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  • Articles: DFG German National Licenses  (13)
  • Biochemistry and Biotechnology  (13)
  • 1
    ISSN: 0887-3585
    Keywords: antiparallel β-sheet ; twist ; protein folding ; side chain interactions ; branched amino acids ; cystine-rich proteins ; side chain packing ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Cross-strand pair correlations are calculated for residue pairs in antiparallel β-sheet for two cases: pairs whose backbone atoms are hydrogen bonded together (H-bonded site) and pairs which are not (non-H-bonded site). The statistics show that this distinction is important. When glycine is located on the edge of a sheet, it shows a 3:1 preference for the H-bonded site. Thestrongest observed correlations are for pairs of disulfide-bonded cystines, many of which adopt a close-packed conformation with each cystine in a spiral conformation of opposite chirality to its partner. It is likely that these pairs are a signature for the family of small, cystine-rich proteins. Most other strong positive and negative correlations involve charged and polar residues. It appears that electrostatic compatibility is the strongest factor affecting pair correlation. Significant correlations are observed for β- and γ-branched residues inthe non-H-bonded site. An examination of the structures showsa directionality in side chain packing. There is a correlation between (1) the directionality in the packing interactions of non-H-bonded β- and γ-branched residue pairs, (2) the handedness of the observed enantiomers of chiral β-branched side chains, and (3) the handedness of the twist of β-sheet. These findings have implications for the formation of β-sheets during protein folding and the mechanism by which the sheet becomes twisted. © 1995 Wiley-Liss, Inc.
    Additional Material: 7 Ill.
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  • 2
    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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  • 3
    ISSN: 0006-3592
    Keywords: chemostat ; glucose limitation ; glycosylation ; CHO cells ; interferon-γ ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: The physiology of a recombinant Chinese hamster ovary cell line in glucose-limited chemostat culture was studied over a range of dilution rates (D = 0.008 to 0.20 h-1). The specific growth rate (μ) deviated from D at low dilution rates due to an increased specific death rate. Extrapolation of these data suggested a minimum specific growth rate of 0.011 h-1 (μmax = 0.025 h-1) The metabolism at each steady state was characterized by determining the metabolic quotients for glucose, lactate, ammonia, amino acids, and interferon-γ (IFN-γ). The specific rate of glucose uptake increased linearly with μ, and the saturation constant for glucose (Ks) was calculated to be 59.6 μM. There was a linear increase in the rate of lactate production with a higher yield of lactate from glucose at high growth rates. The decline in the rate of production of lactate, alanine, and serine at low growth rate was consistent with the limitation of the glycolytic pathway by glucose. The specific rate of IFN-γ production increased with μ in a manner indicative of a growth-related product. Despite changes in the IFN-γ production rate and cell physiology, the pattern of IFN-γ glycosylation was similar at all except the lowest growth rates where there was increased production of nonglycosylated IFN-γ. © 1993 John Wiley & Sons, Inc.
    Additional Material: 10 Ill.
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  • 4
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 17 (1975), S. 557-570 
    ISSN: 0006-3592
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Of the experimental methods available for obtaining data to estimate the biological kinetic parameters μm, Ks, and Yeach requires considerable experimental effort, yet often yields somewhat imprecise estimates of the parameters, particularly Ks. Therefore it would be worthwhile to seek ways to get parameter estimates of greater precision using less experimental effort. The precision of parameter estimates is strongly dependent, upon the settings of the independent, variables used in the experiments. This dependence is explained and an attempt made to show how experimental settings can be determined that lead efficiently to precise parameter estimates with minimal effort.
    Additional Material: 9 Ill.
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  • 5
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 38 (1991), S. 371-379 
    ISSN: 0006-3592
    Keywords: plant tissue culture ; Papaver somniferum ; linear growth ; phosphate limitation ; modeling ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: In examining the growth kinetics of cell suspensions of opium poppy (Papaver somniferum), the increase in biomass with time was observed to be linear over the entire batch growth period of up to 20 days. Although batch growth profiles were reproducible utilizing the same inoculum, growth rates varied tremendously when experiments were inoculated with cells from different flasks. Both of these phenomena are difficult to explain with conventional batch growth models. In a series of a experiments, phosphate was determined to be the growth-rate-limiting substrate. By expressing growth rate in terms of the intracellular reserves of phosphorus, a growth model which expresses kinetics in terms of the intracellular phosphorus contents of the cells is shown to predict both linear growth character and inoculum dependent variability in growth. The stationary phase phosphate content of seven plant suspension cultures of different plant species was found to be comparable to phosphorus levels of phosphate-starved poppy cells, which suggests that phosphate limitation may be common for plant tissue culture. The applicability of this model to other biological systems which display similar batch growth patterns when subjected to inorganic nutrient deprivation is discussed.
    Additional Material: 5 Ill.
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  • 6
    ISSN: 0006-3592
    Keywords: plant cell suspensions ; carbon utilization ; growth yield ; maintenance coefficient ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Methodology is presented for the determination of growth yield (Yg) and maintenance coefficient (m) for carbon utilization of plant cells grown in suspension culture. Estimation of Yg and m requires measurements of specific growth rate (µ) and specific rate of substrate uptake (q) at different growth limiting substrate concentrations. Batch culture of tobacco cells did not permit evaluation of Yg and m because µ is constant and maximal during most of the growth cycle. In batch culture, the period of declining specific growth rate is extremely brief because of the rapid transition from logarithmic growth to stationary phase. This occurs because the Km for growth is relatively small compared to the initial sucrose concentration. Thus, when the substrate level reaches the Km, the large mass of cells rapidly depletes the remaining substrate. In contrast, semicontinuous culture facilitates the determination of Yg and m because various steady-state growth rates can be achieved. Mathematical expressions were developed to determine the effective values of µ and q over the semicontinuous replacement interval. The validity of this approach was verified by conducting simulations using experimentally determined parameters.
    Additional Material: 5 Ill.
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  • 7
    ISSN: 0006-3592
    Keywords: Chinese hamster ovary ; interferon-γ ; chemostat culture ; glycosylation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: A Chinese hamster ovary (CHO) cell line expressing recombinant human interferon-γ (IFN-γ) was grown under glucose limitation in a chemostate at a constant dilution rate of 0.015 h-1 with glucose feed concentrations of 2.75 mM and 4.25 mM. The changes in cell concentration that accompanied changes in the glucose feed concentration indicated that the cells were glucose-limited. The cell yield on glucose remained constant, but there was a decline in residual glucose concentration and a reduced lactate yield from glucose in the latter stages of the culture. The consumption rates for many of the essential amino acids were increased later in the culture. The volumetric rate of interferon-γ production was maintained throughout the course of this culture, indicating that IFN-γ expression was stable under these conditions. However, the specific rate of IFN-γ production was significantly lower at the higher glucose feed concentration. Under glucose limitation, the proportion of fully glycosylated IFN-γ produced by these cells was less than that produced in the early stages of batch cultures. The proportion of fully glycosylated IFN-γ increased during transient periods of glucose excess, suggesting that the culture environment influences the glycosylation of IFN-γ.
    Additional Material: 4 Ill.
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  • 8
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 41 (1993), S. 1027-1038 
    ISSN: 0006-3592
    Keywords: sensitivity coefficients ; metabolic sensitivity coefficients ; elasticities ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: The application of metabolic control theory (MCT), or other methods of determining metabolic sensitivity to the rates of specific cellular processes, such as enzymatic reactions, requires knowledge of the elasticity coefficients (system partial derivatives) for the processes under study. Although rate equations are available in the literature for some enzymatic reactions, there are many reactions and processes for which this is not the case. Although one could perform the experiments necessary to determine the rate equations for a given system, these equations are, in fact, not required for the calculation of sensitivities-only the elasticities (the derivatives) are needed. A more direct and efficient approach would be to compute elasticities directly from experimental data. Errors can analysis and alternative regression techniques are presented which not only allow one to eliminate data components with excessive noise, but also provide guidance as to what additional data may be require for accurate sensitivity analysis. This information indicates which measurements require more accuracy and what additional experiments should be conducted to reduce errors in calculated metabolic sensitivity coefficients. © 1993 Wiley & Sons, Inc.
    Additional Material: 1 Ill.
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  • 9
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 38 (1991), S. 241-246 
    ISSN: 0006-3592
    Keywords: fed-batch operation ; continuous approximation ; growth kinetics ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: In Cephalotaxus harringtonia plant cell cultures, periods of batch growth that are limited by hexose uptake are too short to make an accurate estimate of the Monod saturation constant. Continuous cultures are infeasible on a laboratory scale, and semicontinuous cultures require too frequent sampling. Fed-batch operation, consisting of intermittent removal from a culture that is fed continuously, was investigated as a possible solution to these problems. For a constant feed rate, computer simulations showed that a steady state can be achieved which is useful for studying growth at different specific growth rates. In terms of the dilution rate it was confirmed that the operation is essentially equivalent to continuous culture when the samples represent a small fraction of the total culture volume. Experiments with glucose or fructose as the carbon source were carried out in shake flasks fed by a multichannel syringe pump. Results indicate that Monod kinetics based on medium glucose levels cannot adequately describe growth under these conditions. Monod's expression for specific growth rate using internal glucose concentration gives an improved correlation.
    Additional Material: 6 Ill.
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  • 10
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 17 (1975), S. 571-583 
    ISSN: 0006-3592
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Biokinetic parameters are usually calculated from slopes and intercepts taken from plots of experimental data. One response at an item is plotted and used for parameter estimation. Aside from problems that may be caused by transformations made when the data are plotted, this approach has the weakness of not using all the data simultaneously when there is more than one response. This paper shows how multiresponse biological data can be handled to get parameter estimates that are much more precise than those obtained using conventional methods.
    Additional Material: 9 Ill.
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