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  • Engineering  (9)
  • Crystallography, X-Ray  (6)
  • Organic Chemistry
  • 1995-1999  (17)
  • 1
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    A model for the mechanism of human topoisomerase I (1998)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1998-03-21
    Description: The three-dimensional structure of a 70-kilodalton amino terminally truncated form of human topoisomerase I in complex with a 22-base pair duplex oligonucleotide, determined to a resolution of 2.8 angstroms, reveals all of the structural elements of the enzyme that contact DNA. The linker region that connects the central core of the enzyme to the carboxyl-terminal domain assumes a coiled-coil configuration and protrudes away from the remainder of the enzyme. The positively charged DNA-proximal surface of the linker makes only a few contacts with the DNA downstream of the cleavage site. In combination with the crystal structures of the reconstituted human topoisomerase I before and after DNA cleavage, this information suggests which amino acid residues are involved in catalyzing phosphodiester bond breakage and religation. The structures also lead to the proposal that the topoisomerization step occurs by a mechanism termed "controlled rotation."〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stewart, L -- Redinbo, M R -- Qiu, X -- Hol, W G -- Champoux, J J -- CA65656/CA/NCI NIH HHS/ -- GM16713/GM/NIGMS NIH HHS/ -- GM49156/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1998 Mar 6;279(5356):1534-41.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Biomolecular Structure Center and Department of Biological Structure, School of Medicine, University of Washington, Seattle, WA 98195-7742, USA. emerald_biostructures@rocketmail.com〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9488652" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Arginine/chemistry/metabolism ; Binding Sites ; Catalysis ; Crystallography, X-Ray ; DNA/chemistry/*metabolism ; DNA Topoisomerases, Type I/*chemistry/*metabolism ; Humans ; Hydrogen Bonding ; *Models, Chemical ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Oligodeoxyribonucleotides/chemistry/metabolism ; *Protein Conformation ; Protein Structure, Secondary ; Tyrosine/chemistry/metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 2
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    Structure of the VHL-ElonginC-ElonginB complex: implications for VHL tumor suppressor function (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-04-16
    Description: Mutation of the VHL tumor suppressor is associated with the inherited von Hippel-Lindau (VHL) cancer syndrome and the majority of kidney cancers. VHL binds the ElonginC-ElonginB complex and regulates levels of hypoxia-inducible proteins. The structure of the ternary complex at 2.7 angstrom resolution shows two interfaces, one between VHL and ElonginC and another between ElonginC and ElonginB. Tumorigenic mutations frequently occur in a 35-residue domain of VHL responsible for ElonginC binding. A mutational patch on a separate domain of VHL indicates a second macromolecular binding site. The structure extends the similarities to the SCF (Skp1-Cul1-F-box protein) complex that targets proteins for degradation, supporting the hypothesis that VHL may function in an analogous pathway.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stebbins, C E -- Kaelin, W G Jr -- Pavletich, N P -- New York, N.Y. -- Science. 1999 Apr 16;284(5413):455-61.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Structural Biology, Joan and Sanford I. Weill Graduate School of Medical Sciences, Cornell University, New York, NY 10021, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10205047" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Cell Cycle Proteins/chemistry/metabolism ; Cloning, Molecular ; Crystallography, X-Ray ; *Genes, Tumor Suppressor ; Humans ; Hydrogen Bonding ; *Ligases ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Mutation, Missense ; Neoplasms/genetics ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Proteins/*chemistry/genetics/metabolism ; S-Phase Kinase-Associated Proteins ; Surface Properties ; Transcription Factors/*chemistry/metabolism ; *Tumor Suppressor Proteins ; *Ubiquitin-Protein Ligases ; Von Hippel-Lindau Tumor Suppressor Protein ; von Hippel-Lindau Disease/*genetics
    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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    Inhibition of the hammerhead ribozyme cleavage reaction by site-specific binding of Tb (1998)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1998-01-24
    Description: Terbium(III) [Tb(III)] was shown to inhibit the hammerhead ribozyme by competing with a single magnesium(II) ion. X-ray crystallography revealed that the Tb(III) ion binds to a site adjacent to an essential guanosine in the catalytic core of the ribozyme, approximately 10 angstroms from the cleavage site. Synthetic modifications near this binding site yielded an RNA substrate that was resistant to Tb(III) binding and capable of being cleaved, even in the presence of up to 20 micromolar Tb(III). It is suggested that the magnesium(II) ion thought to bind at this site may act as a switch, affecting the conformational changes required to achieve the transition state.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Feig, A L -- Scott, W G -- Uhlenbeck, O C -- GM-36944/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1998 Jan 2;279(5347):81-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9417029" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Binding, Competitive ; Catalysis ; Crystallography, X-Ray ; Magnesium/metabolism ; Models, Molecular ; Nucleic Acid Conformation ; RNA, Catalytic/*antagonists & inhibitors/chemistry/*metabolism ; Terbium/*metabolism/pharmacology
    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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    Crystal structures of human topoisomerase I in covalent and noncovalent complexes with DNA (1998)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1998-03-21
    Description: Topoisomerases I promote the relaxation of DNA superhelical tension by introducing a transient single-stranded break in duplex DNA and are vital for the processes of replication, transcription, and recombination. The crystal structures at 2.1 and 2.5 angstrom resolution of reconstituted human topoisomerase I comprising the core and carboxyl-terminal domains in covalent and noncovalent complexes with 22-base pair DNA duplexes reveal an enzyme that "clamps" around essentially B-form DNA. The core domain and the first eight residues of the carboxyl-terminal domain of the enzyme, including the active-site nucleophile tyrosine-723, share significant structural similarity with the bacteriophage family of DNA integrases. A binding mode for the anticancer drug camptothecin is proposed on the basis of chemical and biochemical information combined with these three-dimensional structures of topoisomerase I-DNA complexes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Redinbo, M R -- Stewart, L -- Kuhn, P -- Champoux, J J -- Hol, W G -- CA65656/CA/NCI NIH HHS/ -- GM49156/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1998 Mar 6;279(5356):1504-13.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Biomolecular Structure Center and Department of Biological Structure, Box 357742, School of Medicine, University of Washington, Seattle, WA 98195, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9488644" target="_blank"〉PubMed〈/a〉
    Keywords: Antineoplastic Agents, Phytogenic/metabolism/pharmacology ; Binding Sites ; Camptothecin/analogs & derivatives/metabolism/pharmacology ; Crystallography, X-Ray ; DNA/chemistry/*metabolism ; DNA Topoisomerases, Type I/*chemistry/genetics/metabolism ; *DNA-Binding Proteins ; Homeodomain Proteins/chemistry ; Host Cell Factor C1 ; Humans ; Hydrogen Bonding ; Integrases/chemistry ; Models, Molecular ; Mutation ; Nucleic Acid Conformation ; Octamer Transcription Factor-1 ; Oligodeoxyribonucleotides/chemistry/metabolism ; *Protein Conformation ; Protein Structure, Secondary ; Recombinant Proteins/chemistry ; Transcription Factors/chemistry ; Tyrosine/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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  • 5
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    Capturing the structure of a catalytic RNA intermediate: the hammerhead ribozyme (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-12-20
    Description: The crystal structure of an unmodified hammerhead RNA in the absence of divalent metal ions has been solved, and it was shown that this ribozyme can cleave itself in the crystal when divalent metal ions are added. This biologically active RNA fold is the same as that found previously for two modified hammerhead ribozymes. Addition of divalent cations at low pH makes it possible to capture the uncleaved RNA in metal-bound form. A conformational intermediate, having an additional Mg(II) bound to the cleavage-site phosphate, was captured by freeze-trapping the RNA at an active pH prior to cleavage. The most significant conformational changes were limited to the active site of the ribozyme, and the changed conformation requires only small additional movements to reach a proposed transition-state.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Scott, W G -- Murray, J B -- Arnold, J R -- Stoddard, B L -- Klug, A -- GM-49857/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1996 Dec 20;274(5295):2065-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, England.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8953035" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Crystallization ; Crystallography, X-Ray ; Freezing ; Hydrogen-Ion Concentration ; Magnesium/metabolism ; Manganese/metabolism ; Models, Molecular ; *Nucleic Acid Conformation ; RNA, Catalytic/*chemistry/metabolism
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 6
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    Structure of the heat shock protein chaperonin-10 of Mycobacterium leprae (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-01-12
    Description: Members of the chaperonin-10 (cpn10) protein family, also called heat shock protein 10 and in Escherichia coli GroES, play an important role in ensuring the proper folding of many proteins. The crystal structure of the Mycobacterium leprae cpn10 (Ml-cpn10) oligomer has been elucidated at a resolution of 3.5 angstroms. The architecture of the Ml-cpn10 heptamer resembles a dome with an oculus in its roof. The inner surface of the dome is hydrophilic and highly charged. A flexible region, known to interact with cpn60, extends from the lower rim of the dome. With the structure of a cpn10 heptamer now revealed and the structure of the E. coli GroEL previously known, models of cpn10:cpn60 and GroEL:GroES complexes are proposed.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mande, S C -- Mehra, V -- Bloom, B R -- Hol, W G -- AI07118/AI/NIAID NIH HHS/ -- AI23545/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 1996 Jan 12;271(5246):203-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Structure, University of Washington, Seattle 98195, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8539620" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Chaperonin 10/*chemistry/metabolism ; Chaperonin 60/chemistry/metabolism ; Crystallography, X-Ray ; Models, Molecular ; Molecular Sequence Data ; Mycobacterium leprae/*chemistry ; *Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Sequence Alignment
    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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  • 7
    Electronic Resource
    Electronic Resource
    A linearized implicit pseudo-spectral method for certain non-linear water wave equations (1998)
    Chichester : Wiley-Blackwell
    Communications in Numerical Methods in Engineering 14 (1998), S. 977-993 
    Details
    ISSN: 1069-8299
    Keywords: third-order KdV equation ; fifth-order KdV equation ; pseudo-spectral ; implicit method ; unconditional stability ; Engineering ; Numerical Methods and Modeling
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics , Technology
    Notes: An efficient numerical method is developed for the numerical solution of non-linear wave equations typified by the third- and fifth-order Korteweg-de Vries equations and their generalizations. The method developed uses a pseudo-spectral (Fourier transform) treatment of the space dependence together with a linearized implicit scheme in time.An important advantage to be gained from the use of this method over the pseudo-spectral scheme proposed by Fornberg and Whitham (a Fourier transform treatment of the space variable together with a leap-frog scheme in time) which is conditionally stable, is the ability to vary the mesh length, thereby reducing the computational time. Using a linearized stability analysis, it is shown that the proposed method is unconditionally stable.The method presented here is for the Korteweg-de Vries equations and their generalized forms, but it can be implemented to a broad class of non-linear wave equations (equation (1)), with obvious changes in the various formulae.To illustrate the application of this method, numerical results portraying a single soliton solution and the collision of two solitons are reported for the third- and fifth-order Korteweg-de Vries equations. © 1998 John Wiley & Sons, Ltd.
    Additional Material: 6 Ill.
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  • 8
    Electronic Resource
    Electronic Resource
    A second order finite element method for the solution of the transonic Euler and Navier-Stokes equations (1995)
    Chichester : Wiley-Blackwell
    International Journal for Numerical Methods in Fluids 20 (1995), S. 671-693 
    Details
    ISSN: 0271-2091
    Keywords: airfoil ; artificial viscosity ; upwinding ; Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: The numerical solution of the compressible Euler and Navier-Stokes equations in primitive variables form requires the use of artificial viscosity or upwinding. Methods that are first-order-accurate are too dissipative and reduce the effective Reynolds number substantially unless a very fine grid is used. A first-order finite element method for the solution of the Euler and Navier-Stokes equations can be constructed by adding Laplacians of the primitive variables to the governing equations. Second-order schemes may require a fourth-order dissipation and higher-order elements. A finite element approach is proposed in which the fourth-order dissipation is recast as the difference of two Laplacian operators, allowing the use of bilinear elements. The Laplacians of the primitive variables of the first-order scheme are thus balanced by additional terms obtained from the governing equations themselves, tensor identities or other forms of nodal averaging. To demonstrate formally the accuracy of this scheme, an exact solution is introduced which satisfies the continuity equation identically and the momentum equations through forcing functions. The solutions of several transonic and supersonic inviscid and laminar viscous test cases are also presented and compared to other available numerical data.
    Additional Material: 17 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/fld.1650200802
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  • 9
    Electronic Resource
    Electronic Resource
    BOUNDARY CONDITIONS IN SHALLOW WATER MODELS - AN ALTERNATIVE IMPLEMENTATION FOR FINITE ELEMENT CODES (1996)
    Chichester : Wiley-Blackwell
    International Journal for Numerical Methods in Fluids 22 (1996), S. 603-618 
    Details
    ISSN: 0271-2091
    Keywords: shallow water equations ; wave continuity equation ; boundary conditions ; finite elements ; generalized functions ; Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: Finite element solution of the shallow water wave equations has found increasing use by researchers and practitioners in the modelling of oceans and coastal areas. Wave equation models, most of which use equal-orderC0 interpolants for both the velocity and the surface elevation, do not introduce spurious oscillation modes, hence avoiding the need for artificial or numerical damping. An important question for both primitive equation and wave equation models is the interpretation of boundary conditions. Analysis of the characteristics of the governing equations shows that for most geophysical flows a single condition at each boundary is sufficient, yet there is not a consensus in the literature as to what that boundary condition must be or how it should be implemented in a finite element code. Traditionally (partly because of limited data), surface elevation is specified at open ocean boundaries while the normal flux is specified as zero at land boundaries. In most finite element wave equation models both of these boundary conditions are implemented as essential conditions. Our recent work focuses on alternative ways to numerically implement normal flow boundary conditions with an eye towards improving the mass-conserving properties of wave equation models. A unique finite element formulation using generalized functions demonstrates that boundary conditions should be implemented by treating normal fluxes as natural conditions with the flux interpreted as external to the computational domain. Results from extensive numerical experiments show that the scheme does conserve mass for all parameter values. Furthermore, convergence studies demonstrate that the algorithm is consistent, as residual errors at the boundary diminish as the grid is refined.
    Additional Material: 6 Ill.
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  • 10
    Electronic Resource
    Electronic Resource
    A DIRECTIONALLY ADAPTIVE METHODOLOGY USING AN EDGE-BASED ERROR ESTIMATE ON QUADRILATERAL GRIDS (1996)
    Chichester : Wiley-Blackwell
    International Journal for Numerical Methods in Fluids 23 (1996), S. 673-690 
    Details
    ISSN: 0271-2091
    Keywords: Euler equations ; directionally adaptive meshes ; edge-based error estimate ; structured grids ; mesh movement ; finite element method ; high-speed flows ; Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: The present paper describes a directionally adaptive finite element method for high-speed flows, using an edge-based error estimate on quadrilateral grids. The error of the numerical solution is estimated through its second derivatives and the resulting Hessian tensor is used to define a Riemannian metric. An improved mesh movement strategy, based on a spring analogy, but with no orthogonality constraints, is introduced to equidistribute the lengths of the edges of the elements in the defined metric. The grid adaptation procedure is validated on an analytical test case and the efficiency of the overall methodology is investigated on supersonic and hypersonic benchmarks.
    Additional Material: 21 Ill.
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