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  • 1990-1994  (11)
  • Biochemistry and Biotechnology  (6)
  • Engineering General  (5)
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  • 1
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 18 (1994), S. 205-215 
    ISSN: 0887-3585
    Keywords: peptide folding ; disulfide framework ; insect toxins ; NMR ; distance geometry ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: An analysis of the sequences of scyllatoxin and charybdotoxin suggested that it would be possible to design a core peptide sequence which would still fold to give the β-hairpin and helix seen in the toxins, but which would eliminate one disulfide and connecting residues. The core sequence was modeled, then synthesized and purified. The cysteines oxidize in air to give the same disulfide pairings as seen in the parent toxins as the major product. The three-dimensional structure of the core sequence peptide, termed Max, was determined using proton NMR spectroscopy and found to be identical in secondary structure to the toxins. However differences were found in the relative orientation of the β-hairpin and helix. The use of this structural motif, found in many insect toxins, as a disulfide framework for exploring sequence/structure/activity relationships is discussed. © 1994 John Wiley & Sons, Inc.
    Additional Material: 9 Ill.
    Type of Medium: Electronic Resource
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  • 2
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 11 (1991), S. 142-152 
    ISSN: 0887-3585
    Keywords: AMBER ; electrostatics ; protein-protein interactions ; intermolecular bonding ; electron transfer ; redox proteins ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Molecular dynamics simulations have been carried out on the complex formed between the tetraheme cytochrome c3 and the iron protein rubredoxin from the sulfate-reducing bacterium Desulfovibrio vulgaris. These simulations were performed both with explicit solvent water molecules included, and without solvent molecules using a distance-dependent dielectric constant to approximate the screening effects of solvent. The results of both simulations are strikingly different, indicating that the representation of environmental effects is important in such simulations. For example, a striking adaptation of the two proteins seen in the nonsolvated simulation is not seen when explicit solvent water is included; in fact, the complex appears to become weaker in the solvated simulation. Nonetheless, the iron-iron distance decreases more significantly in the solvated simulation than in the nonsolvated simulation. It was found that in both cases molecular dynamics optimized the structures further than energy minimization alone.
    Additional Material: 11 Ill.
    Type of Medium: Electronic Resource
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  • 3
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 16 (1993), S. 306-308 
    ISSN: 0887-3585
    Keywords: rubredoxin ; lgG antibody ; lgM antibody ; immunogen ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The immunogenicity of a folded, all D-amino acid protein- rubredoxin, has been compared with that for the corresponding L-protein enantiomer. Following multiple administrations with alum adjuvant, the L-protein induced a strong, specific lgG antibody response, whereas the D-protein did not. This relative lack of responsiveness to the D-protein cannot be attributed to rapid excretion, since it is retained at least 4 times longer than the natural L-protein. These observations provide the first direct evidence that a folded D-amino acid protein has low immunogenicity and is long lived in vivo. Proteins with such properties may be useful as molecular platforms in a variety of chemical and pharmaco-logical applications. © 1993 Wiley-Liss, Inc.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
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  • 4
    ISSN: 0887-3585
    Keywords: α-helix capping ; α-helix initiation ; α-helix termination ; synthetic peptides ; protein folding ; circular dichroism ; 1H nmr ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A significant fraction of the amino acids in proteins are alpha helical in conformation. Alpha helices in globular proteins are short, with an average length of about twelve residues, so that residues at the ends of helices make up an important fraction of all helical residues. In the middle of a helix, H-bonds connect the NH and CO groups of each residue to partners four residues along the chain. At the ends of a helix, the H-bond potential of the main chain remains unfulfilled, and helix capping interactions involving bonds from polar side chains to the NH or CO of the backbone have been proposed and detected. In a study of synthetic helical peptides, we have found that the sequence Ser-Glu-Asp-Glu stabilizes the alpha helix in a series of helical peptides with consensus sequences. Following the report by Harper and Rose, which identifies SerXaaXaaGlu as a member of a class of common motifs at the N termini of alpha helices in proteins that they refer to as “capping boxes,” we have reexamined the side chain-main chain interactions in a varient sequence using 1H NMR, and find that the postulated reciprocal side chain-backbone bonding between the first Ser and last Glu side chains and their peptide NH partners can be resolved: Deletion of two residues N terminal to the Ser-Glu-Asp-Glu sequence in these peptides has no effect on the initiation of helical structure, as defined by two-dimensional (2D) NMR experiments on this variant. Thus the capping box sequence Ser-Glu-Asp-Glu inhibits N terminal fraying of the N terminus of alpha helix in these peptides, and shows the side chain-main chain interactions proposed by Harper and Rose. It thus acts as a helix initiating signal. Since normal a helix cannot propagate beyond the N terminus of this structure, the box acts as a termination signal in this direction as well. © 1994 John Wiley & Sons, Inc.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
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  • 5
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 37 (1991), S. 519-527 
    ISSN: 0006-3592
    Keywords: papain ; organic solvent ; ester synthesis ; enzyme inactivation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Synthesis of N-CBZ-(N-Carbobenzoxy)-1-amino-acid methyl esters from N-CBZ-amino acids and methanol has been used as an assay to examine the properties of papain in organic solvents containing small amounts of water. Papain is active in solvents ranging in polarity from acetonitrile to tetrachloromethane. The optimal activity in each solvent varied only about three to four fold, but the amount of added water required to achieve it varied from 4% (v/v) in acetonitrile to 0.05% (v/v) in tetrachloromethane. The enzyme was generally more stable in hydrophobic solvents and at lower water contents. The apparent Km value of CBZ-glycine was 26 times higher in acetonitrile than in toluene due to differential partitioning of the substrate between aqueous and organic phases. The substrate specificity of the enzyme was qualitatively little different from that in aqueous solution, with amino acid derivatives still the best substrates. Nitrile analogs of substrates inhibited the enzyme, as they do in aqueous solution, and inhibition by a variety of substituted aromatic hydrocarbons showed that the main specificity of papain for hydrophobic side chains at its S2 subsite, was little affected. The results show that papain can catalyze reactions under a variety of conditions in organic solvents but its substrate specificity is little changed from that in aqueous media.
    Additional Material: 4 Ill.
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  • 6
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 42 (1993), S. 657-666 
    ISSN: 0006-3592
    Keywords: β-galactosidase ; lactose ; β-galactopyranoside ; synthesis ; organic solvent ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Commercially available lactase (β-D-galactoside galactohydrolase, EC 3.2.1.23) enzymes produced from Kluyveromyces fragilis and Kluyveromyces lactis were accessed as catalysts for use in the production of β-galactopyranosides of various alcohols using lactose as galactosyl donor. The yield of galactoside was enhanced by using the highest practical concentrations of both lactose and alcohol acceptor. The concentrations and thus yield, were limited by the solubility of the substrates. The increase in galactoside yield with increasing lactose concentration appeared to be specific to the lactose substrate and not due to water activity alterations, because addition of maltose to a fixed concentration of lactose had no effect. During the course of the reaction, the yield of galactoside peaked after around 70% to 80% of the lactose was consumed, due to hydrolysis of the product by the enzyme. A wide variety of compounds with primary or secondary hydroxyl groups could act as acceptors, the essential requirement being at least some water solubility. Addition of organic cosolvents had little effect on galactoside yield except when it increased the water solubility of sparingly soluble alcohols. Some galactosides were synthesized on a gram scale to determine practical product recoveries and improve purification methods for large-scale synthesis. Initial purification by hydrophobic chromatography (for galactosides of hydrophobic alcohols) or strong anion-exchange chromatography (for galactosides of hydrophilic alcohols) separated galactosides, galactobiosides, and higher oligomers from reducing sugars. A facile separation of the galactoside and galactobioside could then be effected by flash chromatography on silica gel. © 1993 John Wiley & Sons, Inc.
    Additional Material: 6 Ill.
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  • 7
    Electronic Resource
    Electronic Resource
    Chichester [u.a.] : Wiley-Blackwell
    International Journal for Numerical Methods in Engineering 37 (1994), S. 3905-3919 
    ISSN: 0029-5981
    Keywords: Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics , Technology
    Notes: This paper presents a parallel implementation of the boundary element method for MIMD computer architectures to determine the effective properties of two heterogeneous physical systems. The first physical system is comprised of spheres sedimenting in a viscous fluid at low Reynolds numbers. The effective property is characterized by the hindered settling function which is a measure of the average sedimentation velocity. The second physical system is a short-fibre reinforced composite. The effective property for this system is the composite modulus. The determination of effective properties of heterogeneous media requires performing statistical analyses of several realizations of physical systems based on defining characteristics of the media. The boundary element method is particularly well suited for studying such systems because of the simplification in the discretization associated with the method. However, as the number of heterogeneities to be modeled is increased so are the computational demands. Parallel computation offers the opportunity to model systems of greater complexity. We discuss a parallel boundary element formulation based on the torus-wrap mapping. In this approach, blocks of the coefficient matrix associated with the discretized boundary element equations are assigned to processors as opposed to more traditional parallel boundary element implementations where rows or columns are assigned to processors. The torus-wrap mapping can be shown to minimize communication volume between processors during the LU factorization. Therefore, the present formulation scales well with increases in the number of processors.
    Additional Material: 5 Ill.
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  • 8
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Numerical Linear Algebra with Applications 1 (1994), S. 477-504 
    ISSN: 1070-5325
    Keywords: Domain decomposition ; Preconditioning ; Iterative methods ; Nonsymmetric and/or indefinite elliptic problems ; Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: In recent years, competitive domain-decomposed preconditioned iterative techniques of Krylov-Schwarz type have been developed for nonsymmetric linear elliptic systems. Such systems arise when convection-diffusion-reaction problems from computational fluid dynamics or heat and mass transfer are linearized for iterative solution. Through domain decomposition, a large problem is divided into many smaller problems whose requirements for coordination can be controlled to allow effective solution on parallel machines. A central question is how to choose these small problems and how to arrange the order of their solution. Different specifications of decomposition and solution order lead to a plethora of algorithms possessing complementary advantages and disadvantages. In this report we compare several methods, including the additive Schwarz algorithm, the classical multiplicative Schwarz algorithm, an accelerated multiplicative Schwarz algorithm, the tile algorithm, the CGK algorithm, the CSPD algorithm, and also the popular global ILU-family of preconditioners, on some nonsymmetric or indefinite elliptic model problems discretized by finite difference methods. The preconditioned problems are solved by the unrestarted GMRES method. A version of the accelerated multiplicative Schwarz method is a consistently good performer.
    Additional Material: 7 Ill.
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  • 9
    Electronic Resource
    Electronic Resource
    Chichester : Wiley-Blackwell
    International Journal for Numerical Methods in Fluids 14 (1992), S. 147-165 
    ISSN: 0271-2091
    Keywords: Domain decomposition ; Computational fluid dynamics ; Preconditioned Krylov iteration ; Newton's method ; Locally uniform mesh refinement ; 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 divide-and-conquer paradigm of iterative domain decomposition or substructuring has become a practical tool in computational fluid dynamics applications because of its flexibility in accommodating adaptive refinement through locally uniform (or quasi-uniform) grids, its ability to exploit multiple discretizations of the operator equations, and the modular pathway it provides towards parallelism. We illustrate these features on the classic model problem of flow over a backstep using Newton's method as the non-linear iteration. Multiple discretizations (second-order in the operator and first-order in the preconditioner) and locally uniform mesh refinement pay dividends separately and can be combined synergistically. We include sample performance results from an Intel iPSC/860 hypercube implementation.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
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  • 10
    Electronic Resource
    Electronic Resource
    Chichester : Wiley-Blackwell
    International Journal for Numerical Methods in Fluids 11 (1990), S. 127-150 
    ISSN: 0271-2091
    Keywords: Ocean model ; Grid convergence ; Energy conservation ; 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: Five numerical schemes are compared using convergence studies in the framework of the hydrostatic Sandia Ocean Modeling System (SOMS). Three resolutions are used, 40, 20 and 10 km, with respectively three, seven and 15 layers and time steps of 60, 30 and 15 min, so 15 convergence calculations are performed. The same geophysical prototype problem (exhibiting baroclinic instability in a statically stable environment) is used for all calculations.All five schemes are second-order-accurate in space, but those using four-point interpolations for the Coriolis and pressure gradient terms are shown to produce much more accurate results, with relatively little extra computation, than schemes using two-point interpolations.Convergence is also indicated with decreasing horizontal diffusivities of 107, 106, and 105 cm2s-1. Using 107 cm2s-1 diffusivities causes substantial damping of the dominant instabilities during the 30-day integrations performed, but using 106 cm2 s-1 results in little damping and yields results very close to those using 105 cm2 s-1.A barotropic (vertically averaged flow) cyclonic northern basin gyre is explained as a weakly forced circulation. Its equilibrium amplitude is determined by a balance between dissipation effects due to horizontal mixing and diffusion, and weak second-order driving associated with thermodynamic forcing and vorticity dissipation at the basin bottom. It is thus quite sensitive to model dissipation but can be well described by SOMS owing to SOMS' low numerical dissipation.
    Additional Material: 10 Ill.
    Type of Medium: Electronic Resource
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