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA. ; Department of Mechanical Engineering, University of California, Berkeley, Berkeley, CA 94720, USA. ; Department of Chemistry, MIT, Cambridge, MA 02139, USA. ; Mechanobiology Institute, National University of Singapore, Singapore. ; Department of Chemistry and Nano-Science Center, University of Copenhagen, Copenhagen, Denmark. ; Department of Chemical Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA. Department of Chemistry, MIT, Cambridge, MA 02139, USA. Department of Biological Engineering, MIT, Cambridge, MA 02139, USA. Ragon Institute of Massachusetts General Hospital, MIT, and Harvard, Cambridge, MA 02139, USA. Department of Physics, MIT, Cambridge, MA 02139, USA. Institute for Medical Engineering and Science, MIT, Cambridge, MA 02139, USA. ; Howard Hughes Medical Institute, Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA. Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA. Physical Biosciences and Materials Sciences Divisions, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. ; Howard Hughes Medical Institute, Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA. Mechanobiology Institute, National University of Singapore, Singapore. Physical Biosciences and Materials Sciences Divisions, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. Berkeley Education Alliance for Research in Singapore, 1 Create Way, CREATE tower level 11, University Town, Singapore 138602. jtgroves@lbl.gov.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24994643" target="_blank"〉PubMed〈/a〉
    Keywords: Allosteric Regulation ; Catalytic Domain ; Crystallography, X-Ray ; Enzyme Activation ; Humans ; Kinetics ; Nucleotides/chemistry ; *Protein Interaction Domains and Motifs ; Proto-Oncogene Proteins p21(ras)/*agonists ; Son of Sevenless Protein, Drosophila/*chemistry/genetics
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  • 15
    Publication Date: 2014-12-20
    Description: Variability in gene expression among genetically identical cells has emerged as a central preoccupation in the study of gene regulation; however, a divide exists between the predictions of molecular models of prokaryotic transcriptional regulation and genome-wide experimental studies suggesting that this variability is indifferent to the underlying regulatory architecture. We constructed a set of promoters in Escherichia coli in which promoter strength, transcription factor binding strength, and transcription factor copy numbers are systematically varied, and used messenger RNA (mRNA) fluorescence in situ hybridization to observe how these changes affected variability in gene expression. Our parameter-free models predicted the observed variability; hence, the molecular details of transcription dictate variability in mRNA expression, and transcriptional noise is specifically tunable and thus represents an evolutionarily accessible phenotypic parameter.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4388425/" 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/PMC4388425/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jones, Daniel L -- Brewster, Robert C -- Phillips, Rob -- 1 U54 CA143869/CA/NCI NIH HHS/ -- DP1 OD000217/OD/NIH HHS/ -- R01 GM085286/GM/NIGMS NIH HHS/ -- U54 CA143869/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2014 Dec 19;346(6216):1533-6. doi: 10.1126/science.1255301. Epub 2014 Dec 18.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Applied Physics, California Institute of Technology, Pasadena, CA 91125, USA. ; Department of Applied Physics, California Institute of Technology, Pasadena, CA 91125, USA. Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA. ; Department of Applied Physics, California Institute of Technology, Pasadena, CA 91125, USA. Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA. phillips@pboc.caltech.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25525251" target="_blank"〉PubMed〈/a〉
    Keywords: Cells/*metabolism ; DNA-Directed RNA Polymerases/metabolism ; Escherichia coli/genetics ; Gene Dosage ; *Gene Expression Regulation ; *Genetic Variation ; In Situ Hybridization ; Kinetics ; Lac Repressors/genetics/metabolism ; Models, Genetic ; *Promoter Regions, Genetic ; Protein Binding ; RNA, Messenger/genetics ; Transcription, Genetic
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  • 16
    Publication Date: 2013-07-03
    Description: Wheat stem rust, caused by Puccinia graminis f. sp. tritici (Pgt), is a devastating disease that can cause severe yield losses. A previously uncharacterized Pgt race, designated Ug99, has overcome most of the widely used resistance genes and is threatening major wheat production areas. Here, we demonstrate that the Sr35 gene from Triticum monococcum is a coiled-coil, nucleotide-binding, leucine-rich repeat gene that confers near immunity to Ug99 and related races. This gene is absent in the A-genome diploid donor and in polyploid wheat but is effective when transferred from T. monococcum to polyploid wheat. The cloning of Sr35 opens the door to the use of biotechnological approaches to control this devastating disease and to analyses of the molecular interactions that define the wheat-rust pathosystem.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4748951/" 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/PMC4748951/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Saintenac, Cyrille -- Zhang, Wenjun -- Salcedo, Andres -- Rouse, Matthew N -- Trick, Harold N -- Akhunov, Eduard -- Dubcovsky, Jorge -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2013 Aug 16;341(6147):783-6. doi: 10.1126/science.1239022. Epub 2013 Jun 27.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23811222" target="_blank"〉PubMed〈/a〉
    Keywords: Alternative Splicing ; Amino Acid Sequence ; *Basidiomycota/pathogenicity ; Cloning, Molecular ; Disease Resistance/genetics ; *Genes, Plant ; Haplotypes ; Molecular Sequence Annotation ; Molecular Sequence Data ; Mutation ; Phylogeny ; Plant Diseases/genetics/*immunology/microbiology ; Plant Proteins/chemistry/genetics ; Plant Stems/microbiology ; Plants, Genetically Modified ; Polymorphism, Single Nucleotide ; Polyploidy ; Sequence Analysis, DNA ; Triticum/*genetics/immunology/microbiology
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  • 17
    Publication Date: 2013-12-07
    Description: In individual cells, transcription is a random process obeying single-molecule kinetics. Often, it occurs in a bursty, intermittent manner. The frequency and size of these bursts affect the magnitude of temporal fluctuations in messenger RNA and protein content within a cell, creating variation or "noise" in gene expression. It is still unclear to what degree transcriptional kinetics are specific to each gene and determined by its promoter sequence. Alternative scenarios have been proposed, in which the kinetics of transcription are governed by cellular constraints and follow universal rules across the genome. Evidence from genome-wide noise studies and from systematic perturbations of promoter sequences suggest that both scenarios-namely gene-specific versus genome-wide regulation of transcription kinetics-may be present to different degrees in bacteria, yeast, and animal cells.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4045091/" 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/PMC4045091/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sanchez, Alvaro -- Golding, Ido -- R01 GM082837/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2013 Dec 6;342(6163):1188-93. doi: 10.1126/science.1242975.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Rowland Institute at Harvard, Harvard University, Cambridge, MA 02142, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24311680" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Escherichia coli/genetics/metabolism ; Eukaryota/genetics/metabolism ; *Gene Expression Regulation ; Genome ; Kinetics ; Models, Genetic ; Promoter Regions, Genetic ; RNA, Messenger/genetics/metabolism ; Single-Cell Analysis ; Stochastic Processes ; *Transcription, Genetic ; Yeasts/genetics/metabolism
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  • 18
    Publication Date: 2013-03-09
    Description: RNA chaperones are ubiquitous, heterogeneous proteins essential for RNA structural biogenesis and function. We investigated the mechanism of chaperone-mediated RNA folding by following the time-resolved dimerization of the packaging domain of a retroviral RNA at nucleotide resolution. In the absence of the nucleocapsid (NC) chaperone, dimerization proceeded through multiple, slow-folding intermediates. In the presence of NC, dimerization occurred rapidly through a single structural intermediate. The RNA binding domain of heterogeneous nuclear ribonucleoprotein A1 protein, a structurally unrelated chaperone, also accelerated dimerization. Both chaperones interacted primarily with guanosine residues. Replacing guanosine with more weakly pairing inosine yielded an RNA that folded rapidly without a facilitating chaperone. These results show that RNA chaperones can simplify RNA folding landscapes by weakening intramolecular interactions involving guanosine and explain many RNA chaperone activities.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4338410/" 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/PMC4338410/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Grohman, Jacob K -- Gorelick, Robert J -- Lickwar, Colin R -- Lieb, Jason D -- Bower, Brian D -- Znosko, Brent M -- Weeks, Kevin M -- GM031819/GM/NIGMS NIH HHS/ -- GM064803/GM/NIGMS NIH HHS/ -- GM072518/GM/NIGMS NIH HHS/ -- HHSN261200800001E/PHS HHS/ -- R01 GM031819/GM/NIGMS NIH HHS/ -- R01 GM064803/GM/NIGMS NIH HHS/ -- T32 GM007092/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2013 Apr 12;340(6129):190-5. doi: 10.1126/science.1230715. Epub 2013 Mar 7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599-3290, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23470731" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Dimerization ; Guanosine/chemistry/*metabolism ; Heterogeneous-Nuclear Ribonucleoprotein Group A-B/chemistry/metabolism ; Inosine/chemistry/metabolism ; Kinetics ; Models, Molecular ; Molecular Chaperones/chemistry/*metabolism ; Moloney murine leukemia virus/genetics/*metabolism ; Nucleic Acid Conformation ; Nucleocapsid Proteins/chemistry/*metabolism ; Protein Binding ; RNA, Viral/*chemistry/metabolism
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  • 19
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2013-12-21
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Xie, X Sunney -- New York, N.Y. -- Science. 2013 Dec 20;342(6165):1457-9. doi: 10.1126/science.1248859.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA, and Biodynamic Optical Imaging Center (BIOPIC), Peking University, Beijing 100871, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24357307" target="_blank"〉PubMed〈/a〉
    Keywords: Catalysis ; Enzymes/*chemistry ; Fluorescence ; Kinetics ; Molecular Imaging ; Optical Imaging
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  • 20
    Publication Date: 2013-07-03
    Description: Wheat stem rust, caused by the fungus Puccinia graminis f. sp. tritici, afflicts bread wheat (Triticum aestivum). New virulent races collectively referred to as "Ug99" have emerged, which threaten global wheat production. The wheat gene Sr33, introgressed from the wild relative Aegilops tauschii into bread wheat, confers resistance to diverse stem rust races, including the Ug99 race group. We cloned Sr33, which encodes a coiled-coil, nucleotide-binding, leucine-rich repeat protein. Sr33 is orthologous to the barley (Hordeum vulgare) Mla mildew resistance genes that confer resistance to Blumeria graminis f. sp. hordei. The wheat Sr33 gene functions independently of RAR1, SGT1, and HSP90 chaperones. Haplotype analysis from diverse collections of Ae. tauschii placed the origin of Sr33 resistance near the southern coast of the Caspian Sea.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Periyannan, Sambasivam -- Moore, John -- Ayliffe, Michael -- Bansal, Urmil -- Wang, Xiaojing -- Huang, Li -- Deal, Karin -- Luo, Mingcheng -- Kong, Xiuying -- Bariana, Harbans -- Mago, Rohit -- McIntosh, Robert -- Dodds, Peter -- Dvorak, Jan -- Lagudah, Evans -- New York, N.Y. -- Science. 2013 Aug 16;341(6147):786-8. doi: 10.1126/science.1239028. Epub 2013 Jun 27.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Commonwealth Scientific and Industrial Research Organization (CSIRO) Plant Industry, Canberra, ACT 2601, Australia.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23811228" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; *Basidiomycota/pathogenicity ; Cloning, Molecular ; Disease Resistance/genetics ; *Genes, Plant ; Haplotypes ; Hordeum/genetics ; Hybridization, Genetic ; Molecular Chaperones/genetics/metabolism ; Molecular Sequence Data ; Mutation ; Plant Diseases/genetics/*immunology/microbiology ; Plant Proteins/chemistry/genetics/metabolism ; Plant Stems/microbiology ; Plants, Genetically Modified ; Poaceae/*genetics ; Synteny ; Triticum/*genetics/*microbiology
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  • 21
    Publication Date: 2013-10-05
    Description: The chromatin immunoprecipitation (ChIP) assay is widely used to capture interactions between chromatin and regulatory proteins, but it is unknown how stable most native interactions are. Although live-cell imaging suggests short-lived interactions at tandem gene arrays, current methods cannot measure rapid binding dynamics at single-copy genes. We show, by using a modified ChIP assay with subsecond temporal resolution, that the time dependence of formaldehyde cross-linking can be used to extract in vivo on and off rates for site-specific chromatin interactions varying over a ~100-fold dynamic range. By using the method, we show that a regulatory process can shift weakly bound TATA-binding protein to stable promoter interactions, thereby facilitating transcription complex formation. This assay provides an approach for systematic, quantitative analyses of chromatin binding dynamics in vivo.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3997053/" 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/PMC3997053/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Poorey, Kunal -- Viswanathan, Ramya -- Carver, Melissa N -- Karpova, Tatiana S -- Cirimotich, Shana M -- McNally, James G -- Bekiranov, Stefan -- Auble, David T -- GM55763/GM/NIGMS NIH HHS/ -- R01 GM055763/GM/NIGMS NIH HHS/ -- Intramural NIH HHS/ -- New York, N.Y. -- Science. 2013 Oct 18;342(6156):369-72. doi: 10.1126/science.1242369. Epub 2013 Oct 3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA 22908, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24091704" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphatases/chemistry/metabolism ; Chromatin/chemistry/*metabolism ; Chromatin Immunoprecipitation/*methods ; Cross-Linking Reagents/chemistry ; DNA-Binding Proteins/chemistry/metabolism ; Formaldehyde/chemistry ; Gene Dosage ; *Gene Expression Regulation ; Kinetics ; Promoter Regions, Genetic ; Saccharomyces cerevisiae Proteins/chemistry/metabolism ; TATA-Binding Protein Associated Factors/chemistry/metabolism ; TATA-Box Binding Protein/chemistry/*metabolism ; Transcription Factors/chemistry/metabolism
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 22
    Publication Date: 2013-02-09
    Description: Piperidines are prevalent in natural products and pharmaceutical agents and are important synthetic targets for drug discovery and development. We report on a methodology that provides highly substituted piperidine derivatives with regiochemistry selectively tunable by varying the strength of acid used in the reaction. Readily available starting materials are first converted to dihydropyridines via a cascade reaction initiated by rhodium-catalyzed carbon-hydrogen bond activation. Subsequent divergent regio- and diastereoselective protonation of the dihydropyridines under either kinetic or thermodynamic control provides two distinct iminium ion intermediates that then undergo highly diastereoselective nucleophilic additions. X-ray structural characterization of both the kinetically and thermodynamically favored iminium ions along with density functional theory calculations provide a theoretical underpinning for the high selectivities achieved for the reaction sequences.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3809088/" 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/PMC3809088/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Duttwyler, Simon -- Chen, Shuming -- Takase, Michael K -- Wiberg, Kenneth B -- Bergman, Robert G -- Ellman, Jonathan A -- GM069559/GM/NIGMS NIH HHS/ -- R01 GM069559/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2013 Feb 8;339(6120):678-82. doi: 10.1126/science.1230704.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Yale University, New Haven, CT 06520, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23393259" target="_blank"〉PubMed〈/a〉
    Keywords: Acids ; Catalysis ; Crystallography, X-Ray ; Dihydropyridines/chemistry ; Heterocyclic Compounds/*chemical synthesis/chemistry ; Hydrogen Bonding ; Kinetics ; Molecular Conformation ; Molecular Structure ; Nitrogen/*chemistry ; Piperidines/*chemical synthesis/*chemistry ; *Protons ; Rhodium ; Stereoisomerism ; Thermodynamics
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  • 23
    Publication Date: 2012-11-10
    Description: Despite more than 30 years of work on the Wnt signaling pathway, the basic mechanism of how the extracellular Wnt signal increases the intracellular concentration of beta-catenin is still contentious. Circumventing much of the detailed biochemistry, we used basic principles of chemical kinetics coupled with quantitative measurements to define the reactions on beta-catenin directly affected by the Wnt signal. We conclude that the core signal transduction mechanism is relatively simple, with only two regulated phosphorylation steps. Their partial inhibition gives rise to the full dynamics of the response and subsequently maintains a steady state in which the concentration of beta-catenin is increased.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hernandez, Ana R -- Klein, Allon M -- Kirschner, Marc W -- New York, N.Y. -- Science. 2012 Dec 7;338(6112):1337-40. doi: 10.1126/science.1228734. Epub 2012 Nov 8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23138978" target="_blank"〉PubMed〈/a〉
    Keywords: Casein Kinase I/chemistry/metabolism ; Cell Line, Tumor ; Cysteine Proteinase Inhibitors/pharmacology ; Glycogen Synthase Kinase 3/metabolism ; HEK293 Cells ; Humans ; Kinetics ; Leupeptins/pharmacology ; Phosphorylation ; *Signal Transduction ; Wnt Proteins/*metabolism ; Wnt3A Protein/metabolism ; beta Catenin/*metabolism
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  • 24
    Publication Date: 2012-03-01
    Description: The genetic changes responsible for morphological differences between species are largely unidentified. Such changes can involve modifications of growth that are relevant to understanding evolution, development, and disease. We identified a gene that induces male-specific wing size and shape differences between Nasonia wasp species. Fine-scale mapping and in situ hybridization reveal that changes in at least three regions (two strictly in noncoding sequence) around the gene unpaired-like (upd-like) cause changes in spatial and temporal expression of upd-like in the developing wing and corresponding changes in wing width. Upd-like shows homology to the Drosophila unpaired gene, a well-studied signaling protein that regulates cell proliferation and differentiation. Our results indicate how multiple changes in the regulation of upd-like are involved in microevolution of morphological and sex-specific differences between species.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3520604/" 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/PMC3520604/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Loehlin, David W -- Werren, John H -- 5R01 GM070026-04/GM/NIGMS NIH HHS/ -- 5R24 GM084917-04/GM/NIGMS NIH HHS/ -- R01 GM070026/GM/NIGMS NIH HHS/ -- R24 GM084917/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2012 Feb 24;335(6071):943-7. doi: 10.1126/science.1215193.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, University of Rochester, Rochester, NY 14627, USA. loehlin@wisc.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22363002" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; *Biological Evolution ; Cloning, Molecular ; Drosophila/genetics ; Drosophila Proteins/genetics ; Female ; Gene Expression Profiling ; Gene Expression Regulation, Developmental ; Genes, Insect ; Insect Proteins/*genetics/metabolism ; Male ; Molecular Sequence Data ; Morphogenesis/genetics ; Organ Size ; Quantitative Trait Loci ; Sex Characteristics ; Species Specificity ; Transcription Factors/genetics ; Wasps/anatomy & histology/*genetics/*growth & development ; Wings, Animal/*anatomy & histology/*growth & development/metabolism
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  • 25
    Publication Date: 2012-03-01
    Description: The transition path is the tiny fraction of an equilibrium molecular trajectory when a transition occurs as the free-energy barrier between two states is crossed. It is a single-molecule property that contains all the mechanistic information on how a process occurs. As a step toward observing transition paths in protein folding, we determined the average transition-path time for a fast- and a slow-folding protein from a photon-by-photon analysis of fluorescence trajectories in single-molecule Forster resonance energy transfer experiments. Whereas the folding rate coefficients differ by a factor of 10,000, the transition-path times differ by a factor of less than 5, which shows that a fast- and a slow-folding protein take almost the same time to fold when folding actually happens. A very simple model based on energy landscape theory can explain this result.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3878298/" 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/PMC3878298/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chung, Hoi Sung -- McHale, Kevin -- Louis, John M -- Eaton, William A -- Z99 DK999999/Intramural NIH HHS/ -- New York, N.Y. -- Science. 2012 Feb 24;335(6071):981-4. doi: 10.1126/science.1215768.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health (NIH), Bethesda, MD 20892-0520, USA. chunghoi@niddk.nih.gov〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22363011" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacterial Proteins/*chemistry ; Carrier Proteins/*chemistry ; Fluorescence Resonance Energy Transfer ; Kinetics ; Likelihood Functions ; Models, Molecular ; Molecular Sequence Data ; Photons ; Protein Conformation ; *Protein Folding ; Protein Interaction Domains and Motifs ; Protein Structure, Tertiary ; Thermodynamics
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  • 26
    Publication Date: 2012-10-23
    Description: Growing RNA chains fold cotranscriptionally as they are synthesized by RNA polymerase. Riboswitches, which regulate gene expression by adopting alternative RNA folds, are sensitive to cotranscriptional events. We developed an optical-trapping assay to follow the cotranscriptional folding of a nascent RNA and used it to monitor individual transcripts of the pbuE adenine riboswitch, visualizing distinct folding transitions. We report a particular folding signature for the riboswitch aptamer whose presence directs the gene-regulatory transcription outcome, and we measured the termination frequency as a function of adenine level and tension applied to the RNA. Our results demonstrate that the outcome is kinetically controlled. These experiments furnish a means to observe conformational switching in real time and enable the precise mapping of events during cotranscriptional folding.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3496414/" 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/PMC3496414/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Frieda, Kirsten L -- Block, Steven M -- R37 GM057035/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2012 Oct 19;338(6105):397-400. doi: 10.1126/science.1225722.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Biophysics Program, Stanford University, Stanford, CA 94305, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23087247" target="_blank"〉PubMed〈/a〉
    Keywords: Adenine/*chemistry/metabolism ; Bacillus subtilis/genetics ; Base Sequence ; Kinetics ; Molecular Sequence Data ; *Optical Tweezers ; *RNA Folding ; Riboswitch/*genetics ; *Transcription, Genetic
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  • 27
    Publication Date: 2012-09-08
    Description: Spontaneous electrical signals in the retina's photoreceptors impose a limit on visual sensitivity. Their origin is attributed to a thermal, rather than photochemical, activation of the transduction cascade. Although the mechanism of such a process is under debate, the observation of a relationship between the maximum absorption wavelength (lambda(max)) and the thermal activation kinetic constant (k) of different visual pigments (the Barlow correlation) indicates that the thermal and photochemical activations are related. Here we show that a quantum chemical model of the bovine rod pigment provides a molecular-level understanding of the Barlow correlation. The transition state mediating thermal activation has the same electronic structure as the photoreceptor excited state, thus creating a direct link between lambda(max) and k. Such a link appears to be the manifestation of intrinsic chromophore features associated with the existence of a conical intersection between its ground and excited states.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gozem, Samer -- Schapiro, Igor -- Ferre, Nicolas -- Olivucci, Massimo -- New York, N.Y. -- Science. 2012 Sep 7;337(6099):1225-8. doi: 10.1126/science.1220461.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Bowling Green State University, Bowling Green, OH 43403, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22955833" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cattle ; Isomerism ; Kinetics ; Models, Chemical ; Photochemical Processes ; Quantum Theory ; Retinal Rod Photoreceptor Cells/*chemistry/physiology ; Rhodopsin/*chemistry/*physiology ; Rod Opsins/chemistry/physiology ; Schiff Bases ; Temperature ; Thermodynamics
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  • 28
    Publication Date: 2012-06-23
    Description: Transcription factors (TFs) are proteins that regulate the expression of genes by binding sequence-specific sites on the chromosome. It has been proposed that to find these sites fast and accurately, TFs combine one-dimensional (1D) sliding on DNA with 3D diffusion in the cytoplasm. This facilitated diffusion mechanism has been demonstrated in vitro, but it has not been shown experimentally to be exploited in living cells. We have developed a single-molecule assay that allows us to investigate the sliding process in living bacteria. Here we show that the lac repressor slides 45 +/- 10 base pairs on chromosomal DNA and that sliding can be obstructed by other DNA-bound proteins near the operator. Furthermore, the repressor frequently (〉90%) slides over its natural lacO(1) operator several times before binding. This suggests a trade-off between rapid search on nonspecific sequences and fast binding at the specific sequence.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hammar, Petter -- Leroy, Prune -- Mahmutovic, Anel -- Marklund, Erik G -- Berg, Otto G -- Elf, Johan -- New York, N.Y. -- Science. 2012 Jun 22;336(6088):1595-8. doi: 10.1126/science.1221648.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22723426" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Chromosomes, Bacterial/metabolism ; DNA, Bacterial/*metabolism ; Escherichia coli/genetics/*metabolism ; Escherichia coli Proteins/*metabolism ; Facilitated Diffusion ; Kinetics ; *Lac Operon ; Lac Repressors/*metabolism ; *Operator Regions, Genetic ; Protein Binding ; Transcription Factors/metabolism
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  • 29
    Publication Date: 2012-04-14
    Description: microRNAs (miRNAs) regulate gene expression through translational repression and/or messenger RNA (mRNA) deadenylation and decay. Because translation, deadenylation, and decay are closely linked processes, it is important to establish their ordering and thus to define the molecular mechanism of silencing. We have investigated the kinetics of these events in miRNA-mediated gene silencing by using a Drosophila S2 cell-based controllable expression system and show that mRNAs with both natural and engineered 3' untranslated regions with miRNA target sites are first subject to translational inhibition, followed by effects on deadenylation and decay. We next used a natural translational elongation stall to show that miRNA-mediated silencing inhibits translation at an early step, potentially translation initiation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3971879/" 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/PMC3971879/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Djuranovic, Sergej -- Nahvi, Ali -- Green, Rachel -- R01 GM059425/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2012 Apr 13;336(6078):237-40. doi: 10.1126/science.1215691.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute (HHMI) and Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22499947" target="_blank"〉PubMed〈/a〉
    Keywords: 3' Untranslated Regions ; Animals ; Cell Line ; Drosophila Proteins/genetics ; Drosophila melanogaster/*genetics/metabolism ; *Gene Silencing ; Kinetics ; MicroRNAs/*genetics/metabolism ; Peptide Chain Elongation, Translational ; Peptide Chain Initiation, Translational ; *Protein Biosynthesis ; *RNA Stability ; RNA, Messenger/genetics/*metabolism
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  • 30
    Publication Date: 2012-08-04
    Description: The synaptic adhesion molecules neurexin and neuroligin alter the development and function of synapses and are linked to autism in humans. Here, we found that Caenorhabditis elegans neurexin (NRX-1) and neuroligin (NLG-1) mediated a retrograde synaptic signal that inhibited neurotransmitter release at neuromuscular junctions. Retrograde signaling was induced in mutants lacking a muscle microRNA (miR-1) and was blocked in mutants lacking NLG-1 or NRX-1. Release was rapid and abbreviated when the retrograde signal was on, whereas release was slow and prolonged when retrograde signaling was blocked. The retrograde signal adjusted release kinetics by inhibiting exocytosis of synaptic vesicles (SVs) that are distal to the site of calcium entry. Inhibition of release was mediated by increased presynaptic levels of tomosyn, an inhibitor of SV fusion.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3791080/" 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/PMC3791080/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hu, Zhitao -- Hom, Sabrina -- Kudze, Tambudzai -- Tong, Xia-Jing -- Choi, Seungwon -- Aramuni, Gayane -- Zhang, Weiqi -- Kaplan, Joshua M -- NS32196/NS/NINDS NIH HHS/ -- R37 NS032196/NS/NINDS NIH HHS/ -- New York, N.Y. -- Science. 2012 Aug 24;337(6097):980-4. doi: 10.1126/science.1224896. Epub 2012 Aug 2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22859820" target="_blank"〉PubMed〈/a〉
    Keywords: Acetylcholine/metabolism ; Animals ; Caenorhabditis elegans/genetics/*physiology ; Caenorhabditis elegans Proteins/genetics/*metabolism ; Cell Adhesion Molecules, Neuronal/genetics/*metabolism ; Cholinergic Neurons/physiology ; Excitatory Postsynaptic Potentials ; Exocytosis ; Kinetics ; Mice ; MicroRNAs/genetics/metabolism ; Motor Neurons/physiology ; Mutation ; Neural Inhibition ; Neuromuscular Junction/*physiology ; Neurotransmitter Agents/metabolism ; *Synaptic Transmission ; Synaptic Vesicles/physiology ; Transcription Factors/genetics/metabolism ; Transfection
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  • 31
    Publication Date: 2012-04-14
    Description: Biological systems involving short-range activators and long-range inhibitors can generate complex patterns. Reaction-diffusion models postulate that differences in signaling range are caused by differential diffusivity of inhibitor and activator. Other models suggest that differential clearance underlies different signaling ranges. To test these models, we measured the biophysical properties of the Nodal/Lefty activator/inhibitor system during zebrafish embryogenesis. Analysis of Nodal and Lefty gradients revealed that Nodals have a shorter range than Lefty proteins. Pulse-labeling analysis indicated that Nodals and Leftys have similar clearance kinetics, whereas fluorescence recovery assays revealed that Leftys have a higher effective diffusion coefficient than Nodals. These results indicate that differential diffusivity is the major determinant of the differences in Nodal/Lefty range and provide biophysical support for reaction-diffusion models of activator/inhibitor-mediated patterning.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3525670/" 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/PMC3525670/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Muller, Patrick -- Rogers, Katherine W -- Jordan, Ben M -- Lee, Joon S -- Robson, Drew -- Ramanathan, Sharad -- Schier, Alexander F -- 5R01GM56211/GM/NIGMS NIH HHS/ -- R01 GM056211/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2012 May 11;336(6082):721-4. doi: 10.1126/science.1221920. Epub 2012 Apr 12.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA. pmueller@fas.harvard.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22499809" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Blastula/*metabolism ; *Body Patterning ; Diffusion ; Embryonic Development ; Fluorescence Recovery After Photobleaching ; Half-Life ; Intracellular Signaling Peptides and Proteins/genetics/*metabolism ; Kinetics ; Left-Right Determination Factors/genetics/*metabolism ; Models, Biological ; Nodal Signaling Ligands/genetics/*metabolism ; Recombinant Fusion Proteins/metabolism ; Zebrafish/*embryology/metabolism ; Zebrafish Proteins/genetics/*metabolism
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  • 32
    Publication Date: 2012-01-24
    Description: Tethering a single lysozyme molecule to a carbon nanotube field-effect transistor produced a stable, high-bandwidth transducer for protein motion. Electronic monitoring during 10-minute periods extended well beyond the limitations of fluorescence techniques to uncover dynamic disorder within a single molecule and establish lysozyme as a processive enzyme. On average, 100 chemical bonds are processively hydrolyzed, at 15-hertz rates, before lysozyme returns to its nonproductive, 330-hertz hinge motion. Statistical analysis differentiated single-step hinge closure from enzyme opening, which requires two steps. Seven independent time scales governing lysozyme's activity were observed. The pH dependence of lysozyme activity arises not from changes to its processive kinetics but rather from increasing time spent in either nonproductive rapid motions or an inactive, closed conformation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3914775/" 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/PMC3914775/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Choi, Yongki -- Moody, Issa S -- Sims, Patrick C -- Hunt, Steven R -- Corso, Brad L -- Perez, Israel -- Weiss, Gregory A -- Collins, Philip G -- R01 CA133592/CA/NCI NIH HHS/ -- R01 CA133592-01/CA/NCI NIH HHS/ -- T32 CA009054/CA/NCI NIH HHS/ -- T32CA009054/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2012 Jan 20;335(6066):319-24. doi: 10.1126/science.1214824.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Surface and Interface Science, University of California Irvine, Irvine, CA 92697-2375, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22267809" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteriophage T4/enzymology ; Biocatalysis ; Electric Conductivity ; Fluorescence Resonance Energy Transfer ; Hydrogen-Ion Concentration ; Kinetics ; Microscopy, Atomic Force ; Muramidase/*chemistry/*metabolism ; Nanotubes, Carbon ; Peptidoglycan/metabolism ; Protein Conformation ; Pyrenes ; Static Electricity ; Thermodynamics ; Transistors, Electronic
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  • 33
    Publication Date: 2012-06-02
    Description: We describe a general computational method for designing proteins that self-assemble to a desired symmetric architecture. Protein building blocks are docked together symmetrically to identify complementary packing arrangements, and low-energy protein-protein interfaces are then designed between the building blocks in order to drive self-assembly. We used trimeric protein building blocks to design a 24-subunit, 13-nm diameter complex with octahedral symmetry and a 12-subunit, 11-nm diameter complex with tetrahedral symmetry. The designed proteins assembled to the desired oligomeric states in solution, and the crystal structures of the complexes revealed that the resulting materials closely match the design models. The method can be used to design a wide variety of self-assembling protein nanomaterials.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4138882/" 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/PMC4138882/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉King, Neil P -- Sheffler, William -- Sawaya, Michael R -- Vollmar, Breanna S -- Sumida, John P -- Andre, Ingemar -- Gonen, Tamir -- Yeates, Todd O -- Baker, David -- RR-15301/RR/NCRR NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2012 Jun 1;336(6085):1171-4. doi: 10.1126/science.1219364.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22654060" target="_blank"〉PubMed〈/a〉
    Keywords: Chromatography, Gel ; Cloning, Molecular ; Computational Biology ; Computer Simulation ; Crystallography, X-Ray ; Escherichia coli/genetics/metabolism ; Hydrogen Bonding ; Microscopy, Electron ; Models, Molecular ; Molecular Weight ; Mutation ; *Nanostructures ; *Protein Engineering ; *Protein Multimerization ; Protein Structure, Secondary ; Protein Subunits/*chemistry/genetics ; Proteins/*chemistry/genetics
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  • 34
    Publication Date: 2011-04-23
    Description: Cellular messenger RNA levels are achieved by the combinatorial complexity of factors controlling transcription, yet the small number of molecules involved in these pathways fluctuates stochastically. It has not yet been experimentally possible to observe the activity of single polymerases on an endogenous gene to elucidate how these events occur in vivo. Here, we describe a method of fluctuation analysis of fluorescently labeled RNA to measure dynamics of nascent RNA--including initiation, elongation, and termination--at an active yeast locus. We find no transcriptional memory between initiation events, and elongation speed can vary by threefold throughout the cell cycle. By measuring the abundance and intranuclear mobility of an upstream transcription factor, we observe that the gene firing rate is directly determined by trans-activating factor search times.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3152976/" 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/PMC3152976/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Larson, Daniel R -- Zenklusen, Daniel -- Wu, Bin -- Chao, Jeffrey A -- Singer, Robert H -- 57071/PHS HHS/ -- 86217/PHS HHS/ -- R01 GM057071/GM/NIGMS NIH HHS/ -- R01 GM057071-10/GM/NIGMS NIH HHS/ -- R01 GM057071-11/GM/NIGMS NIH HHS/ -- R01 GM057071-12/GM/NIGMS NIH HHS/ -- R01 GM086217/GM/NIGMS NIH HHS/ -- R01 GM086217-01/GM/NIGMS NIH HHS/ -- R01 GM086217-02/GM/NIGMS NIH HHS/ -- R01 GM086217-03/GM/NIGMS NIH HHS/ -- R01 GM086217-04/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2011 Apr 22;332(6028):475-8. doi: 10.1126/science.1202142.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21512033" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphatases/genetics ; Cell Cycle ; Cell Nucleus/metabolism ; DNA Polymerase I/genetics ; Facilitated Diffusion ; *Genes, Fungal ; Glutamate Synthase/genetics ; Green Fluorescent Proteins ; Kinetics ; Microscopy, Fluorescence ; Models, Genetic ; Promoter Regions, Genetic ; RNA Polymerase II/metabolism ; RNA Precursors/genetics/metabolism ; RNA, Fungal/biosynthesis/*genetics ; RNA, Messenger/biosynthesis/*genetics ; Saccharomyces cerevisiae/*genetics/metabolism ; Saccharomyces cerevisiae Proteins/genetics/metabolism ; Spectrometry, Fluorescence ; Transcription Factors/metabolism ; *Transcription, Genetic ; Transcriptional Activation
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  • 35
    facet.materialart.
    Unknown
    American Association for the Advancement of Science (AAAS)
    Publication Date: 2011-07-09
    Description: Both engineering and evolution are constrained by trade-offs between efficiency and robustness, but theory that formalizes this fact is limited. For a simple two-state model of glycolysis, we explicitly derive analytic equations for hard trade-offs between robustness and efficiency with oscillations as an inevitable side effect. The model describes how the trade-offs arise from individual parameters, including the interplay of feedback control with autocatalysis of network products necessary to power and catalyze intermediate reactions. We then use control theory to prove that the essential features of these hard trade-off "laws" are universal and fundamental, in that they depend minimally on the details of this system and generalize to the robust efficiency of any autocatalytic network. The theory also suggests worst-case conditions that are consistent with initial experiments.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chandra, Fiona A -- Buzi, Gentian -- Doyle, John C -- R01GM078992A/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2011 Jul 8;333(6039):187-92. doi: 10.1126/science.1200705.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Bioengineering, California Institute of Technology, Pasadena, CA 91125, USA. fiona@caltech.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21737735" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Monophosphate/metabolism ; Adenosine Triphosphate/metabolism ; Allosteric Regulation ; Biocatalysis ; Feedback, Physiological ; Glucose/metabolism ; *Glycolysis ; Kinetics ; Linear Models ; *Models, Biological ; NAD/metabolism ; Nonlinear Dynamics ; Phosphofructokinases/antagonists & inhibitors/metabolism ; Pyruvate Kinase/antagonists & inhibitors/metabolism ; Saccharomyces cerevisiae/*metabolism ; Single-Cell Analysis
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  • 36
    Publication Date: 2011-02-26
    Description: Metarhizium anisopliae infects mosquitoes through the cuticle and proliferates in the hemolymph. To allow M. anisopliae to combat malaria in mosquitoes with advanced malaria infections, we produced recombinant strains expressing molecules that target sporozoites as they travel through the hemolymph to the salivary glands. Eleven days after a Plasmodium-infected blood meal, mosquitoes were treated with M. anisopliae expressing salivary gland and midgut peptide 1 (SM1), which blocks attachment of sporozoites to salivary glands; a single-chain antibody that agglutinates sporozoites; or scorpine, which is an antimicrobial toxin. These reduced sporozoite counts by 71%, 85%, and 90%, respectively. M. anisopliae expressing scorpine and an [SM1](8):scorpine fusion protein reduced sporozoite counts by 98%, suggesting that Metarhizium-mediated inhibition of Plasmodium development could be a powerful weapon for combating malaria.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4153607/" 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/PMC4153607/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fang, Weiguo -- Vega-Rodriguez, Joel -- Ghosh, Anil K -- Jacobs-Lorena, Marcelo -- Kang, Angray -- St Leger, Raymond J -- 5R21A1079429-02/PHS HHS/ -- R01 AI031478/AI/NIAID NIH HHS/ -- R21 AI079429/AI/NIAID NIH HHS/ -- R21 AI088033/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2011 Feb 25;331(6020):1074-7. doi: 10.1126/science.1199115.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Entomology, University of Maryland, 4112 Plant Sciences Building, College Park, MD 20742, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21350178" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Anopheles gambiae/*microbiology/*parasitology/physiology ; Antibodies, Protozoan/immunology ; Base Sequence ; Cloning, Molecular ; Defensins/genetics/metabolism ; Feeding Behavior ; Female ; Hemolymph/metabolism/microbiology/parasitology ; Humans ; Insect Vectors/*microbiology/*parasitology/physiology ; Malaria, Falciparum/transmission ; Metarhizium/*genetics/physiology ; Molecular Sequence Data ; Oligopeptides/genetics/metabolism ; Organisms, Genetically Modified ; Pest Control, Biological ; Plasmodium falciparum/*physiology ; Protozoan Proteins/immunology ; Salivary Glands/metabolism/parasitology ; Spores, Fungal/physiology ; Sporozoites/physiology ; Transformation, Genetic ; Transgenes
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  • 37
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    Unknown
    American Association for the Advancement of Science (AAAS)
    Publication Date: 2011-04-23
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nair, Gautham -- Raj, Arjun -- New York, N.Y. -- Science. 2011 Apr 22;332(6028):431-2. doi: 10.1126/science.1205995.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21512026" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; DNA-Directed RNA Polymerases/metabolism ; Fibroblasts ; *Gene Expression ; *Gene Silencing ; Genes, Fungal ; Kinetics ; Mice ; Models, Genetic ; RNA, Messenger/*genetics/metabolism ; Signal Processing, Computer-Assisted ; Stochastic Processes ; *Transcription, Genetic ; *Transcriptional Activation ; Yeasts/genetics
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  • 38
    Publication Date: 2011-03-12
    Description: The spliceosome is the complex macromolecular machine responsible for removing introns from precursors to messenger RNAs (pre-mRNAs). We combined yeast genetic engineering, chemical biology, and multiwavelength fluorescence microscopy to follow assembly of single spliceosomes in real time in whole-cell extracts. We find that individual spliceosomal subcomplexes associate with pre-mRNA sequentially via an ordered pathway to yield functional spliceosomes and that association of every subcomplex is reversible. Further, early subcomplex binding events do not fully commit a pre-mRNA to splicing; rather, commitment increases as assembly proceeds. These findings have important implications for the regulation of alternative splicing. This experimental strategy should prove widely useful for mechanistic analysis of other macromolecular machines in environments approaching the complexity of living cells.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3086749/" 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/PMC3086749/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hoskins, Aaron A -- Friedman, Larry J -- Gallagher, Sarah S -- Crawford, Daniel J -- Anderson, Eric G -- Wombacher, Richard -- Ramirez, Nicholas -- Cornish, Virginia W -- Gelles, Jeff -- Moore, Melissa J -- F32 GM079971/GM/NIGMS NIH HHS/ -- F32 GM079971-03/GM/NIGMS NIH HHS/ -- GM079971/GM/NIGMS NIH HHS/ -- GM759628/GM/NIGMS NIH HHS/ -- K99 GM086471/GM/NIGMS NIH HHS/ -- K99 GM086471-02/GM/NIGMS NIH HHS/ -- K99/R00 GM086471/GM/NIGMS NIH HHS/ -- R01 GM043369/GM/NIGMS NIH HHS/ -- R01 GM053007/GM/NIGMS NIH HHS/ -- R01 GM053007-15/GM/NIGMS NIH HHS/ -- R01 GM081648/GM/NIGMS NIH HHS/ -- R01 GM081648-04/GM/NIGMS NIH HHS/ -- R01 GM54469/GM/NIGMS NIH HHS/ -- R01 GM81648/GM/NIGMS NIH HHS/ -- R37 GM043369/GM/NIGMS NIH HHS/ -- R37 GM043369-21/GM/NIGMS NIH HHS/ -- RC1 GM091804/GM/NIGMS NIH HHS/ -- RC1 GM091804-02/GM/NIGMS NIH HHS/ -- T32 GM007596/GM/NIGMS NIH HHS/ -- T32 GM007596-30/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2011 Mar 11;331(6022):1289-95. doi: 10.1126/science.1198830.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Pharmacology, Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21393538" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/metabolism ; Fluorescent Dyes ; Introns ; Kinetics ; Microscopy, Fluorescence ; Protein Binding ; RNA Precursors/*metabolism ; *RNA Splicing ; RNA, Fungal/*metabolism ; Ribonucleoprotein, U1 Small Nuclear/metabolism ; Ribonucleoprotein, U2 Small Nuclear/metabolism ; Ribonucleoprotein, U4-U6 Small Nuclear/metabolism ; Ribonucleoprotein, U5 Small Nuclear/metabolism ; Ribonucleoproteins, Small Nuclear/*metabolism ; Saccharomyces cerevisiae/genetics/*metabolism/ultrastructure ; Saccharomyces cerevisiae Proteins/*metabolism ; Spliceosomes/*metabolism
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  • 39
    Publication Date: 2011-09-24
    Description: Nonhexameric helicases use adenosine triphosphate (ATP) to unzip base pairs in double-stranded nucleic acids (dsNAs). Studies have suggested that these helicases unzip dsNAs in single-base pair increments, consuming one ATP molecule per base pair, but direct evidence for this mechanism is lacking. We used optical tweezers to follow the unwinding of double-stranded RNA by the hepatitis C virus NS3 helicase. Single-base pair steps by NS3 were observed, along with nascent nucleotide release that was asynchronous with base pair opening. Asynchronous release of nascent nucleotides rationalizes various observations of its dsNA unwinding and may be used to coordinate the translocation speed of NS3 along the RNA during viral replication.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4172460/" 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/PMC4172460/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cheng, Wei -- Arunajadai, Srikesh G -- Moffitt, Jeffrey R -- Tinoco, Ignacio Jr -- Bustamante, Carlos -- 5R01GM010840/GM/NIGMS NIH HHS/ -- 5R01GM032543/GM/NIGMS NIH HHS/ -- R01 GM010840/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2011 Sep 23;333(6050):1746-9. doi: 10.1126/science.1206023.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan, Ann Arbor, MI 48109, USA. chengwe@umich.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21940894" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/metabolism ; Algorithms ; Base Pairing ; Hepacivirus/*enzymology ; Kinetics ; Models, Biological ; Nucleic Acid Conformation ; Optical Tweezers ; RNA Helicases/*metabolism ; RNA, Double-Stranded/chemistry/*metabolism ; RNA, Viral/chemistry/*metabolism ; Viral Nonstructural Proteins/*metabolism
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  • 40
    Publication Date: 2011-03-19
    Description: In prokaryotes and eukaryotes, most genes appear to be transcribed during short periods called transcriptional bursts, interspersed by silent intervals. We describe how such bursts generate gene-specific temporal patterns of messenger RNA (mRNA) synthesis in mammalian cells. To monitor transcription at high temporal resolution, we established various gene trap cell lines and transgenic cell lines expressing a short-lived luciferase protein from an unstable mRNA, and recorded bioluminescence in real time in single cells. Mathematical modeling identified gene-specific on- and off-switching rates in transcriptional activity and mean numbers of mRNAs produced during the bursts. Transcriptional kinetics were markedly altered by cis-regulatory DNA elements. Our analysis demonstrated that bursting kinetics are highly gene-specific, reflecting refractory periods during which genes stay inactive for a certain time before switching on again.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Suter, David M -- Molina, Nacho -- Gatfield, David -- Schneider, Kim -- Schibler, Ueli -- Naef, Felix -- New York, N.Y. -- Science. 2011 Apr 22;332(6028):472-4. doi: 10.1126/science.1198817. Epub 2011 Mar 17.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, Sciences III, University of Geneva, 30 Quai Ernest Ansermet, 1211 Geneva, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21415320" target="_blank"〉PubMed〈/a〉
    Keywords: Acetylation ; Animals ; Cells, Cultured ; Chromatin/physiology ; Circadian Rhythm/genetics ; Down-Regulation ; *Gene Expression ; Histones/metabolism ; Kinetics ; Luminescent Measurements ; Mice ; Models, Genetic ; NIH 3T3 Cells ; Promoter Regions, Genetic ; Protein Biosynthesis ; RNA, Messenger/genetics/metabolism ; Stochastic Processes ; *Transcription, Genetic ; Transcriptional Activation ; Transgenes ; Up-Regulation
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  • 41
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    Unknown
    American Association for the Advancement of Science (AAAS)
    Publication Date: 2011-10-29
    Description: An outstanding challenge in the field of molecular biology has been to understand the process by which proteins fold into their characteristic three-dimensional structures. Here, we report the results of atomic-level molecular dynamics simulations, over periods ranging between 100 mus and 1 ms, that reveal a set of common principles underlying the folding of 12 structurally diverse proteins. In simulations conducted with a single physics-based energy function, the proteins, representing all three major structural classes, spontaneously and repeatedly fold to their experimentally determined native structures. Early in the folding process, the protein backbone adopts a nativelike topology while certain secondary structure elements and a small number of nonlocal contacts form. In most cases, folding follows a single dominant route in which elements of the native structure appear in an order highly correlated with their propensity to form in the unfolded state.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lindorff-Larsen, Kresten -- Piana, Stefano -- Dror, Ron O -- Shaw, David E -- New York, N.Y. -- Science. 2011 Oct 28;334(6055):517-20. doi: 10.1126/science.1208351.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉D. E. Shaw Research, New York, NY 10036, USA. kresten.lindorff-larsen@DEShawResearch.com〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22034434" target="_blank"〉PubMed〈/a〉
    Keywords: Kinetics ; Molecular Dynamics Simulation ; Protein Conformation ; *Protein Folding ; Protein Structure, Secondary ; Proteins/*chemistry ; Thermodynamics
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  • 42
    Publication Date: 2011-10-15
    Description: Periodic stripe patterns are ubiquitous in living organisms, yet the underlying developmental processes are complex and difficult to disentangle. We describe a synthetic genetic circuit that couples cell density and motility. This system enabled programmed Escherichia coli cells to form periodic stripes of high and low cell densities sequentially and autonomously. Theoretical and experimental analyses reveal that the spatial structure arises from a recurrent aggregation process at the front of the continuously expanding cell population. The number of stripes formed could be tuned by modulating the basal expression of a single gene. The results establish motility control as a simple route to establishing recurrent structures without requiring an extrinsic pacemaker.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Liu, Chenli -- Fu, Xiongfei -- Liu, Lizhong -- Ren, Xiaojing -- Chau, Carlos K L -- Li, Sihong -- Xiang, Lu -- Zeng, Hualing -- Chen, Guanhua -- Tang, Lei-Han -- Lenz, Peter -- Cui, Xiaodong -- Huang, Wei -- Hwa, Terence -- Huang, Jian-Dong -- New York, N.Y. -- Science. 2011 Oct 14;334(6053):238-41. doi: 10.1126/science.1209042.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, The University of Hong Kong, Pokfulam, Hong Kong, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21998392" target="_blank"〉PubMed〈/a〉
    Keywords: Acyl-Butyrolactones/metabolism ; Bacterial Load ; Cell Proliferation ; Culture Media ; Diffusion ; Escherichia coli K12/cytology/genetics/*growth & development/*physiology ; Gene Expression Regulation, Bacterial ; Gene Regulatory Networks ; Kinetics ; Models, Biological ; Movement ; Quorum Sensing ; Synthetic Biology
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  • 43
    Publication Date: 2011-04-23
    Description: Amination of alkanes has generally required metal catalysts and/or high temperatures. Here we report that simple exposure of a broad range of alkanes to N-triflylimino-lambda(3)-bromane 1 at ambient temperature results in C-H insertion of the nitrogen functionality to afford triflyl-substituted amines in moderate to high yields. Marked selectivity for tertiary over secondary C-H bonds was observed; primary (methyl) C-H bonds were inert. Addition of hexafluoroisopropanol to inhibit decomposition of 1 dramatically improved the C-H amination efficiencies. Second-order kinetics, activation parameters (negative activation entropy), deuterium isotope effects, and theoretical calculations suggest a concerted asynchronous bimolecular transition state for the metal-free C-H amination event.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ochiai, Masahito -- Miyamoto, Kazunori -- Kaneaki, Takao -- Hayashi, Satoko -- Nakanishi, Waro -- New York, N.Y. -- Science. 2011 Apr 22;332(6028):448-51. doi: 10.1126/science.1201686.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Graduate School of Pharmaceutical Sciences, University of Tokushima, 1-78 Shomachi, Tokushima 770-8505, Japan. mochiai@ph.tokushima-u.ac.jp〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21512029" target="_blank"〉PubMed〈/a〉
    Keywords: Adamantane/chemistry ; Alkanes/*chemistry ; Amination ; Amines/*chemistry ; Bromobenzenes/*chemistry ; Carbon/chemistry ; Hydrocarbons, Brominated/*chemistry ; Hydrogen/chemistry ; Kinetics ; Physicochemical Processes ; Stereoisomerism ; Temperature ; Thermodynamics
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  • 44
    Publication Date: 2011-07-19
    Description: Passive transfer of broadly neutralizing HIV antibodies can prevent infection, which suggests that vaccines that elicit such antibodies would be protective. Thus far, however, few broadly neutralizing HIV antibodies that occur naturally have been characterized. To determine whether these antibodies are part of a larger group of related molecules, we cloned 576 new HIV antibodies from four unrelated individuals. All four individuals produced expanded clones of potent broadly neutralizing CD4-binding-site antibodies that mimic binding to CD4. Despite extensive hypermutation, the new antibodies shared a consensus sequence of 68 immunoglobulin H (IgH) chain amino acids and arise independently from two related IgH genes. Comparison of the crystal structure of one of the antibodies to the broadly neutralizing antibody VRC01 revealed conservation of the contacts to the HIV spike.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3351836/" 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/PMC3351836/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Scheid, Johannes F -- Mouquet, Hugo -- Ueberheide, Beatrix -- Diskin, Ron -- Klein, Florian -- Oliveira, Thiago Y K -- Pietzsch, John -- Fenyo, David -- Abadir, Alexander -- Velinzon, Klara -- Hurley, Arlene -- Myung, Sunnie -- Boulad, Farid -- Poignard, Pascal -- Burton, Dennis R -- Pereyra, Florencia -- Ho, David D -- Walker, Bruce D -- Seaman, Michael S -- Bjorkman, Pamela J -- Chait, Brian T -- Nussenzweig, Michel C -- P01 AI081677/AI/NIAID NIH HHS/ -- P30 AI060354/AI/NIAID NIH HHS/ -- R01 AI033292/AI/NIAID NIH HHS/ -- RR00862/RR/NCRR NIH HHS/ -- RR022220/RR/NCRR NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2011 Sep 16;333(6049):1633-7. doi: 10.1126/science.1207227. Epub 2011 Jul 14.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21764753" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Antibodies, Neutralizing/*chemistry/*immunology/metabolism ; Antibody Affinity ; Antibody Specificity ; Antigens, CD4/immunology/*metabolism ; Binding Sites ; Binding Sites, Antibody ; Cloning, Molecular ; Consensus Sequence ; Crystallography, X-Ray ; Genes, Immunoglobulin Heavy Chain ; HIV Antibodies/*chemistry/*immunology/metabolism ; HIV Envelope Protein gp120/chemistry/*immunology/metabolism ; HIV Infections/immunology ; Humans ; Immunoglobulin Fab Fragments/chemistry ; Immunoglobulin Heavy Chains/chemistry ; Immunoglobulin Light Chains/chemistry ; Molecular Mimicry ; Molecular Sequence Data ; Mutation ; Protein Conformation
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  • 45
    Publication Date: 2011-01-06
    Description: Rhizobium-root nodule symbiosis is generally considered to be unique for legumes. However, there is one exception, and that is Parasponia. In this nonlegume, the rhizobial nodule symbiosis evolved independently and is, as in legumes, induced by rhizobium Nod factors. We used Parasponia andersonii to identify genetic constraints underlying evolution of Nod factor signaling. Part of the signaling cascade, downstream of Nod factor perception, has been recruited from the more-ancient arbuscular endomycorrhizal symbiosis. However, legume Nod factor receptors that activate this common signaling pathway are not essential for arbuscular endomycorrhizae. Here, we show that in Parasponia a single Nod factor-like receptor is indispensable for both symbiotic interactions. Therefore, we conclude that the Nod factor perception mechanism also is recruited from the widespread endomycorrhizal symbiosis.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Op den Camp, Rik -- Streng, Arend -- De Mita, Stephane -- Cao, Qingqin -- Polone, Elisa -- Liu, Wei -- Ammiraju, Jetty S S -- Kudrna, Dave -- Wing, Rod -- Untergasser, Andreas -- Bisseling, Ton -- Geurts, Rene -- New York, N.Y. -- Science. 2011 Feb 18;331(6019):909-12. doi: 10.1126/science.1198181. Epub 2010 Dec 23.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Plant Sciences, Wageningen University, Wageningen, Netherlands.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21205637" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Calcium-Calmodulin-Dependent Protein Kinases/metabolism ; Cloning, Molecular ; Evolution, Molecular ; Gene Duplication ; Genes, Plant ; Glomeromycota/physiology ; Lipopolysaccharides/*metabolism ; Molecular Sequence Data ; Mycorrhizae/*physiology ; Nitrogen Fixation ; Phylogeny ; Plant Proteins/genetics/*metabolism ; Plant Root Nodulation ; Protein Kinases/genetics/*metabolism ; RNA Interference ; Root Nodules, Plant/microbiology/physiology ; Signal Transduction ; Sinorhizobium/*physiology ; *Symbiosis ; Ulmaceae/genetics/*microbiology/*physiology
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  • 46
    Publication Date: 2011-04-09
    Description: Conformational dynamics play a key role in enzyme catalysis. Although protein motions have clear implications for ligand flux, a role for dynamics in the chemical step of enzyme catalysis has not been clearly established. We generated a mutant of Escherichia coli dihydrofolate reductase that abrogates millisecond-time-scale fluctuations in the enzyme active site without perturbing its structural and electrostatic preorganization. This dynamic knockout severely impairs hydride transfer. Thus, we have found a link between conformational fluctuations on the millisecond time scale and the chemical step of an enzymatic reaction, with broad implications for our understanding of enzyme mechanisms and for design of novel protein catalysts.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3151171/" 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/PMC3151171/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bhabha, Gira -- Lee, Jeeyeon -- Ekiert, Damian C -- Gam, Jongsik -- Wilson, Ian A -- Dyson, H Jane -- Benkovic, Stephen J -- Wright, Peter E -- GM080209/GM/NIGMS NIH HHS/ -- GM75995/GM/NIGMS NIH HHS/ -- R01 GM075995/GM/NIGMS NIH HHS/ -- U54 GM094586/GM/NIGMS NIH HHS/ -- Y1-CO-1020/CO/NCI NIH HHS/ -- Y1-GM-1104/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2011 Apr 8;332(6026):234-8. doi: 10.1126/science.1198542.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology and Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21474759" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Biocatalysis ; Catalytic Domain ; Crystallography, X-Ray ; Escherichia coli/*enzymology ; Folic Acid/chemistry ; Kinetics ; Models, Molecular ; Molecular Sequence Data ; Mutant Proteins/chemistry/metabolism ; NADP/chemistry ; Protein Conformation ; Tetrahydrofolate Dehydrogenase/*chemistry/genetics/*metabolism
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  • 47
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2011-03-19
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bradforth, Stephen -- New York, N.Y. -- Science. 2011 Mar 18;331(6023):1398-9. doi: 10.1126/science.1203629.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of Southern California, Los Angeles, CA 90089-0482, USA. stephen.bradforth@usc.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21415344" target="_blank"〉PubMed〈/a〉
    Keywords: Chemical Phenomena ; Cyclohexanes/*chemistry ; Free Radicals ; Hydrogen/*chemistry ; Hydrogen Cyanide/*chemistry ; Kinetics ; Solutions ; Solvents/chemistry
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  • 48
    Publication Date: 2011-09-03
    Description: A deeper mechanistic understanding of the saccharification of cellulosic biomass could enhance the efficiency of biofuels development. We report here the real-time visualization of crystalline cellulose degradation by individual cellulase enzymes through use of an advanced version of high-speed atomic force microscopy. Trichoderma reesei cellobiohydrolase I (TrCel7A) molecules were observed to slide unidirectionally along the crystalline cellulose surface but at one point exhibited collective halting analogous to a traffic jam. Changing the crystalline polymorphic form of cellulose by means of an ammonia treatment increased the apparent number of accessible lanes on the crystalline surface and consequently the number of moving cellulase molecules. Treatment of this bulky crystalline cellulose simultaneously or separately with T. reesei cellobiohydrolase II (TrCel6A) resulted in a remarkable increase in the proportion of mobile enzyme molecules on the surface. Cellulose was completely degraded by the synergistic action between the two enzymes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Igarashi, Kiyohiko -- Uchihashi, Takayuki -- Koivula, Anu -- Wada, Masahisa -- Kimura, Satoshi -- Okamoto, Tetsuaki -- Penttila, Merja -- Ando, Toshio -- Samejima, Masahiro -- New York, N.Y. -- Science. 2011 Sep 2;333(6047):1279-82. doi: 10.1126/science.1208386.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan. aquarius@mail.ecc.u-tokyo.ac.jp〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21885779" target="_blank"〉PubMed〈/a〉
    Keywords: Adsorption ; Biomass ; Cellobiose/metabolism ; Cellulose/chemistry/*metabolism ; Cellulose 1,4-beta-Cellobiosidase/*metabolism ; Crystallization ; Hydrolysis ; Kinetics ; Microscopy, Atomic Force ; Trichoderma/enzymology
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  • 49
    Publication Date: 2011-06-11
    Description: Aromatic molecules are key constituents of many pharmaceuticals, electronic materials, and commodity plastics. The utility of these molecules directly reflects the identity and pattern of substituents on the aromatic ring. Here, we report a palladium(II) catalyst system, incorporating an unconventional ortho-dimethylaminopyridine ligand, for the conversion of substituted cyclohexanones to the corresponding phenols. The reaction proceeds via successive dehydrogenation of two saturated carbon-carbon bonds of the six-membered ring and uses molecular oxygen as the hydrogen acceptor. This reactivity demonstrates a versatile and efficient strategy for the synthesis of substituted aromatic molecules with fundamentally different selectivity constraints from the numerous known synthetic methods that rely on substitution of a preexisting aromatic ring.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3174491/" 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/PMC3174491/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Izawa, Yusuke -- Pun, Doris -- Stahl, Shannon S -- RC1 GM091161/GM/NIGMS NIH HHS/ -- RC1 GM091161-01/GM/NIGMS NIH HHS/ -- RC1 GM091161-02/GM/NIGMS NIH HHS/ -- RC1-GM091161/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2011 Jul 8;333(6039):209-13. doi: 10.1126/science.1204183. Epub 2011 Jun 9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21659567" target="_blank"〉PubMed〈/a〉
    Keywords: Aerobiosis ; Catalysis ; Cyclohexanones/*chemistry ; Hydrogen/chemistry ; Kinetics ; Ligands ; Molecular Structure ; Organic Chemistry Processes ; Palladium/*chemistry ; Phenols/*chemical synthesis/*chemistry
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  • 50
    Publication Date: 2011-02-05
    Description: Solvent collisions can often mask initial disposition of energy to the products of solution-phase chemical reactions. Here, we show with transient infrared absorption spectra obtained with picosecond time resolution that the nascent HCN products of reaction of CN radicals with cyclohexane in chlorinated organic solvents exhibit preferential excitation of one quantum of the C-H stretching mode and up to two quanta of the bending mode. On time scales of approximately 100 to 300 picoseconds, the HCN products undergo relaxation to the vibrational ground state by coupling to the solvent bath. Comparison with reactions of CN radicals with alkanes in the gas phase, known to produce HCN with greater C-H stretch and bending mode excitation (up to two and approximately six quanta, respectively), indicates partial damping of the nascent product vibrational motion by the solvent. The transient infrared spectra therefore probe solvent-induced modifications to the reaction free energy surface and chemical dynamics.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Greaves, Stuart J -- Rose, Rebecca A -- Oliver, Thomas A A -- Glowacki, David R -- Ashfold, Michael N R -- Harvey, Jeremy N -- Clark, Ian P -- Greetham, Gregory M -- Parker, Anthony W -- Towrie, Michael -- Orr-Ewing, Andrew J -- ST/501784/Biotechnology and Biological Sciences Research Council/United Kingdom -- New York, N.Y. -- Science. 2011 Mar 18;331(6023):1423-6. doi: 10.1126/science.1197796. Epub 2011 Feb 3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Chemistry, University of Bristol, Cantock's Close, Bristol, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21292937" target="_blank"〉PubMed〈/a〉
    Keywords: Chemical Phenomena ; Cyclohexanes/*chemistry ; Free Radicals ; Hydrogen/*chemistry ; Hydrogen Cyanide/*chemistry ; Kinetics ; Models, Chemical ; Physicochemical Processes ; Solutions ; Solvents/chemistry ; Spectrophotometry, Infrared
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  • 51
    Publication Date: 2011-10-29
    Description: Direct observation of the detailed conformational fluctuations of a single protein molecule en route to its folded state has so far been realized only in silico. We have used single-molecule force spectroscopy to study the folding transitions of single calmodulin molecules. High-resolution optical tweezers assays in combination with hidden Markov analysis reveal a complex network of on- and off-pathway intermediates. Cooperative and anticooperative interactions across domain boundaries can be observed directly. The folding network involves four intermediates. Two off-pathway intermediates exhibit non-native interdomain interactions and compete with the ultrafast productive folding pathway.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stigler, Johannes -- Ziegler, Fabian -- Gieseke, Anja -- Gebhardt, J Christof M -- Rief, Matthias -- New York, N.Y. -- Science. 2011 Oct 28;334(6055):512-6. doi: 10.1126/science.1207598.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Physik Department E22, Technische Universitat Munchen, James-Franck-Strasse, 85748 Garching, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22034433" target="_blank"〉PubMed〈/a〉
    Keywords: Calcium/chemistry ; Calmodulin/*chemistry ; Kinetics ; Markov Chains ; Optical Tweezers ; Protein Conformation ; Protein Folding ; Protein Structure, Tertiary ; Thermodynamics
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  • 52
    Publication Date: 2011-11-15
    Description: Silent information regulator 2 (Sir2) proteins (sirtuins) are nicotinamide adenine dinucleotide-dependent deacetylases that regulate important biological processes. Mammals have seven sirtuins, Sirt1 to Sirt7. Four of them (Sirt4 to Sirt7) have no detectable or very weak deacetylase activity. We found that Sirt5 is an efficient protein lysine desuccinylase and demalonylase in vitro. The preference for succinyl and malonyl groups was explained by the presence of an arginine residue (Arg(105)) and tyrosine residue (Tyr(102)) in the acyl pocket of Sirt5. Several mammalian proteins were identified with mass spectrometry to have succinyl or malonyl lysine modifications. Deletion of Sirt5 in mice appeared to increase the level of succinylation on carbamoyl phosphate synthase 1, which is a known target of Sirt5. Thus, protein lysine succinylation may represent a posttranslational modification that can be reversed by Sirt5 in vivo.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3217313/" 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/PMC3217313/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Du, Jintang -- Zhou, Yeyun -- Su, Xiaoyang -- Yu, Jiu Jiu -- Khan, Saba -- Jiang, Hong -- Kim, Jungwoo -- Woo, Jimin -- Kim, Jun Huyn -- Choi, Brian Hyun -- He, Bin -- Chen, Wei -- Zhang, Sheng -- Cerione, Richard A -- Auwerx, Johan -- Hao, Quan -- Lin, Hening -- 231138/European Research Council/International -- DK58920/DK/NIDDK NIH HHS/ -- P41 RR001646/RR/NCRR NIH HHS/ -- P41 RR001646-27/RR/NCRR NIH HHS/ -- R01 GM086703/GM/NIGMS NIH HHS/ -- R01 GM086703-03/GM/NIGMS NIH HHS/ -- R01 GM086703-03S1/GM/NIGMS NIH HHS/ -- R01GM086703/GM/NIGMS NIH HHS/ -- RR01646/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 2011 Nov 11;334(6057):806-9. doi: 10.1126/science.1207861.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22076378" target="_blank"〉PubMed〈/a〉
    Keywords: Acetylation ; Animals ; Carbamoyl-Phosphate Synthase (Ammonia)/metabolism ; Cattle ; Crystallography, X-Ray ; Histones/metabolism ; Humans ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Kinetics ; Lysine/*metabolism ; Male ; Mice ; Mice, Knockout ; Mitochondria, Liver/metabolism ; NAD/metabolism ; Peptides/*metabolism ; Protein Processing, Post-Translational ; Sirtuins/chemistry/genetics/*metabolism ; Succinic Acid/*metabolism
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  • 53
    Publication Date: 2011-10-25
    Description: Inhibitor of apoptosis (IAP) proteins are negative regulators of cell death. IAP family members contain RING domains that impart E3 ubiquitin ligase activity. Binding of endogenous or small-molecule antagonists to select baculovirus IAP repeat (BIR) domains within cellular IAP (cIAP) proteins promotes autoubiquitination and proteasomal degradation and so releases inhibition of apoptosis mediated by cIAP. Although the molecular details of antagonist-BIR domain interactions are well understood, it is not clear how this binding event influences the activity of the RING domain. Here biochemical and structural studies reveal that the unliganded, multidomain cIAP1 sequesters the RING domain within a compact, monomeric structure that prevents RING dimerization. Antagonist binding induces conformational rearrangements that enable RING dimerization and formation of the active E3 ligase.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dueber, Erin C -- Schoeffler, Allyn J -- Lingel, Andreas -- Elliott, J Michael -- Fedorova, Anna V -- Giannetti, Anthony M -- Zobel, Kerry -- Maurer, Brigitte -- Varfolomeev, Eugene -- Wu, Ping -- Wallweber, Heidi J A -- Hymowitz, Sarah G -- Deshayes, Kurt -- Vucic, Domagoj -- Fairbrother, Wayne J -- P41RR001209/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 2011 Oct 21;334(6054):376-80. doi: 10.1126/science.1207862.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Early Discovery Biochemistry, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22021857" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Cell Line ; Cell Line, Tumor ; Cloning, Molecular ; Humans ; Hydrophobic and Hydrophilic Interactions ; Inhibitor of Apoptosis Proteins/*antagonists & inhibitors/*chemistry/metabolism ; Mice ; Models, Biological ; Models, Molecular ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; Proteasome Endopeptidase Complex/metabolism ; Protein Conformation ; Protein Interaction Domains and Motifs ; Protein Multimerization ; Protein Structure, Secondary ; Scattering, Small Angle ; Ubiquitin-Protein Ligases/chemistry/metabolism ; Ubiquitinated Proteins/chemistry/metabolism ; Ubiquitination
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  • 54
    Publication Date: 2011-12-24
    Description: DNA replication machineries have been studied extensively, but the kinetics of action of their components remains largely unknown. We report a study of DNA synthesis during replication in living Escherichia coli cells. Using single-molecule microscopy, we observed repetitive fluorescence bursts of single polymerase IIIs (Pol IIIs), indicating polymerase exchange at the replication fork. Fluctuations in the amount of DNA-bound single-stranded DNA-binding protein (SSB) reflect different speeds for the leading- and lagging-strand DNA polymerases. Coincidence analyses of Pol III and SSB fluctuations show that they correspond to the lagging-strand synthesis and suggest the use of a new Pol III for each Okazaki fragment. Based on exchanges involving two Pol IIIs, we propose that the third polymerase in the replisome is involved in lagging-strand synthesis.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lia, Giuseppe -- Michel, Benedicte -- Allemand, Jean-Francois -- New York, N.Y. -- Science. 2012 Jan 20;335(6066):328-31. doi: 10.1126/science.1210400. Epub 2011 Dec 22.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉CNRS, Centre de Genetique Moleculaire, UPR3404, Gif-sur-Yvette F-91198, France. lia@cgm.cnrs-gif.fr〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22194411" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/metabolism ; DNA/*biosynthesis ; DNA Polymerase III/*metabolism ; *DNA Replication ; DNA, Bacterial/*biosynthesis ; DNA, Single-Stranded/metabolism ; DNA-Binding Proteins/*metabolism ; Escherichia coli/*metabolism ; Escherichia coli Proteins/*metabolism ; Fluorescence ; Kinetics ; Luminescent Proteins/metabolism ; Models, Biological ; Photobleaching ; Recombinant Fusion Proteins/metabolism
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  • 55
    Publication Date: 2010-05-22
    Description: Cell surface receptors convert extracellular cues into receptor activation, thereby triggering intracellular signaling networks and controlling cellular decisions. A major unresolved issue is the identification of receptor properties that critically determine processing of ligand-encoded information. We show by mathematical modeling of quantitative data and experimental validation that rapid ligand depletion and replenishment of the cell surface receptor are characteristic features of the erythropoietin (Epo) receptor (EpoR). The amount of Epo-EpoR complexes and EpoR activation integrated over time corresponds linearly to ligand input; this process is carried out over a broad range of ligand concentrations. This relation depends solely on EpoR turnover independent of ligand binding, which suggests an essential role of large intracellular receptor pools. These receptor properties enable the system to cope with basal and acute demand in the hematopoietic system.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Becker, Verena -- Schilling, Marcel -- Bachmann, Julie -- Baumann, Ute -- Raue, Andreas -- Maiwald, Thomas -- Timmer, Jens -- Klingmuller, Ursula -- New York, N.Y. -- Science. 2010 Jun 11;328(5984):1404-8. doi: 10.1126/science.1184913. Epub 2010 May 20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division Systems Biology of Signal Transduction, DKFZ-ZMBH Alliance, German Cancer Research Center, 69120 Heidelberg, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20488988" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Line ; Cell Membrane/*metabolism ; Computer Simulation ; Endocytosis ; Epoetin Alfa ; Erythropoietin/metabolism/pharmacology ; Kinetics ; Ligands ; Mice ; Models, Biological ; Protein Binding ; Receptors, Erythropoietin/*metabolism ; Recombinant Proteins ; Signal Transduction
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  • 56
    Publication Date: 2010-09-11
    Description: Fungal degradation of plant biomass may provide insights for improving cellulosic biofuel production. We show that the model cellulolytic fungus Neurospora crassa relies on a high-affinity cellodextrin transport system for rapid growth on cellulose. Reconstitution of the N. crassa cellodextrin transport system in Saccharomyces cerevisiae promotes efficient growth of this yeast on cellodextrins. In simultaneous saccharification and fermentation experiments, the engineered yeast strains more rapidly convert cellulose to ethanol when compared with yeast lacking this system.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Galazka, Jonathan M -- Tian, Chaoguang -- Beeson, William T -- Martinez, Bruno -- Glass, N Louise -- Cate, Jamie H D -- New York, N.Y. -- Science. 2010 Oct 1;330(6000):84-6. doi: 10.1126/science.1192838. Epub 2010 Sep 9.〈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/20829451" target="_blank"〉PubMed〈/a〉
    Keywords: *Biofuels ; Biological Transport ; Biomass ; Cellobiose/metabolism ; Cellulase/metabolism ; Cellulose/*analogs & derivatives/*metabolism ; Dextrins/*metabolism ; Ethanol/metabolism ; Fermentation ; Fungal Proteins/genetics/*metabolism ; Genetic Engineering ; Kinetics ; Membrane Transport Proteins/genetics/*metabolism ; Neurospora crassa/genetics/growth & development/*metabolism ; Saccharomyces cerevisiae/genetics/growth & development/*metabolism ; Saccharomyces cerevisiae Proteins/metabolism ; beta-Glucosidase/metabolism
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 57
    Publication Date: 2010-07-10
    Description: Self-organization of nanoparticles is an efficient strategy for producing nanostructures with complex, hierarchical architectures. The past decade has witnessed great progress in nanoparticle self-assembly, yet the quantitative prediction of the architecture of nanoparticle ensembles and of the kinetics of their formation remains a challenge. We report on the marked similarity between the self-assembly of metal nanoparticles and reaction-controlled step-growth polymerization. The nanoparticles act as multifunctional monomer units, which form reversible, noncovalent bonds at specific bond angles and organize themselves into a colloidal polymer. We show that the kinetics and statistics of step-growth polymerization enable a quantitative prediction of the architecture of linear, branched, and cyclic self-assembled nanostructures; their aggregation numbers and size distribution; and the formation of structural isomers.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Liu, Kun -- Nie, Zhihong -- Zhao, Nana -- Li, Wei -- Rubinstein, Michael -- Kumacheva, Eugenia -- 1-R01-HL077546-03A2/HL/NHLBI NIH HHS/ -- New York, N.Y. -- Science. 2010 Jul 9;329(5988):197-200. doi: 10.1126/science.1189457.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of Toronto, 80 Saint George Street, Toronto, Ontario M5S 3H6, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20616274" target="_blank"〉PubMed〈/a〉
    Keywords: Cetrimonium Compounds/chemistry ; Colloids ; Cyclization ; Gold ; Isomerism ; Kinetics ; Metal Nanoparticles/*chemistry ; Microscopy, Electron, Transmission ; Nanotechnology/methods ; Physicochemical Processes ; Polymers ; Polystyrenes/chemistry
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  • 58
    Publication Date: 2010-09-18
    Description: Proliferating cells, including cancer cells, require altered metabolism to efficiently incorporate nutrients such as glucose into biomass. The M2 isoform of pyruvate kinase (PKM2) promotes the metabolism of glucose by aerobic glycolysis and contributes to anabolic metabolism. Paradoxically, decreased pyruvate kinase enzyme activity accompanies the expression of PKM2 in rapidly dividing cancer cells and tissues. We demonstrate that phosphoenolpyruvate (PEP), the substrate for pyruvate kinase in cells, can act as a phosphate donor in mammalian cells because PEP participates in the phosphorylation of the glycolytic enzyme phosphoglycerate mutase (PGAM1) in PKM2-expressing cells. We used mass spectrometry to show that the phosphate from PEP is transferred to the catalytic histidine (His11) on human PGAM1. This reaction occurred at physiological concentrations of PEP and produced pyruvate in the absence of PKM2 activity. The presence of histidine-phosphorylated PGAM1 correlated with the expression of PKM2 in cancer cell lines and tumor tissues. Thus, decreased pyruvate kinase activity in PKM2-expressing cells allows PEP-dependent histidine phosphorylation of PGAM1 and may provide an alternate glycolytic pathway that decouples adenosine triphosphate production from PEP-mediated phosphotransfer, allowing for the high rate of glycolysis to support the anabolic metabolism observed in many proliferating cells.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3030121/" 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/PMC3030121/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Vander Heiden, Matthew G -- Locasale, Jason W -- Swanson, Kenneth D -- Sharfi, Hadar -- Heffron, Greg J -- Amador-Noguez, Daniel -- Christofk, Heather R -- Wagner, Gerhard -- Rabinowitz, Joshua D -- Asara, John M -- Cantley, Lewis C -- 1K08CA136983/CA/NCI NIH HHS/ -- 1P01CA120964-01A/CA/NCI NIH HHS/ -- 5 T32 CA009361-28/CA/NCI NIH HHS/ -- 5P30CA006516-43/CA/NCI NIH HHS/ -- K08 CA136983/CA/NCI NIH HHS/ -- K08 CA136983-02/CA/NCI NIH HHS/ -- P01 CA089021/CA/NCI NIH HHS/ -- P01 CA089021-10/CA/NCI NIH HHS/ -- P01 CA120964/CA/NCI NIH HHS/ -- P01 CA120964-01A1/CA/NCI NIH HHS/ -- P01 GM047467/GM/NIGMS NIH HHS/ -- P01 GM047467-20/GM/NIGMS NIH HHS/ -- P01CA089021/CA/NCI NIH HHS/ -- P01GM047467/GM/NIGMS NIH HHS/ -- P30 CA006516/CA/NCI NIH HHS/ -- P30 CA006516-43S1/CA/NCI NIH HHS/ -- R01 AI078063/AI/NIAID NIH HHS/ -- R01 GM056203/GM/NIGMS NIH HHS/ -- R01-GM56302/GM/NIGMS NIH HHS/ -- R21 CA128620/CA/NCI NIH HHS/ -- R21/R33 DK070299/DK/NIDDK NIH HHS/ -- R33 DK070299/DK/NIDDK NIH HHS/ -- R33 DK070299-03/DK/NIDDK NIH HHS/ -- T32 CA009172/CA/NCI NIH HHS/ -- T32 CA009361/CA/NCI NIH HHS/ -- T32 CA009361-28/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2010 Sep 17;329(5998):1492-9. doi: 10.1126/science.1188015.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Dana Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20847263" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/metabolism ; Animals ; Cell Line ; Cell Line, Tumor ; *Cell Proliferation ; Female ; Glucose/*metabolism ; Glyceric Acids/metabolism ; *Glycolysis ; Histidine/metabolism ; Humans ; Isoenzymes/metabolism ; Kinetics ; Male ; Mammary Neoplasms, Animal/metabolism ; Mice ; Neoplasms/*metabolism/pathology ; Phosphoenolpyruvate/metabolism ; Phosphoglycerate Mutase/*metabolism ; Phosphopyruvate Hydratase/metabolism ; Phosphorylation ; Prostatic Neoplasms/metabolism ; Pyruvate Kinase/*metabolism ; Pyruvic Acid/metabolism ; Recombinant Proteins/metabolism
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  • 59
    Publication Date: 2010-12-15
    Description: Alzheimer's disease is hypothesized to be caused by an imbalance between beta-amyloid (Abeta) production and clearance that leads to Abeta accumulation in the central nervous system (CNS). Abeta production and clearance are key targets in the development of disease-modifying therapeutic agents for Alzheimer's disease. However, there has not been direct evidence of altered Abeta production or clearance in Alzheimer's disease. By using metabolic labeling, we measured Abeta42 and Abeta40 production and clearance rates in the CNS of participants with Alzheimer's disease and cognitively normal controls. Clearance rates for both Abeta42 and Abeta40 were impaired in Alzheimer's disease compared with controls. On average, there were no differences in Abeta40 or Abeta42 production rates. Thus, the common late-onset form of Alzheimer's disease is characterized by an overall impairment in Abeta clearance.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3073454/" 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/PMC3073454/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mawuenyega, Kwasi G -- Sigurdson, Wendy -- Ovod, Vitaliy -- Munsell, Ling -- Kasten, Tom -- Morris, John C -- Yarasheski, Kevin E -- Bateman, Randall J -- K08 AG027091/AG/NIA NIH HHS/ -- K08 AG027091-03/AG/NIA NIH HHS/ -- K23 AG030946/AG/NIA NIH HHS/ -- K23 AG030946-04/AG/NIA NIH HHS/ -- P01 AG003991/AG/NIA NIH HHS/ -- P01 AG003991-28/AG/NIA NIH HHS/ -- P01 AG03991/AG/NIA NIH HHS/ -- P30 DK056341/DK/NIDDK NIH HHS/ -- P30 DK056341-10/DK/NIDDK NIH HHS/ -- P41 GM103422/GM/NIGMS NIH HHS/ -- P41 RR000954/RR/NCRR NIH HHS/ -- P41 RR000954-34/RR/NCRR NIH HHS/ -- P50 AG005681/AG/NIA NIH HHS/ -- P50 AG005681-28/AG/NIA NIH HHS/ -- P50 AG05681/AG/NIA NIH HHS/ -- P60 DK020579/DK/NIDDK NIH HHS/ -- P60 DK020579-31/DK/NIDDK NIH HHS/ -- R01 NS065667/NS/NINDS NIH HHS/ -- R01 NS065667-03/NS/NINDS NIH HHS/ -- UL1 RR024992/RR/NCRR NIH HHS/ -- UL1 RR024992-05/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 2010 Dec 24;330(6012):1774. doi: 10.1126/science.1197623. Epub 2010 Dec 9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21148344" target="_blank"〉PubMed〈/a〉
    Keywords: Aged ; Aged, 80 and over ; Alzheimer Disease/cerebrospinal fluid/*metabolism ; Amyloid beta-Peptides/cerebrospinal fluid/*metabolism ; Brain/*metabolism ; Female ; Humans ; Kinetics ; Male ; Middle Aged ; Peptide Fragments/cerebrospinal fluid/*metabolism
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  • 60
    Publication Date: 2010-06-05
    Description: Despite the widespread use of axially chiral, or atropisomeric, biaryl ligands in modern synthesis and the occurrence of numerous natural products exhibiting axial chirality, few catalytic methods have emerged for the direct asymmetric preparation of this compound class. Here, we present a tripeptide-derived small-molecule catalyst for the dynamic kinetic resolution of racemic biaryl substrates. The reaction proceeds via an atropisomer-selective electrophilic aromatic substitution reaction using simple bromination reagents. The result is an enantioselective synthesis that delivers chiral nonracemic biaryl compounds with excellent optical purity and good isolated chemical yields (in most cases a 〉95:5 enantiomer ratio and isolated yields of 65 to 87%). A mechanistic model is advanced that accounts for the basis of selectivity observed.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3066098/" 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/PMC3066098/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gustafson, Jeffrey L -- Lim, Daniel -- Miller, Scott J -- GM068649/GM/NIGMS NIH HHS/ -- R01 GM068649/GM/NIGMS NIH HHS/ -- R01 GM068649-10/GM/NIGMS NIH HHS/ -- R37 GM068649/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2010 Jun 4;328(5983):1251-5. doi: 10.1126/science.1188403.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Yale University, 225 Prospect Street, Post Office Box 208107, New Haven, CT 06520-8107, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20522769" target="_blank"〉PubMed〈/a〉
    Keywords: Biphenyl Compounds/*chemical synthesis/chemistry ; Bromine/chemistry ; Catalysis ; *Halogenation ; Kinetics ; Ligands ; Molecular Structure ; Oligopeptides/*chemistry ; Physicochemical Processes ; *Stereoisomerism ; Temperature
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  • 61
    Publication Date: 2010-10-16
    Description: Neutrophils are recruited from the blood to sites of sterile inflammation, where they contribute to wound healing but may also cause tissue damage. By using spinning disk confocal intravital microscopy, we examined the kinetics and molecular mechanisms of neutrophil recruitment to sites of focal hepatic necrosis in vivo. Adenosine triphosphate released from necrotic cells activated the Nlrp3 inflammasome to generate an inflammatory microenvironment that alerted circulating neutrophils to adhere within liver sinusoids. Subsequently, generation of an intravascular chemokine gradient directed neutrophil migration through healthy tissue toward foci of damage. Lastly, formyl-peptide signals released from necrotic cells guided neutrophils through nonperfused sinusoids into the injury. Thus, dynamic in vivo imaging revealed a multistep hierarchy of directional cues that guide neutrophil localization to sites of sterile inflammation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉McDonald, Braedon -- Pittman, Keir -- Menezes, Gustavo B -- Hirota, Simon A -- Slaba, Ingrid -- Waterhouse, Christopher C M -- Beck, Paul L -- Muruve, Daniel A -- Kubes, Paul -- Canadian Institutes of Health Research/Canada -- New York, N.Y. -- Science. 2010 Oct 15;330(6002):362-6. doi: 10.1126/science.1195491.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Immunology Research Group, University of Calgary, Alberta T2N 4N1, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20947763" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/metabolism ; Animals ; Carrier Proteins/metabolism ; Cell Adhesion ; Chemokine CXCL2/metabolism ; Chemokines/metabolism ; Chemotaxis, Leukocyte ; Cues ; Endothelium, Vascular/physiology ; Inflammation/*immunology/metabolism/*pathology ; Kinetics ; Liver/blood supply/*immunology/metabolism/*pathology ; Liver Diseases/*immunology/metabolism/*pathology ; Macrophage-1 Antigen/physiology ; Mice ; Microscopy/methods ; Microscopy, Confocal ; Microvessels/physiology ; Necrosis ; *Neutrophil Infiltration ; Neutrophils/physiology ; Peptides/metabolism ; Receptors, Formyl Peptide/metabolism ; Receptors, Interleukin-8B/metabolism ; Receptors, Purinergic P2/metabolism ; Receptors, Purinergic P2X7 ; Signal Transduction
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  • 62
    Publication Date: 2010-07-22
    Description: The Diels-Alder reaction is a cornerstone in organic synthesis, forming two carbon-carbon bonds and up to four new stereogenic centers in one step. No naturally occurring enzymes have been shown to catalyze bimolecular Diels-Alder reactions. We describe the de novo computational design and experimental characterization of enzymes catalyzing a bimolecular Diels-Alder reaction with high stereoselectivity and substrate specificity. X-ray crystallography confirms that the structure matches the design for the most active of the enzymes, and binding site substitutions reprogram the substrate specificity. Designed stereoselective catalysts for carbon-carbon bond-forming reactions should be broadly useful in synthetic chemistry.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3241958/" 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/PMC3241958/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Siegel, Justin B -- Zanghellini, Alexandre -- Lovick, Helena M -- Kiss, Gert -- Lambert, Abigail R -- St Clair, Jennifer L -- Gallaher, Jasmine L -- Hilvert, Donald -- Gelb, Michael H -- Stoddard, Barry L -- Houk, Kendall N -- Michael, Forrest E -- Baker, David -- R01 GM075962/GM/NIGMS NIH HHS/ -- T32 GM008268/GM/NIGMS NIH HHS/ -- T32 GM008268-24/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2010 Jul 16;329(5989):309-13. doi: 10.1126/science.1190239.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20647463" target="_blank"〉PubMed〈/a〉
    Keywords: Acrylamides/chemistry ; Algorithms ; Butadienes/chemistry ; Carbon/*chemistry ; Catalysis ; Catalytic Domain ; Computer Simulation ; *Computer-Aided Design ; Crystallography, X-Ray ; Enzymes/*chemistry/genetics ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Kinetics ; Models, Molecular ; Mutagenesis ; Physicochemical Processes ; Protein Conformation ; *Protein Engineering ; Proteins/*chemistry/genetics ; Software ; Stereoisomerism ; Substrate Specificity
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  • 63
    Publication Date: 2010-09-11
    Description: Filopodia are finger-like protrusive structures, containing actin bundles. By incubating frog egg extracts with supported lipid bilayers containing phosphatidylinositol 4,5 bisphosphate, we have reconstituted the assembly of filopodia-like structures (FLSs). The actin assembles into parallel bundles, and known filopodial components localize to the tip and shaft. The filopodia tip complexes self-organize--they are not templated by preexisting membrane microdomains. The F-BAR domain protein toca-1 recruits N-WASP, followed by the Arp2/3 complex and actin. Elongation proteins, Diaphanous-related formin, VASP, and fascin are recruited subsequently. Although the Arp2/3 complex is required for FLS initiation, it is not essential for elongation, which involves formins. We propose that filopodia form via clustering of Arp2/3 complex activators, self-assembly of filopodial tip complexes on the membrane, and outgrowth of actin bundles.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2982780/" 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/PMC2982780/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lee, Kwonmoo -- Gallop, Jennifer L -- Rambani, Komal -- Kirschner, Marc W -- GM26875/GM/NIGMS NIH HHS/ -- R01 GM026875/GM/NIGMS NIH HHS/ -- R01 GM026875-34/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2010 Sep 10;329(5997):1341-5. doi: 10.1126/science.1191710.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20829485" target="_blank"〉PubMed〈/a〉
    Keywords: Actin Cytoskeleton/ultrastructure ; Actin-Related Protein 2-3 Complex/metabolism ; Actins/*metabolism ; Animals ; Carrier Proteins/metabolism ; Cell Adhesion Molecules/metabolism ; Cell Membrane/metabolism ; Humans ; Kinetics ; *Lipid Bilayers ; Membrane Microdomains ; Mice ; Microfilament Proteins/metabolism ; Microtubule-Associated Proteins/metabolism ; NADPH Dehydrogenase/metabolism ; Phosphatidylinositol Phosphates/metabolism ; Phosphoproteins/metabolism ; Pseudopodia/*metabolism/*ultrastructure ; Recombinant Fusion Proteins/metabolism ; Signal Transduction ; Wiskott-Aldrich Syndrome Protein, Neuronal/metabolism ; Xenopus ; Xenopus Proteins/metabolism
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  • 64
    Publication Date: 2010-05-08
    Description: Proper protein localization is essential for all cells. However, the precise mechanism by which high fidelity is achieved is not well understood for any protein-targeting pathway. To address this fundamental question, we investigated the signal recognition particle (SRP) pathway in Escherichia coli, which delivers proteins to the bacterial inner membrane through recognition of signal sequences on cargo proteins. Fidelity was thought to arise from the inability of SRP to bind strongly to incorrect cargos. Using biophysical assays, we found that incorrect cargos were also rejected through a series of checkpoints during subsequent steps of targeting. Thus, high fidelity of substrate selection is achieved through the cumulative effect of multiple checkpoints; this principle may be generally applicable to other pathways involving selective signal recognition.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3760334/" 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/PMC3760334/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhang, Xin -- Rashid, Rumana -- Wang, Kai -- Shan, Shu-ou -- GM078024/GM/NIGMS NIH HHS/ -- R01 GM078024/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2010 May 7;328(5979):757-60. doi: 10.1126/science.1186743.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20448185" target="_blank"〉PubMed〈/a〉
    Keywords: Cell Membrane/metabolism ; Escherichia coli/*metabolism ; Escherichia coli Proteins/chemistry/*metabolism ; Fluorescence Resonance Energy Transfer ; Guanosine Triphosphate/metabolism ; Hydrophobic and Hydrophilic Interactions ; Kinetics ; Models, Biological ; Protein Binding ; Protein Biosynthesis ; *Protein Sorting Signals ; *Protein Transport ; Ribosomes/metabolism ; Signal Recognition Particle/*metabolism ; Thermodynamics
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  • 65
    Publication Date: 2010-09-04
    Description: Mechanical stimuli drive many physiological processes, including touch and pain sensation, hearing, and blood pressure regulation. Mechanically activated (MA) cation channel activities have been recorded in many cells, but the responsible molecules have not been identified. We characterized a rapidly adapting MA current in a mouse neuroblastoma cell line. Expression profiling and RNA interference knockdown of candidate genes identified Piezo1 (Fam38A) to be required for MA currents in these cells. Piezo1 and related Piezo2 (Fam38B) are vertebrate multipass transmembrane proteins with homologs in invertebrates, plants, and protozoa. Overexpression of mouse Piezo1 or Piezo2 induced two kinetically distinct MA currents. Piezos are expressed in several tissues, and knockdown of Piezo2 in dorsal root ganglia neurons specifically reduced rapidly adapting MA currents. We propose that Piezos are components of MA cation channels.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3062430/" 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/PMC3062430/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Coste, Bertrand -- Mathur, Jayanti -- Schmidt, Manuela -- Earley, Taryn J -- Ranade, Sanjeev -- Petrus, Matt J -- Dubin, Adrienne E -- Patapoutian, Ardem -- DE016927/DE/NIDCR NIH HHS/ -- NS046303/NS/NINDS NIH HHS/ -- R01 NS046303/NS/NINDS NIH HHS/ -- R01 NS046303-08/NS/NINDS NIH HHS/ -- New York, N.Y. -- Science. 2010 Oct 1;330(6000):55-60. doi: 10.1126/science.1193270. Epub 2010 Sep 2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cell Biology, The Scripps Research Institute (TSRI), La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20813920" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cations/*metabolism ; Cell Line, Tumor ; Cell Membrane/chemistry ; Cloning, Molecular ; Ganglia, Spinal/cytology ; Ion Channels/analysis/chemistry/genetics/*metabolism ; *Mechanotransduction, Cellular ; Membrane Potentials ; Mice ; Molecular Sequence Data ; Neurons/*metabolism ; Patch-Clamp Techniques ; Pressure ; Protein Structure, Tertiary ; RNA Interference ; RNA, Small Interfering/genetics ; Transfection
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  • 66
    facet.materialart.
    Unknown
    American Association for the Advancement of Science (AAAS)
    Publication Date: 2010-07-31
    Description: Spiders and silkworms generate silk protein fibers that embody strength and beauty. Orb webs are fascinating feats of bioengineering in nature, displaying magnificent architectures while providing essential survival utility for spiders. The unusual combination of high strength and extensibility is a characteristic unavailable to date in synthetic materials yet is attained in nature with a relatively simple protein processed from water. This biological template suggests new directions to emulate in the pursuit of new high-performance, multifunctional materials generated with a green chemistry and processing approach. These bio-inspired and high-technology materials can lead to multifunctional material platforms that integrate with living systems for medical materials and a host of other applications.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3136811/" 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/PMC3136811/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Omenetto, Fiorenzo G -- Kaplan, David L -- P41 EB002520/EB/NIBIB NIH HHS/ -- P41 EB002520-07/EB/NIBIB NIH HHS/ -- R01 EY020856/EY/NEI NIH HHS/ -- New York, N.Y. -- Science. 2010 Jul 30;329(5991):528-31. doi: 10.1126/science.1188936.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biomedical Engineering, Tufts University, Medford, MA 02155, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20671180" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biocompatible Materials ; Biomimetic Materials ; Bombyx/genetics/metabolism ; Cloning, Molecular ; Genetic Engineering ; Mechanical Phenomena ; Organisms, Genetically Modified ; Recombinant Proteins/chemistry/metabolism ; *Silk/chemistry/genetics/metabolism ; Spiders/genetics/metabolism ; Textiles
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  • 67
    Publication Date: 2010-05-22
    Description: We report the design, synthesis, and assembly of the 1.08-mega-base pair Mycoplasma mycoides JCVI-syn1.0 genome starting from digitized genome sequence information and its transplantation into a M. capricolum recipient cell to create new M. mycoides cells that are controlled only by the synthetic chromosome. The only DNA in the cells is the designed synthetic DNA sequence, including "watermark" sequences and other designed gene deletions and polymorphisms, and mutations acquired during the building process. The new cells have expected phenotypic properties and are capable of continuous self-replication.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gibson, Daniel G -- Glass, John I -- Lartigue, Carole -- Noskov, Vladimir N -- Chuang, Ray-Yuan -- Algire, Mikkel A -- Benders, Gwynedd A -- Montague, Michael G -- Ma, Li -- Moodie, Monzia M -- Merryman, Chuck -- Vashee, Sanjay -- Krishnakumar, Radha -- Assad-Garcia, Nacyra -- Andrews-Pfannkoch, Cynthia -- Denisova, Evgeniya A -- Young, Lei -- Qi, Zhi-Qing -- Segall-Shapiro, Thomas H -- Calvey, Christopher H -- Parmar, Prashanth P -- Hutchison, Clyde A 3rd -- Smith, Hamilton O -- Venter, J Craig -- New York, N.Y. -- Science. 2010 Jul 2;329(5987):52-6. doi: 10.1126/science.1190719. Epub 2010 May 20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20488990" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/analysis ; Base Sequence ; *Bioengineering ; Cloning, Molecular ; DNA, Bacterial/chemical synthesis/genetics ; Escherichia coli/genetics ; Gene Deletion ; Genes, Bacterial ; *Genetic Engineering ; *Genome, Bacterial ; Molecular Sequence Data ; Mycoplasma capricolum/*genetics ; Mycoplasma mycoides/*genetics/growth & development/physiology/ultrastructure ; Phenotype ; Plasmids ; Polymerase Chain Reaction ; Polymorphism, Genetic ; Saccharomyces cerevisiae/genetics ; Transformation, Bacterial
    Print ISSN: 0036-8075
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  • 68
    Publication Date: 2010-10-16
    Description: Molecular dynamics (MD) simulations are widely used to study protein motions at an atomic level of detail, but they have been limited to time scales shorter than those of many biologically critical conformational changes. We examined two fundamental processes in protein dynamics--protein folding and conformational change within the folded state--by means of extremely long all-atom MD simulations conducted on a special-purpose machine. Equilibrium simulations of a WW protein domain captured multiple folding and unfolding events that consistently follow a well-defined folding pathway; separate simulations of the protein's constituent substructures shed light on possible determinants of this pathway. A 1-millisecond simulation of the folded protein BPTI reveals a small number of structurally distinct conformational states whose reversible interconversion is slower than local relaxations within those states by a factor of more than 1000.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shaw, David E -- Maragakis, Paul -- Lindorff-Larsen, Kresten -- Piana, Stefano -- Dror, Ron O -- Eastwood, Michael P -- Bank, Joseph A -- Jumper, John M -- Salmon, John K -- Shan, Yibing -- Wriggers, Willy -- New York, N.Y. -- Science. 2010 Oct 15;330(6002):341-6. doi: 10.1126/science.1187409.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉D. E. Shaw Research, 120 West 45th Street, New York, NY 10036, USA. David.Shaw@DEShawResearch.com〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20947758" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Substitution ; Aprotinin/*chemistry ; Computational Biology ; Computers ; Kinetics ; Microfilament Proteins/chemistry ; Models, Molecular ; *Molecular Dynamics Simulation ; Mutant Proteins/chemistry ; *Protein Conformation ; *Protein Folding ; Protein Structure, Tertiary ; Proteins/*chemistry ; Solvents ; Thermodynamics
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  • 69
    Publication Date: 2010-01-23
    Description: Viruses are thought to spread across susceptible cells through an iterative process of infection, replication, and release, so that the rate of spread is limited by replication kinetics. Here, we show that vaccinia virus spreads across one cell every 75 minutes, fourfold faster than its replication cycle would permit. To explain this phenomenon, we found that newly infected cells express two surface proteins that mark cells as infected and, via exploitation of cellular machinery, induce the repulsion of superinfecting virions away toward uninfected cells. Mechanistically, early expression of proteins A33 and A36 was critical for virion repulsion and rapid spread, and cells expressing these proteins repelled exogenous virions rapidly. Additional spreading mechanisms may exist for other viruses that also spread faster than predicted by replication kinetics.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4202693/" 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/PMC4202693/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Doceul, Virginie -- Hollinshead, Michael -- van der Linden, Lonneke -- Smith, Geoffrey L -- 061484/Wellcome Trust/United Kingdom -- 090315/Wellcome Trust/United Kingdom -- G0501257/Medical Research Council/United Kingdom -- Medical Research Council/United Kingdom -- New York, N.Y. -- Science. 2010 Feb 12;327(5967):873-6. doi: 10.1126/science.1183173. Epub 2010 Jan 21.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Virology, Faculty of Medicine, Imperial College London, St Mary's Campus, Norfolk Place, London W2 1PG, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20093437" target="_blank"〉PubMed〈/a〉
    Keywords: Actins/metabolism ; Animals ; Cell Membrane/metabolism ; Genes, Viral ; HeLa Cells ; Humans ; Kinetics ; Membrane Glycoproteins/genetics/*metabolism ; Vaccinia virus/genetics/pathogenicity/*physiology ; Viral Envelope Proteins/genetics/*metabolism ; Viral Plaque Assay ; Viral Structural Proteins/genetics/*metabolism ; Virion/physiology ; Virus Release ; Virus Replication
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  • 70
    Publication Date: 2010-09-11
    Description: Proteins can sample conformational states that are critical for function but are seldom detected directly because of their low occupancies and short lifetimes. In this work, we used chemical shifts and bond-vector orientation constraints obtained from nuclear magnetic resonance relaxation dispersion spectroscopy, in concert with a chemical shift-based method for structure elucidation, to determine an atomic-resolution structure of an "invisible" folding intermediate of a small protein module: the FF domain. The structure reveals non-native elements preventing formation of the native conformation in the carboxyl-terminal part of the protein. This is consistent with the kinetics of folding in which a well-structured intermediate forms rapidly and then rearranges slowly to the native state. The approach introduces a general strategy for structure determination of low-populated and transiently formed protein states.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Korzhnev, Dmitry M -- Religa, Tomasz L -- Banachewicz, Wiktor -- Fersht, Alan R -- Kay, Lewis E -- MC_U105484373/Medical Research Council/United Kingdom -- Canadian Institutes of Health Research/Canada -- New York, N.Y. -- Science. 2010 Sep 10;329(5997):1312-6. doi: 10.1126/science.1191723.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Genetics, the University of Toronto, Toronto, Ontario M5S 1A8, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20829478" target="_blank"〉PubMed〈/a〉
    Keywords: Carrier Proteins/*chemistry ; Computational Biology ; Kinetics ; Models, Molecular ; Nuclear Magnetic Resonance, Biomolecular ; Protein Conformation ; *Protein Folding ; Protein Structure, Secondary ; *Protein Structure, Tertiary ; Software ; Thermodynamics
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  • 71
    Publication Date: 2010-10-23
    Description: Transmembrane signals initiated by a broad range of extracellular stimuli converge on nodes that regulate phospholipase C (PLC)-dependent inositol lipid hydrolysis for signal propagation. We describe how heterotrimeric guanine nucleotide-binding proteins (G proteins) activate PLC-betas and in turn are deactivated by these downstream effectors. The 2.7-angstrom structure of PLC-beta3 bound to activated Galpha(q) reveals a conserved module found within PLC-betas and other effectors optimized for rapid engagement of activated G proteins. The active site of PLC-beta3 in the complex is occluded by an intramolecular plug that is likely removed upon G protein-dependent anchoring and orientation of the lipase at membrane surfaces. A second domain of PLC-beta3 subsequently accelerates guanosine triphosphate hydrolysis by Galpha(q), causing the complex to dissociate and terminate signal propagation. Mutations within this domain dramatically delay signal termination in vitro and in vivo. Consequently, this work suggests a dynamic catch-and-release mechanism used to sharpen spatiotemporal signals mediated by diverse sensory inputs.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3046049/" 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/PMC3046049/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Waldo, Gary L -- Ricks, Tiffany K -- Hicks, Stephanie N -- Cheever, Matthew L -- Kawano, Takeharu -- Tsuboi, Kazuhito -- Wang, Xiaoyue -- Montell, Craig -- Kozasa, Tohru -- Sondek, John -- Harden, T Kendall -- EY010852/EY/NEI NIH HHS/ -- GM074001/GM/NIGMS NIH HHS/ -- GM38213/GM/NIGMS NIH HHS/ -- GM57391/GM/NIGMS NIH HHS/ -- GM61454/GM/NIGMS NIH HHS/ -- R01 GM057391/GM/NIGMS NIH HHS/ -- R01 GM057391-13/GM/NIGMS NIH HHS/ -- R01 GM062299/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2010 Nov 12;330(6006):974-80. doi: 10.1126/science.1193438. Epub 2010 Oct 21.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20966218" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Catalytic Domain ; Crystallography, X-Ray ; Enzyme Activation ; GTP-Binding Protein alpha Subunits, Gq-G11/*chemistry/*metabolism ; Guanosine Triphosphate/metabolism ; Humans ; Hydrogen Bonding ; Hydrolysis ; Isoenzymes/chemistry/metabolism ; Kinetics ; Mice ; Models, Molecular ; Molecular Sequence Data ; Mutagenesis ; Phospholipase C beta/*chemistry/metabolism ; Protein Binding ; Protein Structure, Tertiary ; Recombinant Fusion Proteins/chemistry/metabolism ; Signal Transduction
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  • 72
    Publication Date: 2010-05-29
    Description: Nucleosome disruption and replacement are crucial activities that maintain epigenomes, but these highly dynamic processes have been difficult to study. Here, we describe a direct method for measuring nucleosome turnover dynamics genome-wide. We found that nucleosome turnover is most rapid over active gene bodies, epigenetic regulatory elements, and replication origins in Drosophila cells. Nucleosomes turn over faster at sites for trithorax-group than polycomb-group protein binding, suggesting that nucleosome turnover differences underlie their opposing activities and challenging models for epigenetic inheritance that rely on stability of histone marks. Our results establish a general strategy for studying nucleosome dynamics and uncover nucleosome turnover differences across the genome that are likely to have functional importance for epigenome maintenance, gene regulation, and control of DNA replication.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2879085/" 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/PMC2879085/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Deal, Roger B -- Henikoff, Jorja G -- Henikoff, Steven -- 1F32GM083449/GM/NIGMS NIH HHS/ -- 1R21DA025758/DA/NIDA NIH HHS/ -- F32 GM083449-03/GM/NIGMS NIH HHS/ -- R21 DA025758/DA/NIDA NIH HHS/ -- R21 DA025758-02/DA/NIDA NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2010 May 28;328(5982):1161-4. doi: 10.1126/science.1186777.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20508129" target="_blank"〉PubMed〈/a〉
    Keywords: Alanine/analogs & derivatives/metabolism ; Animals ; Cell Line ; Drosophila Proteins/*metabolism ; Drosophila melanogaster ; *Genome, Insect ; Histones/*metabolism ; Kinetics ; Methionine/metabolism ; *Molecular Probe Techniques ; Nucleosomes/*metabolism ; Oligonucleotide Array Sequence Analysis
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  • 73
    Publication Date: 2010-10-16
    Description: No-go decay (NGD) is one of several messenger RNA (mRNA) surveillance systems dedicated to the removal of defective mRNAs from the available pool. Two interacting factors, Dom34 and Hbs1, are genetically implicated in NGD in yeast. Using a reconstituted yeast translation system, we show that Dom34:Hbs1 interacts with the ribosome to promote subunit dissociation and peptidyl-tRNA drop-off. Our data further indicate that these recycling activities are shared by the homologous translation termination factor complex eRF1:eRF3, suggesting a common ancestral function. Because Dom34:Hbs1 activity exhibits no dependence on either peptide length or A-site codon identity, we propose that this quality-control system functions broadly to recycle ribosomes throughout the translation cycle whenever stalls occur.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4022135/" 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/PMC4022135/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shoemaker, Christopher J -- Eyler, Daniel E -- Green, Rachel -- R01 GM059425/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2010 Oct 15;330(6002):369-72. doi: 10.1126/science.1192430.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute and Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20947765" target="_blank"〉PubMed〈/a〉
    Keywords: Cell Cycle Proteins/genetics/*metabolism ; Codon ; Codon, Terminator ; Endoribonucleases/genetics/*metabolism ; GTP-Binding Proteins/genetics/*metabolism ; Guanosine Triphosphate/metabolism ; HSP70 Heat-Shock Proteins/genetics/*metabolism ; Kinetics ; Peptide Chain Termination, Translational ; Peptide Elongation Factors/genetics/*metabolism ; Peptide Termination Factors/metabolism ; Protein Biosynthesis ; *RNA Stability ; RNA, Fungal/genetics/*metabolism ; RNA, Messenger/genetics/*metabolism ; RNA, Transfer, Amino Acyl/genetics/*metabolism ; Recombinant Proteins/metabolism ; Ribosome Subunits/*metabolism ; Saccharomyces cerevisiae/*genetics/metabolism ; Saccharomyces cerevisiae Proteins/genetics/*metabolism
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  • 74
    Publication Date: 2010-03-20
    Description: Self-replicating molecules are likely to have played an important role in the origin of life, and a small number of fully synthetic self-replicators have already been described. Yet it remains an open question which factors most effectively bias the replication toward the far-from-equilibrium distributions characterizing even simple organisms. We report here two self-replicating peptide-derived macrocycles that emerge from a small dynamic combinatorial library and compete for a common feedstock. Replication is driven by nanostructure formation, resulting from the assembly of the peptides into fibers held together by beta sheets. Which of the two replicators becomes dominant is influenced by whether the sample is shaken or stirred. These results establish that mechanical forces can act as a selection pressure in the competition between replicators and can determine the outcome of a covalent synthesis.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Carnall, Jacqui M A -- Waudby, Christopher A -- Belenguer, Ana M -- Stuart, Marc C A -- Peyralans, Jerome J-P -- Otto, Sijbren -- New York, N.Y. -- Science. 2010 Mar 19;327(5972):1502-6. doi: 10.1126/science.1182767.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉University of Cambridge, Department of Chemistry, Lensfield Road, Cambridge CB2 1EW, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20299594" target="_blank"〉PubMed〈/a〉
    Keywords: Circular Dichroism ; Combinatorial Chemistry Techniques ; Cryoelectron Microscopy ; Evolution, Chemical ; Hydrogen-Ion Concentration ; Kinetics ; Leucine/chemistry ; Lysine/chemistry ; Macrocyclic Compounds/*chemistry ; Mechanical Phenomena ; Models, Chemical ; Molecular Conformation ; Origin of Life ; Peptide Library ; Peptides/*chemistry ; Physicochemical Processes ; Spectrum Analysis ; Stress, Mechanical ; Sulfhydryl Compounds/chemistry ; Thermodynamics
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  • 75
    Publication Date: 2010-09-04
    Description: Ultraviolet UV-A and UV-B radiation is harmful to living systems, causing damage to biological macromolecules. An important strategy for dealing with UV exposure is the biosynthesis of small-molecule sunscreens. Among such metabolites, the mycosporine and mycosporine-like amino acids (MAAs) are remarkable for their wide phylogenetic distribution and their unique chemical structures. Here, we report the identification of a MAA biosynthetic gene cluster in a cyanobacterium and the discovery of analogous pathways in other sequenced organisms. We have expressed the cluster in a heterologous bacterial host and characterized all four biosynthetic enzymes in vitro. In addition to clarifying the origin of the MAAs, these efforts have revealed two unprecedented enzymatic strategies for imine formation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3116657/" 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/PMC3116657/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Balskus, Emily P -- Walsh, Christopher T -- F32 GM084625/GM/NIGMS NIH HHS/ -- F32 GM084625-03/GM/NIGMS NIH HHS/ -- GM-084625/GM/NIGMS NIH HHS/ -- GM-20011/GM/NIGMS NIH HHS/ -- R01 GM020011/GM/NIGMS NIH HHS/ -- R01 GM020011-40/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2010 Sep 24;329(5999):1653-6. doi: 10.1126/science.1193637. Epub 2010 Sep 2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20813918" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/metabolism ; Anabaena variabilis/enzymology/*genetics/*metabolism ; Bacterial Proteins/*genetics/metabolism ; Biocatalysis ; Cloning, Molecular ; Cyclohexanols ; Cyclohexylamines/chemistry ; Escherichia coli/genetics/metabolism ; *Genes, Bacterial ; Glycine/*analogs & derivatives/biosynthesis/chemistry ; Imines/metabolism ; Ligases/genetics/metabolism ; Methyltransferases/genetics/metabolism ; Multigene Family ; Nostoc/enzymology/genetics/metabolism ; Open Reading Frames ; Sunscreening Agents/*metabolism ; Ultraviolet Rays
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 76
    Publication Date: 2010-10-30
    Description: Ribosomes are self-assembling macromolecular machines that translate DNA into proteins, and an understanding of ribosome biogenesis is central to cellular physiology. Previous studies on the Escherichia coli 30S subunit suggest that ribosome assembly occurs via multiple parallel pathways rather than through a single rate-limiting step, but little mechanistic information is known about this process. Discovery single-particle profiling (DSP), an application of time-resolved electron microscopy, was used to obtain more than 1 million snapshots of assembling 30S subunits, identify and visualize the structures of 14 assembly intermediates, and monitor the population flux of these intermediates over time. DSP results were integrated with mass spectrometry data to construct the first ribosome-assembly mechanism that incorporates binding dependencies, rate constants, and structural characterization of populated intermediates.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2990404/" 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/PMC2990404/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mulder, Anke M -- Yoshioka, Craig -- Beck, Andrea H -- Bunner, Anne E -- Milligan, Ronald A -- Potter, Clinton S -- Carragher, Bridget -- Williamson, James R -- GM-52468/GM/NIGMS NIH HHS/ -- P41 RR017573/RR/NCRR NIH HHS/ -- P41 RR017573-10/RR/NCRR NIH HHS/ -- R01 GM052468/GM/NIGMS NIH HHS/ -- R01 GM052468-16/GM/NIGMS NIH HHS/ -- R01 RR023093/RR/NCRR NIH HHS/ -- R01 RR023093-09/RR/NCRR NIH HHS/ -- R37 GM053757/GM/NIGMS NIH HHS/ -- R37 GM053757-16/GM/NIGMS NIH HHS/ -- R37-GM-53757/GM/NIGMS NIH HHS/ -- RR023093/RR/NCRR NIH HHS/ -- RR175173/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 2010 Oct 29;330(6004):673-7. doi: 10.1126/science.1193220.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cell Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21030658" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/chemistry/metabolism ; Image Processing, Computer-Assisted ; Kinetics ; Mass Spectrometry ; Microscopy, Electron/methods ; Models, Molecular ; Nucleic Acid Conformation ; Protein Binding ; Protein Conformation ; RNA, Bacterial/chemistry ; RNA, Ribosomal/chemistry ; Ribosomal Proteins/chemistry/*metabolism ; Ribosome Subunits, Small, Bacterial/chemistry/*metabolism/*ultrastructure
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  • 77
    Publication Date: 2010-11-13
    Description: Cytochrome P450 enzymes are responsible for the phase I metabolism of approximately 75% of known pharmaceuticals. P450s perform this and other important biological functions through the controlled activation of C-H bonds. Here, we report the spectroscopic and kinetic characterization of the long-sought principal intermediate involved in this process, P450 compound I (P450-I), which we prepared in approximately 75% yield by reacting ferric CYP119 with m-chloroperbenzoic acid. The Mossbauer spectrum of CYP119-I is similar to that of chloroperoxidase compound I, although its electron paramagnetic resonance spectrum reflects an increase in |J|/D, the ratio of the exchange coupling to the zero-field splitting. CYP119-I hydroxylates the unactivated C-H bonds of lauric acid [D(C-H) ~ 100 kilocalories per mole], with an apparent second-order rate constant of k(app) = 1.1 x 10(7) per molar per second at 4 degrees C. Direct measurements put a lower limit of k 〉/= 210 per second on the rate constant for bound substrate oxidation, whereas analyses involving kinetic isotope effects predict a value in excess of 1400 per second.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rittle, Jonathan -- Green, Michael T -- New York, N.Y. -- Science. 2010 Nov 12;330(6006):933-7. doi: 10.1126/science.1193478.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, 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/21071661" target="_blank"〉PubMed〈/a〉
    Keywords: Biocatalysis ; Catalytic Domain ; Chlorobenzoates/chemistry ; Cytochrome P-450 Enzyme System/*chemistry/*isolation & purification/*metabolism ; Electron Spin Resonance Spectroscopy ; Fatty Acids/chemistry/metabolism ; Freezing ; Hydroxylation ; Kinetics ; Lauric Acids/chemistry/metabolism ; Ligands ; Oxidation-Reduction ; Oxygen/chemistry/metabolism ; Physicochemical Processes ; Spectroscopy, Mossbauer ; Sulfolobus acidocaldarius/enzymology
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  • 78
    Publication Date: 2009-12-17
    Description: We present an analytical treatment of a set of coupled kinetic equations that governs the self-assembly of filamentous molecular structures. Application to the case of protein aggregation demonstrates that the kinetics of amyloid growth can often be dominated by secondary rather than by primary nucleation events. Our results further reveal a range of general features of the growth kinetics of fragmenting filamentous structures, including the existence of generic scaling laws that provide mechanistic information in contexts ranging from in vitro amyloid growth to the in vivo development of mammalian prion diseases.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Knowles, Tuomas P J -- Waudby, Christopher A -- Devlin, Glyn L -- Cohen, Samuel I A -- Aguzzi, Adriano -- Vendruscolo, Michele -- Terentjev, Eugene M -- Welland, Mark E -- Dobson, Christopher M -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2009 Dec 11;326(5959):1533-7. doi: 10.1126/science.1178250.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cavendish Laboratory, University of Cambridge, J. J. Thomson Avenue, Cambridge CB3 0HE, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20007899" target="_blank"〉PubMed〈/a〉
    Keywords: Amyloid/*chemistry ; Biochemical Processes ; Glutathione Peroxidase/chemistry ; Insulin/chemistry ; Kinetics ; Lactoglobulins/chemistry ; Mathematical Concepts ; Multiprotein Complexes/*chemistry ; Peptide Termination Factors/chemistry ; Peptides/chemistry ; Prions/chemistry ; *Protein Multimerization ; Saccharomyces cerevisiae Proteins/chemistry
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  • 79
    Publication Date: 2009-02-07
    Description: Centrosomes, each containing a pair of centrioles, organize microtubules in animal cells, particularly during mitosis. DNA and centrosomes are normally duplicated once before cell division to maintain optimal genome integrity. We report a new role for the Orc1 protein, a subunit of the origin recognition complex (ORC) that is a key component of the DNA replication licensing machinery, in controlling centriole and centrosome copy number in human cells, independent of its role in DNA replication. Cyclin A promotes Orc1 localization to centrosomes where Orc1 prevents Cyclin E-dependent reduplication of both centrioles and centrosomes in a single cell division cycle. The data suggest that Orc1 is a regulator of centriole and centrosome reduplication as well as the initiation of DNA replication.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2653626/" 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/PMC2653626/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hemerly, Adriana S -- Prasanth, Supriya G -- Siddiqui, Khalid -- Stillman, Bruce -- CA13106/CA/NCI NIH HHS/ -- P01 CA013106/CA/NCI NIH HHS/ -- P01 CA013106-310025/CA/NCI NIH HHS/ -- P01 CA013106-36/CA/NCI NIH HHS/ -- P01 CA013106-370025/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2009 Feb 6;323(5915):789-93. doi: 10.1126/science.1166745.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor 11724, NY, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19197067" target="_blank"〉PubMed〈/a〉
    Keywords: Cell Cycle ; Cell Line, Tumor ; Centrioles/*physiology ; Centrosome/*physiology ; Cyclin A/metabolism ; Cyclin E/metabolism ; Cyclin-Dependent Kinase 2/metabolism ; DNA Replication ; HeLa Cells ; Humans ; Kinetics ; Mutant Proteins/metabolism ; Origin Recognition Complex/genetics/*metabolism ; RNA Interference ; RNA, Small Interfering ; Transfection
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  • 80
    Publication Date: 2009-04-11
    Description: Synonymous mutations do not alter the encoded protein, but they can influence gene expression. To investigate how, we engineered a synthetic library of 154 genes that varied randomly at synonymous sites, but all encoded the same green fluorescent protein (GFP). When expressed in Escherichia coli, GFP protein levels varied 250-fold across the library. GFP messenger RNA (mRNA) levels, mRNA degradation patterns, and bacterial growth rates also varied, but codon bias did not correlate with gene expression. Rather, the stability of mRNA folding near the ribosomal binding site explained more than half the variation in protein levels. In our analysis, mRNA folding and associated rates of translation initiation play a predominant role in shaping expression levels of individual genes, whereas codon bias influences global translation efficiency and cellular fitness.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3902468/" 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/PMC3902468/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kudla, Grzegorz -- Murray, Andrew W -- Tollervey, David -- Plotkin, Joshua B -- BB/D019621/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/DO19621/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/DO19621/1/Wellcome Trust/United Kingdom -- P50 GM068763/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2009 Apr 10;324(5924):255-8. doi: 10.1126/science.1170160.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology and Program in Applied Mathematics and Computational Science, University of Pennsylvania, Philadelphia, PA 19104, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19359587" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Substitution ; Base Composition ; Cloning, Molecular ; *Codon ; Escherichia coli/*genetics/growth & development/metabolism ; *Gene Expression ; Gene Library ; Genes, Synthetic ; Green Fluorescent Proteins/*genetics/metabolism ; Mutation ; Nucleic Acid Conformation ; Protein Biosynthesis ; RNA Stability ; RNA, Bacterial/chemistry/genetics/metabolism ; RNA, Messenger/chemistry/*genetics/metabolism ; Spectrometry, Fluorescence
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  • 81
    facet.materialart.
    Unknown
    American Association for the Advancement of Science (AAAS)
    Publication Date: 2009-08-22
    Description: Actin filaments and microtubules polymerize and depolymerize by adding and removing subunits at polymer ends, and these dynamics drive cytoplasmic organization, cell division, and cell motility. Since Wegner proposed the treadmilling theory for actin in 1976, it has largely been assumed that the chemical state of the bound nucleotide determines the rates of subunit addition and removal. This chemical kinetics view is difficult to reconcile with observations revealing multiple structural states of the polymer that influence polymerization dynamics but that are not strictly coupled to the bound nucleotide state. We refer to these phenomena as "structural plasticity" and discuss emerging evidence that they play a central role in polymer dynamics and function.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2864651/" 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/PMC2864651/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kueh, Hao Yuan -- Mitchison, Timothy J -- GM 23928/GM/NIGMS NIH HHS/ -- R01 GM023928/GM/NIGMS NIH HHS/ -- R01 GM023928-31/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2009 Aug 21;325(5943):960-3. doi: 10.1126/science.1168823.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Systems Biology, Harvard Medical School, Boston, MA 02215, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19696342" target="_blank"〉PubMed〈/a〉
    Keywords: Actin Cytoskeleton/*chemistry/metabolism/ultrastructure ; Actin Depolymerizing Factors/metabolism ; Actins/*chemistry/metabolism ; Adenosine Triphosphate/metabolism ; Guanosine Diphosphate/metabolism ; Guanosine Triphosphate/metabolism ; Kinetics ; Microfilament Proteins/metabolism ; Microtubules/*chemistry/metabolism/ultrastructure ; Models, Biological ; Tubulin/*chemistry/metabolism
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  • 82
    Publication Date: 2009-01-10
    Description: Type IV secretion systems (T4SSs) are important virulence factors used by Gram-negative bacterial pathogens to inject effectors into host cells or to spread plasmids harboring antibiotic resistance genes. We report the 15 angstrom resolution cryo-electron microscopy structure of the core complex of a T4SS. The core complex is composed of three proteins, each present in 14 copies and forming a approximately 1.1-megadalton two-chambered, double membrane-spanning channel. The structure is double-walled, with each component apparently spanning a large part of the channel. The complex is open on the cytoplasmic side and constricted on the extracellular side. Overall, the T4SS core complex structure is different in both architecture and composition from the other known double membrane-spanning secretion system that has been structurally characterized.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fronzes, Remi -- Schafer, Eva -- Wang, Luchun -- Saibil, Helen R -- Orlova, Elena V -- Waksman, Gabriel -- 070776/Wellcome Trust/United Kingdom -- BB/C516144/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/C516179/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/F010281/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- Biotechnology and Biological Sciences Research Council/United Kingdom -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2009 Jan 9;323(5911):266-8. doi: 10.1126/science.1166101.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Structural and Molecular Biology, School of Crystallography, Birkbeck College, Malet Street, London, WC1E 7HX, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19131631" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Outer Membrane Proteins/*chemistry/genetics/ultrastructure ; Bacterial Proteins/*chemistry/genetics/*ultrastructure ; Cloning, Molecular ; Cryoelectron Microscopy ; Gram-Negative Bacteria/*chemistry/genetics/pathogenicity ; Imaging, Three-Dimensional ; Models, Molecular ; Multiprotein Complexes/chemistry/ultrastructure ; *Plasmids ; Protein Conformation ; Protein Structure, Quaternary ; Virulence Factors/*chemistry/genetics
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  • 83
    Publication Date: 2009-02-21
    Description: Stripe rust is a devastating fungal disease that afflicts wheat in many regions of the world. New races of Puccinia striiformis, the pathogen responsible for this disease, have overcome most of the known race-specific resistance genes. We report the map-based cloning of the gene Yr36 (WKS1), which confers resistance to a broad spectrum of stripe rust races at relatively high temperatures (25 degrees to 35 degrees C). This gene includes a kinase and a putative START lipid-binding domain. Five independent mutations and transgenic complementation confirmed that both domains are necessary to confer resistance. Yr36 is present in wild wheat but is absent in modern pasta and bread wheat varieties, and therefore it can now be used to improve resistance to stripe rust in a broad set of varieties.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4737487/" 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/PMC4737487/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fu, Daolin -- Uauy, Cristobal -- Distelfeld, Assaf -- Blechl, Ann -- Epstein, Lynn -- Chen, Xianming -- Sela, Hanan -- Fahima, Tzion -- Dubcovsky, Jorge -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2009 Mar 6;323(5919):1357-60. doi: 10.1126/science.1166289. Epub 2009 Feb 19.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Plant Sciences, University of California, Davis, CA 95616, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19228999" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Basidiomycota/*pathogenicity ; Cloning, Molecular ; Crosses, Genetic ; Down-Regulation ; *Genes, Plant ; Hot Temperature ; Immunity, Innate ; Molecular Sequence Data ; Phosphotransferases/chemistry/*genetics/metabolism ; Physical Chromosome Mapping ; *Plant Diseases/immunology/microbiology ; Plant Proteins/chemistry/genetics/metabolism ; Plants, Genetically Modified ; Triticum/*genetics/*microbiology
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  • 84
    facet.materialart.
    Unknown
    American Association for the Advancement of Science (AAAS)
    Publication Date: 2009-08-15
    Description: Dynamin-related proteins (DRPs) can generate forces to remodel membranes. In cells, DRPs require additional proteins [DRP-associated proteins (DAPs)] to conduct their functions. To dissect the mechanistic role of a DAP, we used the yeast mitochondrial division machine as a model, which requires the DRP Dnm1, and two other proteins, Mdv1 and Fis1. Mdv1 played a postmitochondrial targeting role in division by specifically interacting and coassembling with the guanosine triphosphate-bound form of Dnm1. This regulated interaction nucleated and promoted the self-assembly of Dnm1 into helical structures, which drive membrane scission. The nucleation of DRP assembly probably represents a general regulatory strategy for this family of filament-forming proteins, similar to F-actin regulation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lackner, Laura L -- Horner, Jennifer S -- Nunnari, Jodi -- 1F32GM078749/GM/NIGMS NIH HHS/ -- R01 GM062942/GM/NIGMS NIH HHS/ -- R01GM062942/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2009 Aug 14;325(5942):874-7. doi: 10.1126/science.1176921.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19679814" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptor Proteins, Signal Transducing/*metabolism ; GTP Phosphohydrolases/chemistry/genetics/*metabolism ; Guanosine Triphosphate/analogs & derivatives/metabolism ; Intracellular Membranes/physiology ; Kinetics ; Liposomes/metabolism ; Mitochondria/*physiology ; Mitochondrial Proteins/chemistry/genetics/*metabolism ; Models, Biological ; Protein Binding ; Protein Conformation ; Protein Structure, Secondary ; Saccharomyces cerevisiae Proteins/chemistry/genetics/*metabolism
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  • 85
    Publication Date: 2009-03-03
    Description: beta-lactam antibiotics are ineffective against Mycobacterium tuberculosis, being rapidly hydrolyzed by the chromosomally encoded blaC gene product. The carbapenem class of beta-lactams are very poor substrates for BlaC, allowing us to determine the three-dimensional structure of the covalent BlaC-meropenem covalent complex at 1.8 angstrom resolution. When meropenem was combined with the beta-lactamase inhibitor clavulanate, potent activity against laboratory strains of M. tuberculosis was observed [minimum inhibitory concentration (MIC(meropenem)) less than 1 microgram per milliliter], and sterilization of aerobically grown cultures was observed within 14 days. In addition, this combination exhibited inhibitory activity against anaerobically grown cultures that mimic the "persistent" state and inhibited the growth of 13 extensively drug-resistant strains of M. tuberculosis at the same levels seen for drug-susceptible strains. Meropenem and clavulanate are Food and Drug Administration-approved drugs and could potentially be used to treat patients with currently untreatable disease.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2679150/" 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/PMC2679150/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hugonnet, Jean-Emmanuel -- Tremblay, Lee W -- Boshoff, Helena I -- Barry, Clifton E 3rd -- Blanchard, John S -- AI33696/AI/NIAID NIH HHS/ -- Z01 AI000693-15/Intramural NIH HHS/ -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2009 Feb 27;323(5918):1215-8. doi: 10.1126/science.1167498.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19251630" target="_blank"〉PubMed〈/a〉
    Keywords: Acylation ; Antibiotics, Antitubercular/*pharmacology ; Catalytic Domain ; Clavulanic Acid/*pharmacology ; Crystallography, X-Ray ; Drug Combinations ; *Drug Resistance, Multiple, Bacterial ; Enzyme Inhibitors/pharmacology ; Extensively Drug-Resistant Tuberculosis/*microbiology ; Humans ; Kinetics ; Mass Spectrometry ; Microbial Sensitivity Tests ; Mycobacterium tuberculosis/*drug effects/enzymology/growth & development ; Thienamycins/metabolism/*pharmacology ; beta-Lactamase Inhibitors ; beta-Lactamases/*chemistry/metabolism
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  • 86
    Publication Date: 2009-11-07
    Description: Virtually all of the 560 human proteases are stored as inactive proenyzmes and are strictly regulated. We report the identification and characterization of the first small molecules that directly activate proenzymes, the apoptotic procaspases-3 and -6. It is surprising that these compounds induce autoproteolytic activation by stabilizing a conformation that is both more active and more susceptible to intermolecular proteolysis. These procaspase activators bypass the normal upstream proapoptotic signaling cascades and induce rapid apoptosis in a variety of cell lines. Systematic biochemical and biophysical analyses identified a cluster of mutations in procaspase-3 that resist small-molecule activation both in vitro and in cells. Compounds that induce gain of function are rare, and the activators reported here will enable direct control of the executioner caspases in apoptosis and in cellular differentiation. More generally, these studies presage the discovery of other proenzyme activators to explore fundamental processes of proenzyme activation and their fate-determining roles in biology.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2886848/" 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/PMC2886848/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wolan, Dennis W -- Zorn, Julie A -- Gray, Daniel C -- Wells, James A -- F32 CA119641/CA/NCI NIH HHS/ -- F32 CA119641-03/CA/NCI NIH HHS/ -- R01 CA136779/CA/NCI NIH HHS/ -- R21 N5057022/PHS HHS/ -- New York, N.Y. -- Science. 2009 Nov 6;326(5954):853-8. doi: 10.1126/science.1177585.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pharmaceutical Chemistry, University of California, San Francisco, Byers Hall, 1700 4th Street, San Francisco, CA 94158, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19892984" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Apoptosis ; Benzopyrans/chemistry/*metabolism/pharmacology ; Biocatalysis ; Caspase 3/chemistry/genetics/*metabolism ; Caspase 6/chemistry/genetics/*metabolism ; Caspase Inhibitors ; Catalytic Domain ; Cell Line, Transformed ; Cell Line, Tumor ; Cells, Cultured ; Enzyme Activation ; Enzyme Activators/chemistry/*metabolism/pharmacology ; Enzyme Inhibitors/metabolism/pharmacology ; Enzyme Precursors/antagonists & inhibitors/chemistry/genetics/*metabolism ; Granzymes/metabolism ; Humans ; Imidazoles/chemistry/*metabolism/pharmacology ; Kinetics ; Mice ; Molecular Structure ; Mutagenesis ; Pyridines/chemistry/*metabolism/pharmacology ; Signal Transduction ; Small Molecule Libraries/chemistry/metabolism
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  • 87
    Publication Date: 2009-12-08
    Description: Environmental perturbations during mass extinctions were likely manifested differently in epicontinental seas than in open-ocean-facing habitats of comparable depth. Here, we present a dissection of origination and extinction in epicontinental seas versus open-ocean-facing coastal regions in the Permian through Cretaceous periods, an interval through which both settings are well represented in the fossil record. Results demonstrate that extinction rates were significantly higher in open-ocean settings than in epicontinental seas during major mass extinctions but not at other times and that origination rates were significantly higher in open-ocean settings for a protracted interval from the Late Jurassic through the Late Cretaceous. These patterns are manifested even when other paleogeographic and environmental variables are held fixed, indicating that epicontinental seas and open-ocean-facing coastlines carry distinct macroevolutionary signatures.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Miller, Arnold I -- Foote, Michael -- New York, N.Y. -- Science. 2009 Nov 20;326(5956):1106-9. doi: 10.1126/science.1180061.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Geology, University of Cincinnati, Post Office Box 210013, Cincinnati, OH 45221, USA. arnold.miller@uc.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19965428" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Bivalvia ; *Ecosystem ; Environment ; *Extinction, Biological ; Geologic Sediments ; Geological Phenomena ; Kinetics ; Oceans and Seas
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  • 88
    facet.materialart.
    Unknown
    American Association for the Advancement of Science (AAAS)
    Publication Date: 2009-01-10
    Description: An RNA enzyme that catalyzes the RNA-templated joining of RNA was converted to a format whereby two enzymes catalyze each other's synthesis from a total of four oligonucleotide substrates. These cross-replicating RNA enzymes undergo self-sustained exponential amplification in the absence of proteins or other biological materials. Amplification occurs with a doubling time of about 1 hour and can be continued indefinitely. Populations of various cross-replicating enzymes were constructed and allowed to compete for a common pool of substrates, during which recombinant replicators arose and grew to dominate the population. These replicating RNA enzymes can serve as an experimental model of a genetic system. Many such model systems could be constructed, allowing different selective outcomes to be related to the underlying properties of the genetic system.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2652413/" 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/PMC2652413/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lincoln, Tracey A -- Joyce, Gerald F -- R01 GM065130/GM/NIGMS NIH HHS/ -- R01 GM065130-07/GM/NIGMS NIH HHS/ -- R01GM065130/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2009 Feb 27;323(5918):1229-32. doi: 10.1126/science.1167856. Epub 2009 Jan 8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Skaggs Institute for Chemical Biology, Scripps Research Institute, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19131595" target="_blank"〉PubMed〈/a〉
    Keywords: Base Pairing ; Biocatalysis ; Directed Molecular Evolution ; Kinetics ; Nucleic Acid Conformation ; Oligonucleotides/*metabolism ; Polynucleotide Ligases/*chemistry/metabolism ; RNA, Catalytic/chemistry/*metabolism
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  • 89
    Publication Date: 2009-12-19
    Description: Inward-rectifier potassium (K+) channels conduct K+ ions most efficiently in one direction, into the cell. Kir2 channels control the resting membrane voltage in many electrically excitable cells, and heritable mutations cause periodic paralysis and cardiac arrhythmia. We present the crystal structure of Kir2.2 from chicken, which, excluding the unstructured amino and carboxyl termini, is 90% identical to human Kir2.2. Crystals containing rubidium (Rb+), strontium (Sr2+), and europium (Eu3+) reveal binding sites along the ion conduction pathway that are both conductive and inhibitory. The sites correlate with extensive electrophysiological data and provide a structural basis for understanding rectification. The channel's extracellular surface, with large structured turrets and an unusual selectivity filter entryway, might explain the relative insensitivity of eukaryotic inward rectifiers to toxins. These same surface features also suggest a possible approach to the development of inhibitory agents specific to each member of the inward-rectifier K+ channel family.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2819303/" 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/PMC2819303/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tao, Xiao -- Avalos, Jose L -- Chen, Jiayun -- MacKinnon, Roderick -- P30 EB009998/EB/NIBIB NIH HHS/ -- R01 GM043949/GM/NIGMS NIH HHS/ -- R01 GM043949-10/GM/NIGMS NIH HHS/ -- R01 GM043949-11/GM/NIGMS NIH HHS/ -- R01 GM043949-12/GM/NIGMS NIH HHS/ -- R01 GM043949-13/GM/NIGMS NIH HHS/ -- R01 GM043949-14/GM/NIGMS NIH HHS/ -- R01 GM043949-15/GM/NIGMS NIH HHS/ -- R01 GM043949-16/GM/NIGMS NIH HHS/ -- R01 GM043949-17/GM/NIGMS NIH HHS/ -- R01 GM043949-18/GM/NIGMS NIH HHS/ -- R01 GM043949-19/GM/NIGMS NIH HHS/ -- R01 GM043949-20/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2009 Dec 18;326(5960):1668-74. doi: 10.1126/science.1180310.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Molecular Neurobiology and Biophysics, Rockefeller University, Howard Hughes Medical Institute, 1230 York Avenue, New York, NY 10065, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20019282" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Binding Sites ; Chickens ; Cloning, Molecular ; Crystallography, X-Ray ; Europium/metabolism ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Models, Molecular ; Molecular Sequence Data ; Oocytes ; Patch-Clamp Techniques ; Potassium/metabolism ; Potassium Channel Blockers/pharmacology ; Potassium Channels, Inwardly Rectifying/antagonists & ; inhibitors/*chemistry/metabolism ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Subunits/chemistry ; Rubidium/metabolism ; Sequence Alignment ; Strontium/metabolism ; Xenopus laevis
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  • 90
    Publication Date: 2009-11-11
    Description: Highly reducing iterative polyketide synthases are large, multifunctional enzymes that make important metabolites in fungi, such as lovastatin, a cholesterol-lowering drug from Aspergillus terreus. We report efficient expression of the lovastatin nonaketide synthase (LovB) from an engineered strain of Saccharomyces cerevisiae, as well as complete reconstitution of its catalytic function in the presence and absence of cofactors (the reduced form of nicotinamide adenine dinucleotide phosphate and S-adenosylmethionine) and its partner enzyme, the enoyl reductase LovC. Our results demonstrate that LovB retains correct intermediates until completion of synthesis of dihydromonacolin L, but off-loads incorrectly processed compounds as pyrones or hydrolytic products. Experiments replacing LovC with analogous MlcG from compactin biosynthesis demonstrate a gate-keeping function for this partner enzyme. This study represents a key step in the understanding of the functions and structures of this family of enzymes.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2875069/" 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/PMC2875069/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ma, Suzanne M -- Li, Jesse W-H -- Choi, Jin W -- Zhou, Hui -- Lee, K K Michael -- Moorthie, Vijayalakshmi A -- Xie, Xinkai -- Kealey, James T -- Da Silva, Nancy A -- Vederas, John C -- Tang, Yi -- 1R01GM085128/GM/NIGMS NIH HHS/ -- 1R21GM077264/GM/NIGMS NIH HHS/ -- R01 GM085128/GM/NIGMS NIH HHS/ -- R01 GM085128-02/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2009 Oct 23;326(5952):589-92. doi: 10.1126/science.1175602.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19900898" target="_blank"〉PubMed〈/a〉
    Keywords: Aspergillus/enzymology/genetics/metabolism ; Biocatalysis ; Catalytic Domain ; Cloning, Molecular ; Fungal Proteins/metabolism ; Ketones/metabolism ; Lactones/metabolism ; Lovastatin/biosynthesis ; Malonyl Coenzyme A/metabolism ; Molecular Structure ; Multienzyme Complexes/metabolism ; NAD/metabolism ; Naphthalenes/*metabolism ; Polyketide Synthases/chemistry/genetics/isolation & purification/*metabolism ; Pyrones/metabolism ; Recombinant Proteins/chemistry/isolation & purification/metabolism ; S-Adenosylmethionine/metabolism ; Saccharomyces cerevisiae/enzymology/*genetics ; Substrate Specificity
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  • 91
    Publication Date: 2009-08-08
    Description: Posttranslational modifications play key roles in regulating chromatin plasticity. Although various chromatin-remodeling enzymes have been described that respond to specific histone modifications, little is known about the role of poly[adenosine 5'-diphosphate (ADP)-ribose] in chromatin remodeling. Here, we identify a chromatin-remodeling enzyme, ALC1 (Amplified in Liver Cancer 1, also known as CHD1L), that interacts with poly(ADP-ribose) and catalyzes PARP1-stimulated nucleosome sliding. Our results define ALC1 as a DNA damage-response protein whose role in this process is sustained by its association with known DNA repair factors and its rapid poly(ADP-ribose)-dependent recruitment to DNA damage sites. Furthermore, we show that depletion or overexpression of ALC1 results in sensitivity to DNA-damaging agents. Collectively, these results provide new insights into the mechanisms by which poly(ADP-ribose) regulates DNA repair.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3443743/" 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/PMC3443743/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ahel, Dragana -- Horejsi, Zuzana -- Wiechens, Nicola -- Polo, Sophie E -- Garcia-Wilson, Elisa -- Ahel, Ivan -- Flynn, Helen -- Skehel, Mark -- West, Stephen C -- Jackson, Stephen P -- Owen-Hughes, Tom -- Boulton, Simon J -- 064414/Wellcome Trust/United Kingdom -- 11224/Cancer Research UK/United Kingdom -- A3549/Cancer Research UK/United Kingdom -- A5290/Cancer Research UK/United Kingdom -- Biotechnology and Biological Sciences Research Council/United Kingdom -- Cancer Research UK/United Kingdom -- Department of Health/United Kingdom -- New York, N.Y. -- Science. 2009 Sep 4;325(5945):1240-3. doi: 10.1126/science.1177321. Epub 2009 Aug 6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉DNA Damage Response Laboratory, Clare Hall, London Research Institute, South Mimms EN6 3LD, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19661379" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphatases/metabolism ; Adenosine Triphosphate/metabolism ; Cell Line ; Chromatin/*metabolism ; *Chromatin Assembly and Disassembly ; DNA Damage ; DNA Helicases/chemistry/genetics/*metabolism ; *DNA Repair ; DNA-Binding Proteins/chemistry/genetics/*metabolism ; Humans ; Hydrogen Peroxide/pharmacology ; Immunoprecipitation ; Kinetics ; Mutant Proteins/chemistry/metabolism ; Nucleosomes/metabolism ; Phleomycins/pharmacology ; Poly Adenosine Diphosphate Ribose/*metabolism ; Poly(ADP-ribose) Polymerase Inhibitors ; Poly(ADP-ribose) Polymerases/metabolism ; Protein Structure, Tertiary ; Radiation, Ionizing ; Recombinant Proteins/chemistry/metabolism
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  • 92
    facet.materialart.
    Unknown
    American Association for the Advancement of Science (AAAS)
    Publication Date: 2009-03-07
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kliebenstein, Daniel J -- Rowe, Heather C -- New York, N.Y. -- Science. 2009 Mar 6;323(5919):1301-2. doi: 10.1126/science.1171410.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Plant Sciences and Genetics Graduate Group, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA. kliebenstein@ucdavis.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19265010" target="_blank"〉PubMed〈/a〉
    Keywords: ATP-Binding Cassette Transporters/chemistry/genetics/metabolism ; Ascomycota/genetics/*pathogenicity ; Basidiomycota/genetics/*pathogenicity ; Cloning, Molecular ; Evolution, Molecular ; *Genes, Plant ; Immunity, Innate ; Phosphotransferases/chemistry/genetics/metabolism ; *Plant Diseases/immunology/microbiology ; Plant Proteins/chemistry/genetics/metabolism ; Protein Structure, Tertiary ; *Quantitative Trait Loci ; Selection, Genetic ; Triticum/genetics/*microbiology
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  • 93
    Publication Date: 2009-01-10
    Description: Sex determination in maize is controlled by a developmental cascade leading to the formation of unisexual florets derived from an initially bisexual floral meristem. Abortion of pistil primordia in staminate florets is controlled by a tasselseed-mediated cell death process. We positionally cloned and characterized the function of the sex determination gene tasselseed1 (ts1). The TS1 protein encodes a plastid-targeted lipoxygenase with predicted 13-lipoxygenase specificity, which suggests that TS1 may be involved in the biosynthesis of the plant hormone jasmonic acid. In the absence of a functional ts1 gene, lipoxygenase activity was missing and endogenous jasmonic acid concentrations were reduced in developing inflorescences. Application of jasmonic acid to developing inflorescences rescued stamen development in mutant ts1 and ts2 inflorescences, revealing a role for jasmonic acid in male flower development in maize.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Acosta, Ivan F -- Laparra, Helene -- Romero, Sandra P -- Schmelz, Eric -- Hamberg, Mats -- Mottinger, John P -- Moreno, Maria A -- Dellaporta, Stephen L -- R01 GM038148/GM/NIGMS NIH HHS/ -- R01 GM038148-19/GM/NIGMS NIH HHS/ -- R01 GM38148/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2009 Jan 9;323(5911):262-5. doi: 10.1126/science.1164645.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19131630" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Cloning, Molecular ; Cyclopentanes/*metabolism/pharmacology ; Flowers/growth & development ; Genes, Plant ; Lipoxygenase/chemistry/genetics/*metabolism ; Molecular Sequence Data ; Mutation ; Oxylipins/*metabolism/pharmacology ; Plant Proteins/chemistry/*genetics/*metabolism ; Plastids/enzymology ; *Signal Transduction ; Zea mays/enzymology/*genetics/growth & development/*metabolism
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  • 94
    Publication Date: 2009-02-21
    Description: Agricultural crops benefit from resistance to pathogens that endures over years and generations of both pest and crop. Durable disease resistance, which may be partial or complete, can be controlled by several genes. Some of the most devastating fungal pathogens in wheat are leaf rust, stripe rust, and powdery mildew. The wheat gene Lr34 has supported resistance to these pathogens for more than 50 years. Lr34 is now shared by wheat cultivars around the world. Here, we show that the LR34 protein resembles adenosine triphosphate-binding cassette transporters of the pleiotropic drug resistance subfamily. Alleles of Lr34 conferring resistance or susceptibility differ by three genetic polymorphisms. The Lr34 gene, which functions in the adult plant, stimulates senescence-like processes in the flag leaf tips and edges.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Krattinger, Simon G -- Lagudah, Evans S -- Spielmeyer, Wolfgang -- Singh, Ravi P -- Huerta-Espino, Julio -- McFadden, Helen -- Bossolini, Eligio -- Selter, Liselotte L -- Keller, Beat -- New York, N.Y. -- Science. 2009 Mar 6;323(5919):1360-3. doi: 10.1126/science.1166453. Epub 2009 Feb 19.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Plant Biology, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19229000" target="_blank"〉PubMed〈/a〉
    Keywords: ATP-Binding Cassette Transporters/chemistry/*genetics/*metabolism ; Amino Acid Sequence ; Ascomycota/genetics/*pathogenicity ; Basidiomycota/genetics/*pathogenicity ; Chromosome Mapping ; Chromosomes, Plant/genetics ; Cloning, Molecular ; Exons ; Genes, Plant ; Immunity, Innate ; Molecular Sequence Data ; Mutation ; *Plant Diseases/immunology/microbiology ; Plant Leaves/microbiology ; Plant Proteins/chemistry/genetics/metabolism ; Polymorphism, Single Nucleotide ; Quantitative Trait Loci ; Triticum/*genetics/growth & development/immunology/*microbiology
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  • 95
    Publication Date: 2009-08-22
    Description: Blast disease is a devastating fungal disease of rice, one of the world's staple foods. Race-specific resistance to blast disease has usually not been durable. Here, we report the cloning of a previously unknown type of gene that confers non-race-specific resistance and its successful use in breeding. Pi21 encodes a proline-rich protein that includes a putative heavy metal-binding domain and putative protein-protein interaction motifs. Wild-type Pi21 appears to slow the plant's defense responses, which may support optimization of defense mechanisms. Deletions in its proline-rich motif inhibit this slowing. Pi21 is separable from a closely linked gene conferring poor flavor. The resistant pi21 allele, which is found in some strains of japonica rice, could improve blast resistance of rice worldwide.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fukuoka, Shuichi -- Saka, Norikuni -- Koga, Hironori -- Ono, Kazuko -- Shimizu, Takehiko -- Ebana, Kaworu -- Hayashi, Nagao -- Takahashi, Akira -- Hirochika, Hirohiko -- Okuno, Kazutoshi -- Yano, Masahiro -- New York, N.Y. -- Science. 2009 Aug 21;325(5943):998-1001. doi: 10.1126/science.1175550.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉QTL Genomics Research Center, National Institute of Agrobiological Sciences, Kannondai 2-1-2, Tsukuba, Ibaraki 305-8602, Japan. fukusan@affrc.go.jp〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19696351" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Amino Acid Motifs ; Amino Acid Sequence ; Chromosome Mapping ; Cloning, Molecular ; Genes, Plant ; Genetic Variation ; Haplotypes ; Immunity, Innate/*genetics ; Magnaporthe/*pathogenicity ; Molecular Sequence Data ; Oryza/*genetics/metabolism/*microbiology ; Phylogeny ; Plant Diseases/*microbiology ; Plant Proteins/chemistry/*genetics/*physiology ; Proline/analysis ; Protein Interaction Domains and Motifs ; Protein Structure, Tertiary ; Quantitative Trait Loci ; Sequence Deletion ; Transformation, Genetic
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  • 96
    Publication Date: 2009-01-31
    Description: Single-molecule force spectroscopy allows superb mechanical control of protein conformation. We used a custom-built low-drift atomic force microscope to observe mechanically induced conformational equilibrium fluctuations of single molecules of the eukaryotic calcium-dependent signal transducer calmodulin (CaM). From this data, the ligand dependence of the full energy landscape can be reconstructed. We find that calcium ions affect the folding kinetics of the individual CaM domains, whereas target peptides stabilize the already folded structure. Single-molecule data of full length CaM reveal that a wasp venom peptide binds noncooperatively to CaM with 2:1 stoichiometry, whereas a target enzyme peptide binds cooperatively with 1:1 stoichiometry. If mechanical load is applied directly to the target peptide, real-time binding/unbinding transitions can be observed.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Junker, Jan Philipp -- Ziegler, Fabian -- Rief, Matthias -- New York, N.Y. -- Science. 2009 Jan 30;323(5914):633-7. doi: 10.1126/science.1166191.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Physik Department E22, Technische Universitat Munchen, James-Franck-Strasse, 85748 Munchen, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19179531" target="_blank"〉PubMed〈/a〉
    Keywords: Calcium/*metabolism ; Calmodulin/*chemistry/*metabolism ; Humans ; Kinetics ; Ligands ; Microscopy, Atomic Force ; Monte Carlo Method ; Myosin-Light-Chain Kinase/chemistry/*metabolism ; Peptide Fragments/chemistry/metabolism ; Peptides/chemistry/*metabolism ; Protein Binding ; Protein Conformation ; Protein Folding ; Protein Structure, Tertiary ; Thermodynamics ; Wasp Venoms/chemistry/*metabolism
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 97
    Publication Date: 2009-06-06
    Description: Von Willebrand factor (VWF) is secreted as ultralarge multimers that are cleaved in the A2 domain by the metalloprotease ADAMTS13 to give smaller multimers. Cleaved VWF is activated by hydrodynamic forces found in arteriolar bleeding to promote hemostasis, whereas uncleaved VWF is activated at lower, physiologic shear stresses and causes thrombosis. Single-molecule experiments demonstrate that elongational forces in the range experienced by VWF in the vasculature unfold the A2 domain, and only the unfolded A2 domain is cleaved by ADAMTS13. In shear flow, tensile force on a VWF multimer increases with the square of multimer length and is highest at the middle, providing an efficient mechanism for homeostatic regulation of VWF size distribution by force-induced A2 unfolding and cleavage by ADAMTS13, as well as providing a counterbalance for VWF-mediated platelet aggregation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2753189/" 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/PMC2753189/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhang, Xiaohui -- Halvorsen, Kenneth -- Zhang, Cheng-Zhong -- Wong, Wesley P -- Springer, Timothy A -- HL-48675/HL/NHLBI NIH HHS/ -- P01 HL048675/HL/NHLBI NIH HHS/ -- P01 HL048675-16/HL/NHLBI NIH HHS/ -- New York, N.Y. -- Science. 2009 Jun 5;324(5932):1330-4. doi: 10.1126/science.1170905.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Immune Disease Institute, Harvard Medical School, Boston, MA 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19498171" target="_blank"〉PubMed〈/a〉
    Keywords: ADAM Proteins/*metabolism ; Binding Sites ; Blood Coagulation/physiology ; *Hemostasis ; Humans ; Kinetics ; *Mechanical Phenomena ; Optical Tweezers ; Platelet Aggregation ; Protein Conformation ; Protein Folding ; Protein Multimerization ; Protein Structure, Tertiary ; Stress, Mechanical ; Thermodynamics ; von Willebrand Factor/*chemistry/*metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 98
    Publication Date: 2009-01-03
    Description: Retinoic acid inducible-gene I (RIG-I) is a cytosolic multidomain protein that detects viral RNA and elicits an antiviral immune response. Two N-terminal caspase activation and recruitment domains (CARDs) transmit the signal, and the regulatory domain prevents signaling in the absence of viral RNA. 5'-triphosphate and double-stranded RNA (dsRNA) are two molecular patterns that enable RIG-I to discriminate pathogenic from self-RNA. However, the function of the DExH box helicase domain that is also required for activity is less clear. Using single-molecule protein-induced fluorescence enhancement, we discovered a robust adenosine 5'-triphosphate-powered dsRNA translocation activity of RIG-I. The CARDs dramatically suppress translocation in the absence of 5'-triphosphate, and the activation by 5'-triphosphate triggers RIG-I to translocate preferentially on dsRNA in cis. This functional integration of two RNA molecular patterns may provide a means to specifically sense and counteract replicating viruses.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3567915/" 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/PMC3567915/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Myong, Sua -- Cui, Sheng -- Cornish, Peter V -- Kirchhofer, Axel -- Gack, Michaela U -- Jung, Jae U -- Hopfner, Karl-Peter -- Ha, Taekjip -- CA82057/CA/NCI NIH HHS/ -- R01 GM065367/GM/NIGMS NIH HHS/ -- R01-GM065367/GM/NIGMS NIH HHS/ -- U19 AI083025/AI/NIAID NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2009 Feb 20;323(5917):1070-4. doi: 10.1126/science.1168352. Epub 2009 Jan 1.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Champaign, IL 61801, USA. smyong@uiuc.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19119185" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/*metabolism ; Animals ; Cell Line ; Cytosol/metabolism ; DEAD-box RNA Helicases/chemistry/genetics/*metabolism ; Kinetics ; Nucleic Acid Heteroduplexes ; Protein Structure, Tertiary ; RNA/metabolism ; RNA, Double-Stranded/*metabolism ; RNA, Viral/metabolism ; Receptors, Pattern Recognition/chemistry/genetics/*metabolism ; Signal Transduction ; Temperature
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 99
    Publication Date: 2009-01-31
    Description: Populations of certain unicellular organisms, such as suspensions of yeast in nutrient solutions, undergo transitions to coordinated activity with increasing cell density. The collective behavior is believed to arise through communication by chemical signaling via the extracellular solution. We studied large, heterogeneous populations of discrete chemical oscillators (approximately 100,000) with well-defined kinetics to characterize two different types of density-dependent transitions to synchronized oscillatory behavior. For different chemical exchange rates between the oscillators and the surrounding solution, increasing oscillator density led to (i) the gradual synchronization of oscillatory activity, or (ii) the sudden "switching on" of synchronized oscillatory activity. We analyze the roles of oscillator density and exchange rate of signaling species in these transitions with a mathematical model of the interacting chemical oscillators.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Taylor, Annette F -- Tinsley, Mark R -- Wang, Fang -- Huang, Zhaoyang -- Showalter, Kenneth -- New York, N.Y. -- Science. 2009 Jan 30;323(5914):614-7. doi: 10.1126/science.1166253.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Chemistry, University of Leeds, Leeds LS2 9JT, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19179525" target="_blank"〉PubMed〈/a〉
    Keywords: Bromine/*chemistry ; Bromine Compounds/*chemistry ; Catalysis ; Electrochemical Techniques ; Kinetics ; Microspheres ; Models, Chemical ; Oscillometry ; Quorum Sensing
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    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 100
    Publication Date: 2009-09-19
    Description: Zhang et al. (Research Articles, 13 March 2009, p. 1448) reported that synaptic vesicles usually release neurotransmitter through a kiss-and-run mechanism occurring within 1 second but that full collapse of the vesicles becomes more prevalent with repeated stimuli. We report that the kinetics of vesicle retrieval do not change during a stimulus train, with endocytosis occurring in 10 to 15 seconds.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Granseth, Bjorn -- Odermatt, Benjamin -- Royle, Stephen J -- Lagnado, Leon -- MC_U105178794/Medical Research Council/United Kingdom -- Medical Research Council/United Kingdom -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2009 Sep 18;325(5947):1499; author reply 1499. doi: 10.1126/science.1175790.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Clinical and Experimental Medicine, Division of Cell Biology, Linkoping University, SE 581 83 Linkoping, Sweden.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19762627" target="_blank"〉PubMed〈/a〉
    Keywords: Action Potentials ; Animals ; Electric Stimulation ; *Endocytosis ; Green Fluorescent Proteins/metabolism ; Hippocampus/cytology ; Hydrogen-Ion Concentration ; Kinetics ; Membrane Fusion ; Neurotransmitter Agents/*metabolism ; *Quantum Dots ; Synapses/*physiology ; *Synaptic Transmission ; Synaptic Vesicles/*physiology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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