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  • Biochemistry and Biotechnology  (82)
  • Physical Chemistry  (8)
  • 1
    Electronic Resource
    Electronic Resource
    Estimation of parameters in population models for Schizosaccharomyces pombe from chemostat data (1972)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 14 (1972), S. 915-938 
    Details
    ISSN: 0006-3592
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: The integro-differential growth model of Eakman, Fredriekson, and Tsuehiya has been employed to fit cell size distribution data for Schizosaccharomyces pombe grown in a chemostat under severe product inhibition by ethanol. The distributions were obtained with a Coulter aperture and an electronic system patterned after that of Harvey and Marr. Four parameters - mean cell division size, cell division size standard deviation, daughter cell size standard deviation, and a growth rate coefficient - were calculated for models where the cell growth rate was inversely proportional to size, constant, and proportional to size. A fourth model, one where sigmoidal growth behavior was simulated by two linear growth segments, was also investigated. Linear and sigmoidal models fit the distribution data best. While the mean cell division size remained relatively constant at all growth rates, standard deviation of division size distribution increased with increasing holding times. Standard deviation of the daughter size distribution remained small at all dilution rates. Unlike previous findings with other organisms, the average cell size of Schizosaccharomyces pobme increased at low growth rates.
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bit.260140605
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  • 2
    Electronic Resource
    Electronic Resource
    Recombinant antineuraminidase single chain antibody: Expression, characterization, and crystallization in complex with antigen (1993)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 16 (1993), S. 57-63 
    Details
    ISSN: 0887-3585
    Keywords: X-ray crystallography ; antibody domain ; recombinant DNA ; binding affinity ; antigen-antibody complex ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The variable heavy (VH) and variable light (VL) genes of NC10, a monoclonal antibody with specificity toward N9 neuraminidase (NA), were cloned and sequenced. A single chain Fv (scFv) fragment of NC10, consisting of VH and VL domains joined by a peptide linker, was designed, constructed and expressed in the E. coli expression vector pPOW. The N-terminal secretion signal PelB directed the synthesized protein into the periplasm where it was associated with the insoluble membrane fraction. An octapeptide (FLAG) tail was fused to the C-terminus of the single chain Fv to aid in its detection and remained intact throughout the protein purification process. NC10 scFv was purified by solubilization of the E. coli membrane fraction with guanidinium hydrochloride followed by column chromatography. The purified NC10 scFv showed binding affinity for its antigen, NA, 2-fold lower than that of the parent Fab. The complex between NA and the scFv has been crystallized by the vapor diffusion method. The crystals are tetragonal, space group P4212, with unit cell dimensions a = b = 141 Å, c = 218 Å. © 1993 Wiley-Liss, Inc.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340160107
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  • 3
    Electronic Resource
    Electronic Resource
    Towards meeting the paracelsus challenge: The design, synthesis, and characterization of paracelsin-43, an α-helical protein with over 50% sequence identity to an all-β protein (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. 502-513 
    Details
    ISSN: 0887-3585
    Keywords: de novo design ; protein structure ; inverse folding ; genetic algorithms ; 1H NMR ; CD ; peptide ; protein folding ; methanol ; ethylene glycol ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: In response to the Paracelsus Challenge (Rose and Creamer, Proteins, 19:1-3, 1994), we present here the design, synthesis, and characterization of a helical protein, whose sequence is 50% identical to that of an all-β protein. The new sequence was derived by applying an inverse protein folding approach, in which the sequence was optimized to “fit” the new helical structure, but constrained to retain 50% of the original amino acid residues. The program utilizes a genetic algorithm to optimize the sequence, together with empirical potentials of mean force to evaluate the sequence-structure compatibility. Although the designed sequence has little ordered (secondary) structure in water, circular dichroism and nuclear magnetic resonance data show clear evidence for significant helical content in water/ethylene glycol and in water/methanol mixtures at low temperatures, as well as melting behavior indicative of cooperative folding. We believe that this represents a significant step toward meeting the Paracelsus Challenge.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
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  • 4
    Electronic Resource
    Electronic Resource
    Structural aspects of the functional modules in human protein kinase-Cα deduced from comparative analyses (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 26 (1996), S. 217-235 
    Details
    ISSN: 0887-3585
    Keywords: catalytic region ; comparative modeling ; cysteine-rich domain ; phosphorylation ; pseudo-substrate specificity ; synaptotagmin ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Three-dimensional models of the five functional modules in human protein kinase Cα (PKCα) have been generated on the basis of known related structures. The catalytic region at the C-terminus of the sequence and the N-terminal auto-inhibitory pseudo-substrate have been modeled using the crystal structure complex of cAMP-dependent protein kinese (cAPK) and PKI peptide. While the N-terminal helix of the catalytic region of PKCα is predicted to be in a different location compared with cAPK, the C-terminal extension is modeled like that in the cAPK. The predicted permissive phosphorylation site of PKCα, Thr 497, is found to be entirely consistent with the mutagenesis studies. Basic Lys and Arg residues in the pseudo-substrate make several specific interactions with acidic residues in the catalytic region and may interact with the permissive phosphorylation site. Models of the two zinc-binding modules of PKCα are based on nuclear magnetic resonance and crystal structures of such modules in other PKC isoforms while the calcium phospholipid binding module (C2) is based on the crystal structure of a repeating unit in synaptotagmin I. Phorbol ester binding regions in zinc-binding modules and the calcium binding region in the C2 domain are similar to those in the basis structures. A hypothetical model of the relative positions of all five modules has the putative lipid binding ends of the C2 and the two zinc-binding domains pointing in the same direction and may serve as a basis for further experiments. © 1996 Wiley-Liss, Inc.
    Additional Material: 10 Ill.
    Type of Medium: Electronic Resource
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  • 5
    Electronic Resource
    Electronic Resource
    Glucoamylase structural, functional, and evolutionary relationships (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 29 (1997), S. 334-347 
    Details
    ISSN: 0887-3585
    Keywords: evolution ; glucoamylase ; hydrophobic folding ; protein parsimony analysis ; structure/function ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: To correlate structural features with glucoamylase properties, a structure-based multisequence alignment was constructed using information from catalytic and starch-binding domain models. The catalytic domain is composed of three hydrophobic folding units, the most labile and least hydrophobic of them being missing in the most stable glucoamylase. The role of O-glycosylation in stabilizing the most hydrophobic folding unit, the only one where thermostabilizing mutations with unchanged activity have been made, is described. Differences in both length and composition of interhelical loops are correlated with stability and selectivity characteristics. Two new glucoamylase subfamilies are defined by using homology criteria. Protein parsimony analysis suggests an ancient bacterial origin for the glucoamylase gene. Increases in length of the belt surrounding the active site, degree of O-glycosylation, and length of the linker probably correspond to evolutionary steps that increase stability and secretion levels of Aspergillus-related glucoamylases. Proteins 29:334-347, 1997. © 1997 Wiley-Liss, Inc.
    Additional Material: 3 Ill.
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  • 6
    Electronic Resource
    Electronic Resource
    Automated docking of monosaccharide substrates and analogues and methyl α-Acarviosinide in the glucoamylase active site (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 27 (1997), S. 235-248 
    Details
    ISSN: 0887-3585
    Keywords: acarviosinide ; active site ; docking ; glucoamylase ; molecular mechanics ; monosaccharides ; simulated annealing ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Glucoamylase is an important industrial glucohydrolase with a large specificity range. To investigate its interaction with the monosaccharides D-glucose, D-mannose, and D-galactose and with the substrate analogues 1-deoxynojirimycin, D-glucono-1,5-lactone, and methyl αacarviosinide, MM3(92)-optimized structures were docked into its active site using AutoDock 2.1. The results were compared to structures of glucoamylase complexes obtained by protein crystallography. Charged forms of some substrate analogues were also docked to assess the degree of protonation possessed by glucoamylase inhibitors. Many forms of methyl αa-carviosinide were conformationally mapped by using MM3(92), characterizing the conformational pH dependence found for the acarbose family of glucosidase inhibitors. Their significant conformers, representing the most common states of the inhibitor, were used as initial structures for docking. This constitutes a new approach for the exploration of binding modes of carbohydrate chains. Docking results differ slightly from x-ray crystallographic data, the difference being of the order of the crystallographic error. The estimated energetic interactions, even though agreeing in some cases with experimental binding kinetics, are only qualitative due to the large approximations made by AudoDock force field. © 1997 Wiley-Liss, Inc.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
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  • 7
    Electronic Resource
    Electronic Resource
    Automated docking of glucosyl disaccharides in the glucoamylase active site (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 28 (1997), S. 162-173 
    Details
    ISSN: 0887-3585
    Keywords: AutoDock ; cellobioside ; disaccharide ; docking ; gentiobioside ; glucoamylase ; kojibioside ; maltoside ; nigeroside ; simulated annealing ; trehalose ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: To better understand the molecular basis of glucomylase selectivity, low-energy conformers of glucosyl disaccharides obtained from relaxed-residue conformational mapping were flexibly docked into the glucoamylase active site using AutoDock 2.2. This procedure ensures that significant conformational space is searched and can produce bound structures comparable to those obtained by protein crystallography. α-Linked glucosyl disaccharides except α,α-trehalose dock easily into the active site while exclusively β-linked disaccharides do not, explaining why only the former are glucoamylase substrates. The optimized docking modes are similar at the nonreducing end of the different substrates. Individual atomic energies of intermolecular interaction allow the definite identification of key hydroxyl groups for each substrate. This approach confirmed the versatility of the second subsite of the glucoamylase active site in binding different substrates. Proteins 28:162-173, 1997. © 1997 Wiley-Liss Inc.
    Additional Material: 2 Ill.
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  • 8
    Electronic Resource
    Electronic Resource
    1H NMR structure of an antifungal γ-thionin protein SIα1: Similarity to scorpion toxins (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 32 (1998), S. 334-349 
    Details
    ISSN: 0887-3585
    Keywords: antifungal ; thionin ; NMR ; structure ; scorpion ; toxins ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The three-dimensional structure of the Sorghum bicolor seed protein γ-thionin SIα1 has been determined by 2D 1H nuclear magnetic resonance (NMR) spectroscopy. The secondary structure of this 47-residue antifungal protein with four disulphide bridges consists of a three-stranded antiparallel sheet and one helix. The helix is tethered to the sheet by two disulphide bridges which link two successive turns of the helix to alternate residues i, i + 2 in one strand. Possible binding sites for antifungal activity are discussed. The same fold has been observed previously in several scorpion toxins. Proteins 32:334-349, 1998. © 1998 Wiley-Liss, Inc.
    Additional Material: 10 Ill.
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  • 9
    Electronic Resource
    Electronic Resource
    Fold recognition using predicted secondary structure sequences and hidden Markov models of protein folds (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 29 (1997), S. 123-128 
    Details
    ISSN: 0887-3585
    Keywords: protein structure prediction ; hidden Markov models ; fold recognition ; secondary structure ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We present an analysis of the blind predictions submitted to the fold recognition category for the second meeting on the Critical Assessment of techniques for protein Structure Prediction. Our method achieves fold recognition from predicted secondary structure sequences using hidden Markov models (HMMs) of protein folds. HMMs are trained only with experimentally derived secondary structure sequences of proteins having similar fold, therefore protein structures are described by the models at a remarkably simplified level. We submitted predictions for five target sequences, of which four were later found to be suitable for threading. Our approach correctly predicted the fold for three of them. For a fourth sequence the fold could have been correctly predicted if a better model for its structure was available. We conclude that we have additional evidence that secondary structure information represents an important factor for achieving fold recognition. Proteins, Suppl. 1:123-128, 1997. Published 1998 Wiley-Liss, Inc.This article is a US government work and, as such, is in the public domain in the United States of America.
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
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  • 10
    Electronic Resource
    Electronic Resource
    Hydrogen-bonding. Part 4. An analysis of solute hydrogen-bond basicity, in terms of complexation constants (log K), using F1 and F2 factors, the principal components of different kinds of basicityPart 3. M. H. Abraham, P. P. Duce, D. V. Prior, R. A. Schulz, J. J. Morris and P. J. Taylor, J. Chem. Soc. Faraday Trans. 1, 84, 865 (1988). (1989)
    Chichester : Wiley-Blackwell
    Journal of Physical Organic Chemistry 2 (1989), S. 243-254 
    Details
    ISSN: 0894-3230
    Keywords: Organic Chemistry ; Physical Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Physics
    Notes: The principal components factors F1 and F2 in the equation \documentclass{article}\pagestyle{empty}\begin{document}$$ \log K = {\rm BDP}_0 + S_1 F_1 + S_2 F_2 $$\end{document} have been used to obtain S1 and S2 values for sets of hydrogen-bond bases against 32 reference acid/solvent systems. The constants S1 and S2 define an angle θ = tan-1 S2/S1 that is a measure of the electrostatic:covalent bonding ratio in the hydrogen-bond complex. It is shown that θ can vary from 53 (4-fluorophenol in CH2Cl2)to 86 degrees (Ph2NH in CCl4) depending on the reference acid and solvent. This variation in θ can lead to family dependent behaviour in plots of log K for bases against a given reference acid system vs log K for bases against another reference acid system, and precludes the construction of any general scale of hydrogen-bond basicity using log K values. Amongst a quite wide range of reference acid/solvent systems θ varies only from 64 to 73 degrees, and for bases against these reference systems a ‘reasonably general’ scale could be set up. Such a scale could be extended to bases against reference acid/solvent systems outside the 64-73 degree range provided that certain classes of base (e.g. pyridines, alkylamines) were excluded from the additional reference acid/solvent systems.
    Additional Material: 6 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/poc.610020307
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