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  • 1
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    Regulation of an enzyme by phosphorylation at the active site (1990)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1990-08-31
    Description: The isocitrate dehydrogenase of Escherichia coli is an example of a ubiquitous class of enzymes that are regulated by covalent modification. In the three-dimensional structure of the enzyme-substrate complex, isocitrate forms a hydrogen bond with Ser113, the site of regulatory phosphorylation. The structures of Asp113 and Glu113 mutants, which mimic the inactivation of the enzyme by phosphorylation, show minimal conformational changes from wild type, as in the phosphorylated enzyme. Calculations based on observed structures suggest that the change in electrostatic potential when a negative charge is introduced either by phosporylation or site-directed mutagenesis is sufficient to inactivate the enzyme. Thus, direct interaction at a ligand binding site is an alternative mechanism to induced conformational changes from an allosteric site in the regulation of protein activity by phosphorylation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hurley, J H -- Dean, A M -- Sohl, J L -- Koshland, D E Jr -- Stroud, R M -- GM 24485/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1990 Aug 31;249(4972):1012-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Biophysics, University of California, San Francisco 94143-0448.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2204109" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Escherichia coli/*enzymology/genetics ; Homeostasis ; Isocitrate Dehydrogenase/genetics/*metabolism ; Models, Molecular ; Molecular Sequence Data ; Phosphorylation ; Protein Conformation
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 2
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    Electrostatic and steric contributions to regulation at the active site of isocitrate dehydrogenase (1990)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1990-08-31
    Description: The isocitrate dehydrogenase of Escherichia coli is regulated by covalent modification at the active site rather than, as expected, at an allosteric site. As a means of evaluating the mechanism of regulation, the kinetics of the substrate, 2R,3S-isocitrate, and a substrate analog, 2R-malate, were compared for the native, phosphorylated, and mutant enzymes. Phosphorylation decreases activity by more than a factor of 10(6) for the true substrate, but causes minor changes in the activity of the substrate analog. The kinetic results indicate that electrostatic repulsion and steric hindrance between the phosphoryl moiety and the gamma carboxyl group of 2R,3S-isocitrate are the major causes of the inactivation, with a lesser contribution from the loss of a hydrogen bond.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dean, A M -- Koshland, D E Jr -- New York, N.Y. -- Science. 1990 Aug 31;249(4972):1044-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Cell Biology, University of California, Berkeley 94720.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2204110" target="_blank"〉PubMed〈/a〉
    Keywords: Allosteric Site ; Amino Acid Sequence ; Binding Sites ; Escherichia coli/*enzymology/genetics ; Isocitrate Dehydrogenase/genetics/*metabolism ; Models, Molecular ; Mutation ; Protein Conformation
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 3
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    The biochemical architecture of an ancient adaptive landscape (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-10-22
    Description: Molecular evolution is moving from statistical descriptions of adaptive molecular changes toward predicting the fitness effects of mutations. Here, we characterize the fitness landscape of the six amino acids controlling coenzyme use in isopropylmalate dehydrogenase (IMDH). Although all natural IMDHs use nicotinamide adenine dinucleotide (NAD) as a coenzyme, they can be engineered to use nicotinamide adenine dinucleotide phosphate (NADP) instead. Intermediates between these two phenotypic extremes show that each amino acid contributes additively to enzyme function, with epistatic contributions confined to fitness. The genotype-phenotype-fitness map shows that NAD use is a global optimum.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lunzer, Mark -- Miller, Stephen P -- Felsheim, Roderick -- Dean, Antony M -- GM060611/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2005 Oct 21;310(5747):499-501.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉BioTechnology Institute, Evolution and Behavior, University of Minnesota, St. Paul, MN 55108, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16239478" target="_blank"〉PubMed〈/a〉
    Keywords: 3-Isopropylmalate Dehydrogenase/*chemistry/genetics/*metabolism ; Amino Acid Substitution ; Analysis of Variance ; Catalysis ; Epistasis, Genetic ; Escherichia coli/enzymology ; *Evolution, Molecular ; Genotype ; Kinetics ; Leucine/biosynthesis ; Mathematics ; Models, Chemical ; Mutation ; NAD/*metabolism ; NADP/*metabolism ; Oxidation-Reduction ; Phenotype ; Protein Engineering ; Selection, Genetic ; Thermodynamics
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 4
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    The selective cause of an ancient adaptation (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-01-18
    Description: Phylogenetic analysis reveals that the use of nicotinamide adenine dinucleotide phosphate (NADP) by prokaryotic isocitrate dehydrogenase (IDH) arose around the time eukaryotic mitochondria first appeared, about 3.5 billion years ago. We replaced the wild-type gene that encodes the NADP-dependent IDH of Escherichia coli with an engineered gene that possesses the ancestral NAD-dependent phenotype. The engineered enzyme is disfavored during competition for acetate. The selection intensifies in genetic backgrounds where other sources of reduced NADP have been removed. A survey of sequenced prokaryotic genomes reveals that those genomes that encode isocitrate lyase, which is essential for growth on acetate, always have an NADP-dependent IDH. Those with only an NAD-dependent IDH never have isocitrate lyase. Hence, the NADP dependence of prokaryotic IDH is an ancient adaptation to anabolic demand for reduced NADP during growth on acetate.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhu, Guoping -- Golding, G Brian -- Dean, Antony M -- GM060611/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2005 Feb 25;307(5713):1279-82. Epub 2005 Jan 13.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉BioTechnology Institute, University of Minnesota, St. Paul, MN 55108, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15653464" target="_blank"〉PubMed〈/a〉
    Keywords: 3-Isopropylmalate Dehydrogenase ; Acetates/metabolism ; *Adaptation, Physiological ; Alcohol Oxidoreductases/chemistry/metabolism ; Bacteria/*genetics/growth & development/*metabolism ; Binding Sites ; Biological Evolution ; Escherichia coli/enzymology/genetics/metabolism ; Isocitrate Dehydrogenase/chemistry/genetics/*metabolism ; Isocitrate Lyase/genetics/metabolism ; Kinetics ; NAD/*metabolism ; NADP/*metabolism ; Oxidation-Reduction ; Phylogeny ; Protein Engineering ; *Selection, Genetic
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 5
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    Direct demonstration of an adaptive constraint (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-10-21
    Description: The role of constraint in adaptive evolution is an open question. Directed evolution of an engineered beta-isopropylmalate dehydrogenase (IMDH), with coenzyme specificity switched from nicotinamide adenine dinucleotide (NAD) to nicotinamide adenine dinucleotide phosphate (NADP), always produces mutants with lower affinities for NADP. This result is the correlated response to selection for relief from inhibition by NADPH (the reduced form of NADP) expected of an adaptive landscape subject to three enzymatic constraints: an upper limit to the rate of maximum turnover (kcat), a correlation in NADP and NADPH affinities, and a trade-off between NAD and NADP usage. Two additional constraints, high intracellular NADPH abundance and the cost of compensatory protein synthesis, have ensured the conserved use of NAD by IMDH throughout evolution. Our results show that selective mechanisms and evolutionary constraints are to be understood in terms of underlying adaptive landscapes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Miller, Stephen P -- Lunzer, Mark -- Dean, Antony M -- GM060611/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2006 Oct 20;314(5798):458-61.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉BioTechnology Institute, University of Minnesota, St. Paul, MN 55108, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17053145" target="_blank"〉PubMed〈/a〉
    Keywords: 3-Isopropylmalate Dehydrogenase/antagonists & ; inhibitors/chemistry/genetics/*metabolism ; *Adaptation, Physiological ; Amino Acid Substitution ; Binding Sites ; Codon ; *Directed Molecular Evolution ; Escherichia coli/*enzymology/growth & development/physiology ; *Evolution, Molecular ; Kinetics ; Mutation ; NAD/metabolism ; NADP/metabolism ; Phenotype ; Selection, Genetic
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 6
    Electronic Resource
    Electronic Resource
    Predictions of pressure and temperature effects upon radical addition and recombination reactions (1985)
    s.l. : American Chemical Society
    The @journal of physical chemistry 〈Washington, DC〉 89 (1985), S. 4600-4608 
    Details
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology , Physics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/j100267a038
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  • 7
    Electronic Resource
    Electronic Resource
    Radical Chemistry in Methane Oxidative Coupling: Tracing of Ethylene Secondary Reactions with Computer Models and Isotopes (1994)
    s.l. : American Chemical Society
    The @journal of physical chemistry 〈Washington, DC〉 98 (1994), S. 13357-13372 
    Details
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology , Physics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/j100101a041
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  • 8
    Electronic Resource
    Electronic Resource
    Synthesis of new triazoloquinoxalines, pyrroloquinoxalines, and pyrimidopyrroloquinoxalines (1996)
    Springer
    Monatshefte für Chemie 127 (1996), S. 1263-1272 
    Details
    ISSN: 1434-4475
    Keywords: Quinoxaline ; Triazoloquinoxalines ; Pyrroloquinoxalines ; Pyrimidopyrroloquinoxalines
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Description / Table of Contents: Zusammenfassung Wenn man 2-Hydroxychinoxalin-3-carboxamid (1) mit POCl3 inDMF reagieren läßt, erhält man 2-Chlor-3-dimethylaminomethylencarboxamid (2). Die Chlorverbindung2 wurde mit Thioharnstoff und Hydrazinhydrat zu den entsprechenden Mercapto- und Hydrazinderivaten3 und8 umgesetzt. Aus 2-Chlorchinoxalin-3-carbonsäurenitril (13) und Ethylglycinat erhält man14, das durch Erhitzen mit Natriumethylat zum Pyrrolochinoxalin15 cyclisiert wurde. Die Pyrimidopyrrolochinoxalinderivate16 und17 wurden durch Reaktion von15 mit Formamid bzw. Phenylisothiocyanat erhalten.
    Notes: Summary When 2-hydroxyquinoxaline-3-carboxamide (1) was reacted with POCl3 inDMF, 2-chloro-3-dimethylaminomethylenecarboxamide (2) was obtained. The chloro compound2 was reacted with thiourea and hydrazine hydrate to give the corresponding mercapto and hydrazino derivatives3 and8, respectively. On the other hand, 2-chloroquinoxaline-3-carbonitrile (13) reacted with ethyl glycinate to the glycinate derivative14 which was cyclized to pyrroloquinoxaline15 by heating with sodium ethoxide. Pyrimidopyrroloquinoxaline derivatives16 and17 were obtainedvia the reaction of15 with formamide and phenyl isothiocyanate, respectively.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00807794
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  • 9
    Electronic Resource
    Electronic Resource
    Saturated main-effect designs for factorial experiments (1999)
    Springer
    Statistics and computing 9 (1999), S. 179-185 
    Details
    ISSN: 1573-1375
    Keywords: A-efficiency ; D-efficiency ; factorial experiment ; saturated design
    Source: Springer Online Journal Archives 1860-2000
    Topics: Computer Science , Mathematics
    Notes: Abstract The results of a computer search for saturated designs for 2n factorial experiments with n runs is reported, (where n = 2 mod 4). A complete search of the design space is avoided by focussing on designs constructed from cyclic generators. A method of searching quickly for the best generators is given. The resulting designs are as good as, and sometimes better than, designs obtained via search algorithms reported in the literature. The addition of a further factor having three levels is also considered. Here, too, a complete search is avoided by restricting attention to the most efficient part of the design space under p-efficiency.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1008961712217
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  • 10
    Electronic Resource
    Electronic Resource
    Prediction of rate constants for combustion and pyrolysis reactions by bimolecular QRRK (1986)
    Hoboken, NJ : Wiley-Blackwell
    AIChE Journal 32 (1986), S. 1971-1979 
    Details
    ISSN: 0001-1541
    Keywords: Chemistry ; Chemical Engineering
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Bimolecular QRRK (Quantum Rice-Ramsperger-Kassel) analysis is a simple method for calculating rate constants of addition and recombination reactions, based on unimolecular quantum-RRK theory. Input parameters are readily derived, and rate constants and reaction branching can be predicted with remarkable accuracy. Such predictive power makes the method especially useful in developing mechanisms of elementary reactions. Furthermore, from the bimolecular QRRK equations, limiting forms of the rate constants in the limits of low and high pressure are developed. Addition/stabilization is pressure-dependent at low pressure but pressure-independent at high pressure, as is conventionally understood for simple decomposition, its reverse. In distinct contrast, addition with chemically activated decomposition has the opposite behavior: pressure independence at low pressure and pressure dependence [as (pressure)-1] at high pressure. The method is tested against data and illustrated by calculations for O + CO → CO2; for H + O2 → HO2 or O + OH; for H + C2H4 → C2H5 or C2H3 + H2; and for H + C2H3 → C2H4 or H2 + C2H2.
    Additional Material: 9 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/aic.690321206
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