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  • 2015-2019
  • 1995-1999  (60)
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  • 1
    Electronic Resource
    Electronic Resource
    Berlin : Wiley-Blackwell
    Acta Biotechnologica 19 (1999), S. 225-233 
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
    Notes: The potential of using indigenous microorganisms in beach sediments to degrade petroleum hydrocarbons emanating from marine oil spillages in the Straits of Singapore was investigated. A field trial was conducted using oil contaminated beach sediments from Pulau Semakau - a small island 15 km south of Singapore. The results clearly show that the addition of inorganic nutrients to beach sediments significantly enhanced the activity of indigenous microorganisms (measured using the dehydrogenase enzyme assay and viable cell count techniques), as well as the removal of total recoverable petroleum hydrocarbons (TRPH) over a 50-day study period (with up to 44% in the case of nutrient addition). The potential of exploiting in-situ bioremediation techniques for oil spill clean-up operations in tropical marine environments is discussed.
    Additional Material: 3 Ill.
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  • 2
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
    Notes: The biosynthesis of bacterial cellulose by Acetobacter xylinum was optimized by numerically finding the maximum of an arbitrarily chosen second order polynomial model function of several variables (describing the dependence of the cellulose production on the concentrations of the medium components), using multivariable linear regression analysis. The chosen function appeared to describe the analyzed correlation sufficiently well. Consequently, three to six stages of optimization made the determination of the optimum medium compositions possible for 16 days of fermentation at 30°C in a medium based on fructose (wt%: fructose, 3.68; yeast extract, 5.02; (NH4)2NO3, 0.001; KH2PO4, 0.3; MgSO4 × 7 H2O, 0.05; resulting in a cellulose production equal to 0.505 wt.% - namely 5.6 times higher than before the optimization) and for 7 days fermentations at 30°C in a medium based on sucrose and ethanol (wt.%: sucrose, 5.0; ethanol, 1.36; yeast extract, 1.27; (NH4)2SO4, 0.5; KH2PO4, 0.3; MgSO4 × 7 H2O, 0.05; resulting in a cellulose production equal to 0.251 wt.% - namely 1.5 times higher than before the optimization).
    Additional Material: 1 Ill.
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  • 3
    Electronic Resource
    Electronic Resource
    Berlin : Wiley-Blackwell
    Acta Biotechnologica 19 (1999), S. 91-100 
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
    Notes: The stability of a polyphenol oxidase (PPO) preparation from the white-rot fungus Trametes versicolor during a process for the enzymatic decrease of the phenolic content of commercial canola meal (CM) was investigated. The effects of temperature, pH, protein origin and concentration, and meal particles were considered. The results showed that the thermal stability of the enzyme preparation was significantly increased in the presence of CM. The half-life times for the enzyme preparation, pre-incubated with CM at 50, 60, 70 and 75°C, were 45, 10.5, 3.5 and 1.5 hours, respectively; this represents an increase in the thermal stability of the enzyme preparation of up to four times in the presence of CM compared to the stability in the absence of CM. This effect was caused by the protective actions of both the CM particles and CM proteins, with the former responsible for 90% of the observed effect. The thermal stability of the enzyme in the presence of CM, from which 20% of the extractable proteins was extracted, was 5% lower compared to the stability in the presence of untreated CM. Changes in pH level from 5.0 to 3.2 resulted in a loss of stability comparable to that observed when the pre-incubation temperature was increased from 50 to 70°C.A semi-empirical model describing the changes in the concentration of the active enzyme pre-incubated in the presence and absence of CM at various incubation temperatures was proposed. A very good agreement between the model and experimental data was obtained. The proposed model, together with a general set of model parameters, can be used as a tool for the optimization of a process for the upgrade of CM by enzymatically decreasing the meal's phenolic content.
    Additional Material: 5 Ill.
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  • 4
    Electronic Resource
    Electronic Resource
    Berlin : Wiley-Blackwell
    Acta Biotechnologica 19 (1999), S. 111-145 
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
    Notes: A non-comprehensive review of several technical developments in the field of aerobic biological waste-water treatment engineering is carried out, considering the active role the engineers have to play in this field. This paper brings together conventional and advanced problems in the field of aerobic biological waste-water treatment.Such an overview of biological waste-water treatment also precedes comments on some important aspects concerning the microorganisms responsible for waste-water treatment as well as considerations of the application of fundamentals and kinetics to the analysis of the biological processes used most commonly for aerobic biological waste-water treatment.A survey of the development of the biological activated-sludge process and some modifications are given. Some problems implied in the conventional activated-sludge waste-water treatment are analyzed, considering conventional processes and bioreactor models (the continuous stirred-tank reactor model and the plug-flow reactor models of the activated-sludge process) as well as aerated lagoons.Further, modifications of the activated-sludge process are presented. These include additional details on the bioreactor progress and applications, with emphasis on aspects concerning airlift bioreactors and their variants, deep-shaft bioreactors and reciprocating jet bioreactors which are considered as the third generation of bioreactors owing to their important advantages in design, operation and performance in waste-water treatment. Sequencing-batch reactors and aerobic digestion processes, including conventional aerobic digestion, high-purity oxygen digestion, thermophilic aerobic digestion and cryophylic aerobic digestion are also reviewed.Finally, some aspects regarding the operational factors that are involved in the selection of the reactor type are included.
    Additional Material: 11 Ill.
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  • 5
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
    Notes: In the first part of the experiments, the mechanical properties of 1%, 2% and 3% carrageenan and 1%, 2% and 3% carrageenan/locust bean gum (LBG) gels stored in various concentrations of propionic and acetic acids and their mixtures were examined. The stability of these materials was measured by uniaxial compression between two parallel plates using the Instron Universal Testing Machine. A mathematical model explaining the dependence of the destroying force on the storage time was chosen for data analysis. Using this model, the average rate of gel deterioration was calculated. The structural properties of the examined gels were most influenced by the highest concentration of propionic and acetic acids and their mixtures (1% acetic acid and 2% propionic acid). The addition of LBG to carrageenan decreased the gel destroying force and increased its resistance to acids.In the second part of the experiments, the Propionibacterium freudenreichii subsp. shermanii NCFB 1081 and NCFB 566 were immobilized in a living state in 1%, 2% and 3% carrageenan and 1%, 2% and 3% carrageenan/LBG gels. The ammonia consumption, glucose utilization, production of propionic and acetic acids and the biosynthesis of vitamin B12 were examined. An increase in the productivity of propionic acid and a significant decrease in the vitamin B12 produced in the biosynthesis were observed when immobilized cells were used. The immobilization of cells enhanced the productivity of propionic acid by up to 40% compared to free cells. The best results were obtained for the second and third applications of immobilized cells in all concentrations of carrageenan gels and 2% and 3% carrageenan/LBG gels The results showed that carrageenan/LBG is a better support material for the immobilization of propionic acid bacteria than the pure carrageenan.
    Additional Material: 2 Ill.
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  • 6
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
    Type of Medium: Electronic Resource
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  • 7
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
    Type of Medium: Electronic Resource
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  • 8
    Electronic Resource
    Electronic Resource
    Berlin : Wiley-Blackwell
    Acta Biotechnologica 19 (1999), S. 171-177 
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
    Notes: The bioaccumulation of cadmium by the white rot fungus Pleurotus sajor-caju onto dry biomass was investigated using aqueous media with concentrations in the range of 0.125 mM-1.0 mM The highest cadmium uptake (between 88.9 and 91.8%) was observed with aerobic fungal biomass from the exponential growth phase. Up to 1.0 mM cadmium gradually inhibited mycelium development, but never blocked it completely. Freeze-dried, oven-dried and non-metabolizing live Pleurotus sajor-caju biomass types were tested for their capacity to adsorb the test ion Cd2+ within the pH range of 4.5 to 6.0. Freeze-dried biomass proved to be the most efficient biomass type for Cd2+ metal adsorption. Therefore, Pleurotus sajor-caju may be used for heavy metal removal and bioremediation.
    Additional Material: 2 Ill.
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  • 9
    Electronic Resource
    Electronic Resource
    Berlin : Wiley-Blackwell
    Acta Biotechnologica 19 (1999), S. 3-16 
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
    Notes: The kinetics of cellobiose hydrolysis was studied using β-glucosidase from Penicillium funiculosum, both free and immobilized on nylon powder, at different temperatures, pH values, enzymatic activities and initial cellobiose and glucose concentrations.The experimental results were fitted to a kinetic model by considering the substrate and product inhibitions as well as the thermal deactivation of β-glucosidase with a mean deviation of less than 10%. The immobilization of β-glucosidase led to an increase in the stability of the enzyme against changes in the pH value.
    Additional Material: 10 Ill.
    Type of Medium: Electronic Resource
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  • 10
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
    Type of Medium: Electronic Resource
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  • 11
    Electronic Resource
    Electronic Resource
    Berlin : Wiley-Blackwell
    Acta Biotechnologica 19 (1999), S. 27-36 
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
    Notes: Ethanol has been reported to be a gaseous pollutant, originating from the agricultural industry. Interest in its biodegradation has increased over the last two decades. Most of the current studies have focused on its elimination by mixed cultures. This study is part of a broader project intended to utilize Candida utilis strains for gaseous ethanol elimination and to eventually bioconvert them into biomass and/or volatile metabolites. We present here the study of six strains (one from the ATCC and five from the ICIDCA collection) cultivated in a liquid medium, with initial ethanol concentrations of 16 g/l and 32 g/l. At 16 g/l, a maximum ethanol elimination rate of 0.13 g/l × h was obtained in four of the six strains (ATCC 9950, L/375-1, L/375-5 and L/375-10). This rate increased to 0.21 g/l × h with an initial ethanol concentration of 32 g/l. The L/375-5 strain was the best biomass producer (3.3 g/l) at 32 g/l, while the highest ethyl acetate production (0.80 g/l) was obtained with the L/375-1 strain. The L/375-25 and L/375-26 strains which showed very low ethyl acetate production were, by way of contrast, efficient acetaldehyde producers, with 0.54 g/l and 0.66 g/l measured in the broth. While biomass production reached its maximum after two days of culture, the production of acetic acid and ethyl acetate continued during the third day. The results for biomass and metabolite production obtained with the ICIDCA collection strains (L/375-1, L/375-5 and L/375-10) were better than those obtained with the ATCC 9950 strain, although the latter often has been reported to be particularly suitable for metabolite production.
    Additional Material: 5 Ill.
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  • 12
    Electronic Resource
    Electronic Resource
    Berlin : Wiley-Blackwell
    Acta Biotechnologica 19 (1999), S. 77-78 
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
    Type of Medium: Electronic Resource
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  • 13
    Electronic Resource
    Electronic Resource
    Berlin : Wiley-Blackwell
    Acta Biotechnologica 19 (1999), S. 59-68 
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
    Notes: The ability of the Rhizobium sp., isolated from the root nodules of the leguminous pulse yielding shrub Cajanus cajan, to produce extracellular polysaccharides (EPS) was checked. A large amount of EPS (1, 128 μg/ml) was produced by the bacteria in yeast extract mannitol medium. Growth and EPS production started simultaneously, but the production reached its maximum level in the stationary phase of growth at 28 h. The EPS production by this Rhizobium sp. was much higher than by many other strains from nodules of Cajanus cajan which took a much longer time to reach maximum EPS production than this strain. The maximum EPS production (2,561 μg/ml) was obtained when the medium was supplemented with mannitol (1%), cetyl pyridinium chloride (2 μg/ml) and KNO3 (0.2%), in which the production was increased by 276% compared to the control. The EPS production rose in the period up to 65 h with increased mannitol concentration. The EPS contained arabinose, xylose and rhamnose monomers. The possible role of rhizobial EPS production in root nodule symbiosis is discussed.
    Additional Material: 3 Ill.
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  • 14
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
    Type of Medium: Electronic Resource
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  • 15
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
    Type of Medium: Electronic Resource
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  • 16
    Electronic Resource
    Electronic Resource
    Berlin : Wiley-Blackwell
    Acta Biotechnologica 19 (1999), S. 331-339 
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
    Notes: The Rhizobium sp., isolated from the root nodules of the leguminous fodder herb Melilotus alba, produced large amounts of extracellular polysaccharides (EPS) (963.5 μg/ml) in a yeast extract mannitol medium. Growth and EPS production started simultaneously, but EPS production reached its maximum during the stationary phase of growth of the bacteria, at 20 hours. EPS production was increased with all of the thirteen sugars tested. Different nitrogen sources, such as nitrates, glutamic acid, casamino acid and L-asparagine, increased the EPS production although it was inhibited by glycine, nitrite and ammonium salts. Among the vitamins and metal ions, only pyridoxal phosphate and ZnSO4 promoted EPS production. Attempts were made to optimize the cultural requirements for growth and maximum EPS production. Maximum EPS production (1457.0 μg/ml) was obtained when the medium was supplemented with glucose (1%), pyridoxal phosphate (2 μ g/ml), ZnSO4 × 7 H2O (10 μg/ml) and glutamic acid (0.1%). Under these conditions, the production was increased by 254.3% compared to the control. The EPS contained arabinose, xylose and rhamnose monomers. The presence of arabinose and xylose in the EPS produced by a Rhizobium sp. was uncommon.
    Additional Material: 2 Ill.
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  • 17
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
    Notes: In the present work, the use of flame-burned WS as carriers of Z. mobilis and extracellular levansucrase and the effect of the cell fixation method by dehydration on system productivity were investigated. Lyophilization and convective drying of Z. mobilis biomass at 30°C to a moisture content of 10-14% gave the best results for the repeated batch fermentations of a sucrose medium to obtain levan and ethanol. Significant correlation between the product formation and the concentration of free cells in the fermentation medium was established. Clearly, the cells were weakly bound to the newly generated WS and were washed out into the medium during fermentation. Here the hypothesis is presented that components excreted from damaged cells during dehydration can intensify the reactivation of damaged living cells and influence the interactions between the cells and the wire surface.The passive immobilization of extracellular levansucrase in oxidized WS was also observed. The superiority of oxidized WS in comparison with non-treated WS is related to an increase in the number of OH groups. The potential regeneration of WS by burning after the termination of fermentation cycles was also considered.
    Additional Material: 2 Ill.
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  • 18
    Electronic Resource
    Electronic Resource
    Berlin : Wiley-Blackwell
    Acta Biotechnologica 19 (1999), S. 146-146 
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
    Type of Medium: Electronic Resource
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  • 19
    Electronic Resource
    Electronic Resource
    Berlin : Wiley-Blackwell
    Acta Biotechnologica 19 (1999), S. 157-161 
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
    Notes: A xylanase was removed from crude extract of the fungus Penicillium janthinellum under optimized conditions: 0.10M phosphate buffer, pH 7.0, 0.2 M BDBAC (N-benzyl-N-dodeceyl-N-bis (2-hydroxyethyl) ammonium chloride), 7.5% hexanole, 30°C and an agitation time of 1 minute. At 1.42 mg per ml protein concentration, 73% of the xylanase activity was recovered and a 7-fold enrichment factor was obtained. The enzyme had a molecular weight (MW) of 20.1 kDa and the isoelectric point (PI) revealed the presence of two protein bands with a PI of 6.0 and 6.5. The optimum pH and optimum temperature were 4.2 and 50°C, respectively. The low pH differential between the aqueous medium and the protein PI seemed to influence the xylanase transportation into the reversed micelles.
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  • 20
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
    Type of Medium: Electronic Resource
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  • 21
    Electronic Resource
    Electronic Resource
    Berlin : Wiley-Blackwell
    Acta Biotechnologica 19 (1999), S. 163-169 
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
    Notes: The morphogenetic response of Hypericum perforatum seedlings to different auxin and cytokinin concentrations was studied. A stimulation of the concentration-dependent rooting ability was observed under the influence of indole-3-acetic acid and indole-3-butyric acid. Rooting was not enhanced by the effects of 2,4-dichlorophenoxyacetic acid and 1-naphtaleneacetic acid. Differentiated roots were isolated and cultured in liquid media with the same combination of growth-promoting auxins. Chromosome counts in root tip cells after long-term cultivation indicated a high degree of chromosomal instability. Multiple shoot formation occurred under the influence of 6-benzylaminopurine and kinetin. Adenine and 6-(γ,γ-dimethylallylamino)-purine did not stimulate shoot differentiation. No differences in the morphogenetic response to auxins and cytokinis were detected between diploid and tetrapoloid plants.
    Additional Material: 2 Ill.
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  • 22
    Electronic Resource
    Electronic Resource
    Berlin : Wiley-Blackwell
    Acta Biotechnologica 19 (1999) 
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
    Type of Medium: Electronic Resource
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  • 23
    Electronic Resource
    Electronic Resource
    Berlin : Wiley-Blackwell
    Acta Biotechnologica 19 (1999), S. 179-186 
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
    Notes: Spores of Aspergillus niger were exposed to a pulsed electric field. After treatment by the electric field, the viability of the conidia of A. niger varied depending on the field strength, pulse width and frequency. In all cases, these parameters reduced the viability rate of the conidia from 2.0 × 107 to a range from 6.2 × 106 to 8.5 × 106 spores/ml (3.1 to 42.6%). After pulse treatment, the conidia were used as the inoculum for citric acid fermentation in shake flasks. The highest increase in citric acid yield (about 1.4-fold) was reached at a field strength of 2.85 kV/cm, a frequency of 1 Hz and a pulse width of 1 ms. When the parameters of the electric field increased there were important changes in the respiration rate of the Aspergillus niger mycelium (48-h-old) after electric shock treatment. The highest consumption of dissolved oxygen (22.9%) in the medium by Aspergillus niger mycelium was observed at an electric field strength of 2.85 kV/cm, a 1 Hz frequency, a pulse width of 1 ms and a 1-min exposure period. It seems that an electric-field stimulation of the conidia prior to inoculation may offer an important method of improving the efficiency of citric acid. The treatment of the conidia is both simple from the technical point of view and extremely rapid.
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  • 24
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
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  • 25
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
    Notes: The effects of adding some inducers of lignolytic activity to semi-solid-state cultures of Phanerochaete chrysosporium BKM-F-1767 (ATCC 24725) were investigated. The inducers assayed were veratryl alcohol and solid manganese (IV) oxide. The microorganism was cultured on corncob, which functioned both as physical support and source of nutrients.Supplementing the cultures with veratryl alcohol created the situation where manganese-dependent peroxidase (MnP) and lignin peroxidase (LiP) activities of approximately 1,500 U/l and 200 U/l, respectively, could be attained. These activities were considerably higher than those obtained in the reference cultures (about 5 and 4-fold).In the same way, the addition of manganese (IV) oxide led to MnP and LiP activity levels of about 2,000 U/l and 300 U/l, respectively. These activities were also notably above (about 6 and 5-fold, respectively) those achieved in the reference cultures.Moreover, laccase activity (around 200 U/l) was only detected in veratryl alcohol or manganese (IV) oxide supplemented cultures.
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  • 26
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
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  • 27
    Electronic Resource
    Electronic Resource
    Berlin : Wiley-Blackwell
    Acta Biotechnologica 19 (1999), S. 45-56 
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
    Notes: The culture behaviour of Thermus aquaticus was characterized. The response of the bacterium to various carbon (tryptone, glucose, glycerol) and nitrogen sources (yeast extract, NaNO3, (NH4)2SO4, leucine, thymine, thiamine, glutamic acid) was studied. Amino acids did not support growth, but CASTENHOLZ salt medium supplemented with yeast extract and glucose or tryptone resulted in good growth and production. A suitable medium composition giving the highest biomass concentration and enzyme yield was developed. The simple medium containing TYE-NaCl resulted in the highest biomass concentration, whereas CASTENHOLZ mineral medium supplemented with tryptone and yeast extract gave the highest specific activity and enzyme yield. The effect of inoculum age and size on growth was also investigated in order to improve the yield and process consistency. The use of shake flasks inoculated with precultures at their early or late stationary phase resulted in the same biomass concentration (0.56 ± 0.015 g/l) and similar maximum specific growth rates (0.258 ± 0.003 h-1). Inoculum sizes between 1 and 2.5 per cent were optimal for cell growth. As the other papers on thermophilic microorganisms, including the T. aquaticus YT-1 strain, gave qualitative information on growth, the results presented here cannot be compared with others on a quantitative basis. TaqI endonuclease was purified using a 5 step protocol including cell disruption, adsorption, precipitation, column chromatography and final dialysis. The enriched fraction had a specific activity of 33,600 U TaqI endonuclease per mg protein.
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  • 28
    Electronic Resource
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    Berlin : Wiley-Blackwell
    Acta Biotechnologica 19 (1999), S. 88-88 
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
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  • 29
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    Berlin : Wiley-Blackwell
    Acta Biotechnologica 19 (1999), S. 79-86 
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
    Notes: Methylobacterium rhodesianum MB 126, a pink-pigmented facultatively methylotrophic bacterium that uses that serine pathway for the assimilation of reduced C1 compounds, is able to produce poly-3-hydroxybutyrate (PHB) under certain limitation conditions. Mutants of this bacterium, which were isolated after the treatment with sodium nitrite, are impaired in their ability to synthesize PHB, but produce another polymer in addition to PHB, namely an exopolysaccharide (EPS). This paper attempts to explain this surprising behaviour.
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  • 30
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
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  • 31
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    Berlin : Wiley-Blackwell
    Acta Biotechnologica 19 (1999) 
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
    Type of Medium: Electronic Resource
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  • 32
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    Berlin : Wiley-Blackwell
    Acta Biotechnologica 19 (1999), S. 37-44 
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
    Notes: Agar-agar, agarose, carrageenan and calcium alginate were used for the immobilization of Dunaliella salina cells. Out of the four, agar-agar was found to be the most effective and therefore the study was carried out on it using different pH values ranging from 6 to 10 and cell densities from 0.1 to 0.8 μg chlorophyll (chl, a) per bead to find which are is best suited for glycerol production. The maximum glycerol production of 9.2 μM/mg chl a was recorded in agar-agar immobilized algae and this was followed by 8.4 μM/mg chl a in calcium alginate. The maximum cell number 6.2 × 109/ml and the specific growth rate (μ) of 0.80 l/day were reached at pH 8 in agar-agar immobilized algae. It was shown that the maximum amount of glycerol was produced when the cell density was 0.8 μg chl a/ block. Changing the medium after 24 hours affected the rate of glycerol production at different pH values. Using a cell density of 0.8 μg chl a/block at 16 W/m2 light intensity increased the glycerol production in comparison with the use of free living cells.
    Additional Material: 4 Ill.
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  • 33
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    Berlin : Wiley-Blackwell
    Acta Biotechnologica 19 (1999), S. 235-250 
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
    Notes: A new low-cost β-galactosidase (lactase) preparation for whey permeate saccharification was developed and characterized. A biocatalyst with a lactase activity of 10 U/mg, a low transgalactosylase activity and a protein content of 0.22 mg protein/mg was obtained from a fermenter culture of the fungus Penicillium notatum. Factors influencing the enzymatic hydrolysis of lactose, such as reaction time, pH, temperature and enzyme and substrate concentration were standardized to maximize sugar yield from whey permeate. Thus, a 98.1% conversion of 5% lactose in whey permeate to sweet (glucose-galactose) syrup was reached in 48 h using 650 β-galactosidase units/g hydrolyzed substrate. After the immobilization of the acid β-galactosidase from Penicillium notatum on silanized porous glass modified by glutaraldehyde binding, more than 90% of the activity was retained. The marked shifts in the pH value (from 4.0 to 5.0) and optimum temperatures (from 50°C to 60°C) of the solid-phase enzyme were observed and discussed. The immobilized preparation showed high catalytic activity and stability at wider pH and temperature ranges than those of the free enzyme, and under the best operating conditions (lactose, 5%; β-galactosidase, 610-650 U/g lactose; pH 5.0; temperature 55°C), a high efficiency of lactose saccharification (84-88%) in whey permeate was achieved when lactolysis was performed both in a batch process and in a recycling packed-bed bioreactor. It seems that the promising results obtained during the assays performed on a laboratory scale make this immobilizate a new and very viable preparation of β-galactosidase for application in the processing of whey and whey permeates.
    Additional Material: 6 Ill.
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  • 34
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
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  • 35
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    Berlin : Wiley-Blackwell
    Acta Biotechnologica 19 (1999), S. 263-272 
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
    Notes: An acid α-amylase hyperproducing strain, designated as MIR-61, was isolated in a screening procedure from South American soil samples. MIR-61, a 60°C thermoresistant strain, was identified using 98 biochemical and morphological tests and characterized as Bacillus licheniformis by numerical taxonomy. Batch cultures of B. licheniformis MIR-61 showed extracellular α-amylase and α-glucosidase activities during the exponential growth phase.The production of α-amylase was studied at free and constant pH values at 37 and 45°C. Maximum α-amylase activity (4,767 kU/dm3 in a liquid medium) was detected at 45°C at a constant pH (7.0) in the late exponential phase. The α-amylase production by B. licheniformis MIR-61 is 10 to 300 times higher than the enzyme production reported in strains of the same species.Optimum α-amylase activity was found at 50 to 67°C in an acid pH range from 5.5 to 6.0. These properties would allow its use in starch industry processes.
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  • 36
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    Berlin : Wiley-Blackwell
    Acta Biotechnologica 19 (1999) 
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
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  • 37
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
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  • 38
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    Berlin : Wiley-Blackwell
    Acta Biotechnologica 19 (1999), S. 279-292 
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
    Notes: The continuous aerobic degradation of phenoxyalkanoate herbicides by Sphingomonas herbicidovorans MH was investigated in a bubble reactor filled with modified polyurethane-foam (PU 90/51) as a carrier for the adsorptive immobilization of the bacterial cells. The PU-foam was applied in the form of plates (5 × 10 × 10 mm) and the amount added was equivalent to a PU-load of 1.25% [w/v]. Strain MH is capable of detoxifying the dichloro-substituted phenoxyalkanoates 2,4-DP, 2,4-D and 2,4-DB and the methylchloro-substituted phenoxyalkanoates MCPA, MCPP and MCPB. Degradation of the respective substrate was followed by HPLC analyses and by determination of the chloride release. No intermediates of the degradation pathways or “dead end” products were detected by HPLC analyses. The PU-bubble reactor with immobilized 2,4-DP-pre-grown cells was run continuously at 30°C at the high dilution rate of D = 0.5h-1 with 2,4-DP (0.2 g/l), and with subsequent changes to each of the other phenoxyalkanoates as a single substrate in the feed and with an intermittent return to 2,4-DP. Finally, after an intermediate substrate accumulation, 2,4-D, 2,4-DP, MCPA and MCPP could be degraded under the aforementioned conditions corresponding to a maximum degradation rate of Qphen = 100 mg/l × h. In the case of 2,4-DB, a slightly reduced conversion rate of about 94% could be calculated. In contrast to these results, 0.2 g/l of the more recalcitrant MCPB could not be metabolized at this high dilution rate of D = 0.5 h-1 by the biofilm of Sphingomonas herbicidovorans MH, but it was degradable at a reduced dilution rate of D = 0.25 h-1. Complete detoxification of a stoichiometric mixture of the dichloro- and the methylchloro-substituted phenoxyalkanoates including MCPB, respectively, at a total concentration of 0.2 g/l was achieved at D = 0.25 h-1, corresponding to a degradation rate of Qtot = 50 mg/l × h. Finally, the efficiency of the PU-immobilized cells of Sphingomonas herbicidovorans MH in detoxifying mixtures of all six herbicides could be increased to Qtot = 75 mg/l × h by the further addition of PU-foam particles corresponding to a final PU-load of 2.5% [w/v]. This PU-bubble reactor was successfully operated for more than 12 months to clean up synthetically concocted waste waters with fluctuations in phenoxyalkanoate concentration and composition.
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  • 39
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    Berlin : Wiley-Blackwell
    Acta Biotechnologica 19 (1999), S. 307-318 
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
    Notes: The biodesulphurization of Mengen lignite by a mesophilic bacterium, Rhodococcus rhodochrus ATCC 53968, was investigated in a batch stirred and aerated reactor. The experiments were carried out at 28°C with an inoculum percentage, initial pH, initial sodium acetate and lignite concentration of the biodesulphurization medium of 8% [v/v], 6.5 mM, 20 mM and 20 g/l, respectively. Variations in the sulphur contents of the lignite relative to the biodesulphurization period were monitored. The effects of the stirring and aeration rates on the removal of different sulphur forms from coal were investigated in the ranges 450-1,200 rpm and 0.1-0.53 vvm and the optimum values were found to be 500 rpm and 0.18 vvm, respectively. An increase in the total sulphur reduction with increasing biodesulphurization time was observed. The maximum total sulphur removal percentage was found to be 15.2% at 1,200 rpm after four days of incubation. The highest total sulphur removal rate was calculated on the second day of microbial desulphurization for each run. The total and organic sulphur contents of the coal after biodesulphurization were correlated with the stirring and aeration rates by using the non-linear least squares regression method. In the experimental runs lasting 8 days, the highest organic sulphur reducing percentage of 10.1% was obtained at a stirring rate of 500 rpm and an aeration rate of 0.40 vvm.
    Additional Material: 6 Ill.
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  • 40
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
    Notes: Selected strains of basidiomycetes (Abortiporus biennis, Trametes versicolor and Cerrena unicolor) were shown to produce enhanced extracellular peroxidase (EP), superoxide dismutase (SOD) and laccase activities following the exposure of 10-day-old fungal cultures to separate high and low temperature stress. The stressful conditions also caused an increase in the concentrations of phenol compounds and superoxide anion radicals in these cultures. At first, peroxidase activity was observed at 12 hours from the moment of temperature stress application. Laccase activity appeared at 96 hours after the maximum levels of superoxide anion radicals (48 h) and SOD activity (36-72 h). The concentration of phenolic substances grew steadily during the period of cultivation. These relations between laccase, SOD and EP as well as superoxide radicals and phenol levels in the environment of ligninolytic fungi seems to be important in the course of the biosynthesis or biodegradation of lignin, as the consequence of adaptation of these basidiomycetes to environmental temperature conditions.
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  • 41
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    Berlin : Wiley-Blackwell
    Acta Biotechnologica 19 (1999), S. 356-356 
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
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  • 42
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    Berlin : Wiley-Blackwell
    Acta Biotechnologica 19 (1999), S. 349-355 
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
    Notes: Comamonas acidovorans MC1, which is capable of degrading the chiral phenoxypropionate herbicides 2-(2,4-dichlorophenoxy)propionate [dichlorprop, (RS)-2,4-DP] and 2-(4-chloro-2-methylphenoxy)propionate [mecoprop, (RS)-MCPP] and of degrading the phenoxyacetate herbicides 2,4-dichlorophenoxyacetate (2,4-D) and 4-chloro-2-methylphenoxyacetate (MCPA), was investigated with respect to the enzymatic basis of this broad substrate specificity. The initial steps of the degradation pathway of (RS)-2,4-DP and 2,4-D were studied. By applying either ion exchange chromatography or hydrophobic interaction chromatography it was possible to separate two enzyme fractions with etherolytic activity, which exhibited pronounced substrate specificity. One enzyme fraction was highly specific for the degradation of the R-enantiomer of 2,4-DP and did not essentially attack the S-configuration. The other enzyme fraction showed pronounced activity toward the cleavage of the S-enantiomer and additionally utilized 2,4-D with almost equal velocity; (R)-2,4-DP was even cleaved at a low rate by this enzyme. These results confirm the existence of phenoxyalkanoatedegrading enzymes with enantiospecific properties in strain MC1.
    Additional Material: 3 Ill.
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  • 43
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
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  • 44
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    Berlin : Wiley-Blackwell
    Acta Biotechnologica 19 (1999), S. 191-203 
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
    Notes: The population of poly-β-hydroxybutyrate-degrading microorganisms and the biodegradation of PHB in local landfill soils were examined in vitro and in vivo. Forty-two PHB-degraders consisting of 12 bacteria, 25 actinomycetes and 5 moulds were isolated. The total PHB-degraders averaged 4.7 × 107 and 20 × 104 colony forming units (cfu)/g for San Mateo wet and dry soils, respectively, and 2.3 × 107 and 8.5 × 104 cfu/g for Carmona wet and dry samples, respectively. The PHB-degraders formed 0-59% of the total microbial population in San Mateo and 8-42% in Carmona. Complete (100%) degradation of PHB powder was observed for Chryseomonas-27 and Aspergillus-39 on day 5 in shake flask culture and for Streptomyces-4 on day 7. Burial test in landfill soils showed a 90-91% weight loss of PHB film strips within four weeks; the weight loss of polypropylene film strips was up to 0.12% only. Scanning electron micrographs of degraded films revealed the attachment of microbial cells and fungal mycelium and spores on the surfaces. Holes and cavities were also noted due to the microbial degradation processes.
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  • 45
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    Berlin : Wiley-Blackwell
    Acta Biotechnologica 19 (1999), S. 205-210 
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
    Notes: The application of biotechnology in environmental processes is an enormous subject that could remain the topic of a university lecture course for many years. For this reason I wish to limit my lecture to a few examples and to attempt to sketch out particularly promising opportunities for future development.
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  • 46
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
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  • 47
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    Berlin : Wiley-Blackwell
    Acta Biotechnologica 19 (1999), S. 213-223 
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
    Notes: The Acinetobacter sp. E11, isolated from Port Dickson Beach, Malaysia, was able to grow in media containing crude oil as the sole carbon and energy source. Substrate specificity studies showed that the bacterium exhibited substrate preference as growth was observed only in media containing aliphatic hydrocarbons, while aromatic and cyclic hydrocarbons inhibited growth. With the aliphatic hydrocarbons, growth was seen only in the long-chain alkanes tested (pentadecane, dodecane and hexadecane). No growth was recorded in the short-chain alkanes (pentane, hexane and heptane) tested. With complex hydrocarbons, only crude oil and 4T SHELL engine oil supported growth. No growth was observed in kerosene and PETRONAS gasoline. The isolate could grow in up to 10% and 20% [v/v] of the crude oil and alkanes tested, respectively. Among the long-chain alkanes tested, hexadecane was the most preferred, followed by pentadecane and dodecane. Nitrogen and phosphorous supplements were essential for growth and the best growth was achieved with 3% nitrogen/phosphorous additions. Microscopic observation revealed that the bacterium adhered to the hexadecane and crude oil droplets. GC analysis showed that the bacterium was able to degrade more than 60% of the hydrocarbons in the crude oil in 15 days at 37°C compared to the uninoculated media.
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  • 48
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
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  • 49
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
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  • 50
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    Berlin : Wiley-Blackwell
    Acta Biotechnologica 19 (1999), S. 293-304 
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
    Notes: The mineralization of a non-ionic alcohol ethoxylate (AEO) surfactant was investigated over the concentration range occurring in rinsing water from surfactant production processes. For this, an experimental set-up for respirometric batch experiments was developed. The set-up and the method were validated by experiments with glucose as the single carbon source. It was possible to calculate substrate decay from the time course of exogenously consumed oxygen during respirometric batch experiments. The kinetic coefficients calculated by respirometry showed a lower standard deviation than those calculated from emasured glucose concentrations.The degradation mechanism of AEO was investigated by identification of metabolities, occurring during the mineralization process of AEO, using Flow Injection Mass spectrometry (FI-MS). It was concluded that the degradation of AEO occurs in two main steps. First, the enzymatic hydrolysis of AEO into alcohol and polythylene glycol (PEG) is performed. Second, the mineralization of both substances takes place, while the mineralization of the alcohol is faster than that of the PEG. The mineralization kinetics were investigated in respirometric batch experiments. The model used is based on double MONOD kinetics for the substrates being produced by hydrolysis (μmax1 = 0.047 h-1, Ks1 = 15 mg/l DOC for alcohol; μmax2 = 0.027 h-1, KS2 = 4 mg/l DOC for PEG). The validation of the model by calculating the results obtained from measurements in a continuously operated lab scale CSTR with bacteria recycle was successful.
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  • 51
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    Berlin : Wiley-Blackwell
    Acta Biotechnologica 19 (1999), S. 69-75 
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
    Notes: An increase in the molar growth yield (YX/S = 14.3-20.3 g/mol) on glucose (25 mM) was achieved after the transition of Zymomonas mobilis ATCC 29191 from anaerobic to aerobic steady state growth at dilution rates of D = 0.31-0.40 1/h and under oxygen-unlimited conditions. The transfer of anaerobically or aerobically grown steady state cells into a fresh medium resulted in the higher values of YX/S. A positive correlation was established between biomass and acetaldehyde yield within the range of 5-9 mM acetaldehyde in the medium. An inhibitory effect of the exogenously added acetaldehyde (Ki = 16.7 ± 2.8 mM) on the ATPase activity was observed in vitro, using cell-free extracts of anaerobically grown Z. mobilis. The results obtained provide evidence that the increased values of biomass yield could be explained by the redirection of ATP usage during aerobic growth of Z. mobilis.
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  • 52
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
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  • 53
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    Berlin : Wiley-Blackwell
    Acta Biotechnologica 19 (1999), S. 86-87 
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
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  • 54
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    Berlin : Wiley-Blackwell
    Acta Biotechnologica 19 (1999) 
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
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  • 55
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    Berlin : Wiley-Blackwell
    Acta Biotechnologica 19 (1999), S. 101-109 
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
    Notes: Pleurotus sajor-caju (FR.) SINGER was cultivated on different organic wastes, namely sericulture waste, Populus deltoides MARSH, and Eupatorium adenophorum SPRENG. Paddy straw was taken as the control and all the data were compared with it. The mineral contents of the fruiting bodies of Pleurotus sajor-caju and the substrates on which the mushroom was grown were analyzed. Among the eight minerals determined (calcium, phosphorus, potassium, magnesium, sodium, iron, manganese and zinc), the potassium content was highest followed by phosphorus, magnesium and sodium. Analysis of the mineral contents of the substrates before cultivation had also been carried out. The mineral contents of the fruiting bodies of Pleurotus sajor-caju were found to be different on different substrates. It was also observed that the mineral contents of the fruiting bodies of Pleurotus sajor-caju increase when cultivated on substrates with higher mineral contents. The maximum mineral contents per 100 g of the substrates before cultivation were Ca - 347 mg; P - 151 mg; K - 1,805 mg; Na - 127 mg; Mg - 227 mg; Fe - 53 mg; Mn - 10 mg and zn - 3.1 mg. The mineral contents of the fruiting bodies of Pleurotus sajor-caju per 100 g ranged as follows: Ca - 25.1 mg to 35.3 mg; P - 448 mg to 602 mg; K - 2,146 mg to 2350 mg; Na - 139 mg to 229 mg; Mg - 153 mg to 224 mg; Fe - 9.74 mg to 20.75 mg; Mn - 2.5 mg to 4.0 mg and Zn - 2.2 mg to 3.1 mg.
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  • 56
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    Berlin : Wiley-Blackwell
    Acta Biotechnologica 19 (1999), S. 357-363 
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
    Notes: An alternative microbiological method for the production of malate from fumarate is presented. The yeast Dipodascus magnusii was used for this bioconversion.The optimum cell growth temperature was 28°C and the working volume 120 ml. The highest level of fumarase activity during bioconversion was achieved at a pH of 7.5 and a temperature of 37°C. These conditions were determined as optimal. Using sodium fumarate (1M), the maximum specific productivity of malic acid obtained was 1.72 g/(gDCW × h) for intact cells. In the case of ammonium fumarate, it was 2.25 g/(gDCW × h).
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  • 57
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    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
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  • 58
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
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  • 59
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
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  • 60
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
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  • 61
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    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 7 (1990) 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
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  • 62
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    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 7 (1990), S. 16-31 
    ISSN: 0887-3585
    Keywords: BPTI ; dithiothreitol ; DTT-sensitive mutants ; protein folding ; random mutagenesis ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A genetic screening procedure has been developed to identify mutant forms of bovine pancreatic trypsin inhibitor (BPTI) that can fold to an active conformation but are inactivated more rapidly than the wild type protein. Small cultures of Escherichia coli containing plasmids with mutagenized BPTI genes were grown in microtiter plates, lysed, and treated with dithiothreitol (DTT). Under these conditions, unfolding and inactivation of wild-type protein has a half-time of about 10 hours. Variants of BPTI that are inactivated within 1 hour were identified by adding trypsin and a chromogenic substrate. Approximately 11,000 mutagenized clones were screened in this way and 75 clones that produce proteins that can fold but are inactivated by DTT were isolated. The genes coding for 68 “DTT-sensitive” mutant proteins were sequenced, and 25 different single amino acid substitutions at 15 of the 58 residues of the protein were identified. Most of the altered residues are largely buried in the core of the naive wild-type structure and are highly conserved among proteins homologous to BPTI. These results indicate that a large fraction of the sequence of the protein contributes to the kinetic stability of the active conformation, but it also appears that substitutions can be tolerated a most sites without completely preventing folding Because this genetics, further studies of the isolated mutants are expected to provide information about the roles of the altered residues in folding and unfolding.
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  • 63
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    Proteins: Structure, Function, and Genetics 7 (1990) 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
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  • 64
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    Proteins: Structure, Function, and Genetics 7 (1990), S. 74-92 
    ISSN: 0887-3585
    Keywords: thermostability ; bacterial lactate dehydrogenase ; allosteric regulations ; crystallography ; molecular replacement ; coenzyme binding ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Structures have been determined of Bacillus stearothermophilus “apo” and holo lactate dehydrogenase. The holo-enzyme had been co-crystallized with the activator fructose 1,6-biosphosphate. The “apo” lactate dehydrogenase structure was solved by use of the known apo-M4 dogfish lactate dehydrogenase molecule as a starting model. Phases were refined and extended from 4 Å resolution by means of the noncrystallographic molecular 222 symmetry. The R-factor was reduced to 28.7%, using 2.8 Å resolution data, in a restrained least-squares refnement in which the molecula rsymmetry was imposed as a constraint. A low occupancy of coenzyme was found in each of the four subunits of the “apo” enzyme.Further refinement proceeded with the isomorphous holo-enzyume from Bacillus Stearothermophilus. After removing the noncrystallographic constraints, the R-factor dropped from 30.3% to a final value of 26.0% with a 0.019 Å and 1.7° r.m.s. deviation from idealized bond length and angles, respectively.Two sulfate ions per subunit were included in the final model of the “apo” -from-one at the substrate binding site and one close to the molecular P -axis near the location of the fructose 1,6-bisphosphate activator. The final model of the holo-enzyme incorporated two sulfate ions per subunit, one at the substrate binding site and another close to the R-axis. One nicotinamide adenine dinucleotide coenzyme molecule per subunit and two fructose 1,6-bisphosphate molecules per tetramer were also included. The phosphate positions of fructose 1,6-bisphosphate are close to the sulfate ion near the P-axis in the “apo” model.This structure represents the first reported refined model of an allosteric activated lactate dehydrogenase. The structure of the activated holo-enzyme showed far greater similarity to the ternary complex of dogfish M4 lactate dehydrogenase with incotinamide adenine dinucleotide and oxamate than to apo-M4 dogfish lactate dehydrogenase. The conformations of nicotinamide adenine dinucleotide and fructose, 1,6-bisphosphate were also analyzed.
    Additional Material: 15 Ill.
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  • 65
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    Proteins: Structure, Function, and Genetics 7 (1990), S. 185-197 
    ISSN: 0887-3585
    Keywords: restriction enzyme ; DNA-protein interactions ; DNA recognition ; enzyme-substrate interaction ; active site ; site-directed mutagenesis ; protein structure-function ; DNA double-strand breaks ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The EcoRI restriction endonuclease is one of the most widely used tools for recombinant DNA manipulations. Because the EcoRI enzyme has been extremely well characterized biochemically and its structure is known at 3 Å resolution as an enzyme-DNA complex, EcoRI also serves as an important model of DNA-protein interactions. To facilitate a genetic analysis of the EcoRI enzyme, we devised an in vivo DNA scission assay based on our finding that DNA double-strand breaks induce the Escherichia coli SOS response and thereby increase β-galactosidase expression from SOS::lacZ gene fusions. By site-directed mutagenesis, 50 of 60 possible point mutations were generated at three amino acids (E144, R145, and R200) implicated in substrate recognition by the crystal structure. Although several of these mutant enzymes retain partial endonuclease activity, none are altered in substrate specificity in vivo or in vitro. These findings argue that, in addition to the hydrogen bond interactions revealed by the crystal structure, the EcoRI enzyme must make additional contacts to recognize its substrate.
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  • 66
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    Proteins: Structure, Function, and Genetics 7 (1990), S. 234-248 
    ISSN: 0887-3585
    Keywords: computer modelling ; Ca2+-binding proteins ; hydrophobic binding interactions ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Crystals of troponin are stabilized by an intermolecular interaction that involves the packing of helix A from the N-terminal domain of one molecule onto the exposed hydrophobic cleft of the C-terminal domain of a symmetry related molecules. Analysis of this molecular recognition interaction in troponin C suggests a possible mode for the binding of amphiphilic helical molecules to troponin C and to calmodulin. From the template provided by this troponin C packing, it has been possible to build a model of the contact region of mastoporan as it might be bound to the two Ca2+ binding proteins. A possible binding mode of melittin to calmodulin is also proposed. Although some of the characteristics of binding are similar for the two amphiphilic peptides, the increased length of melittin requires a significant bend in the calmodulin central helix similar to that suggested recently for the myosin light chain kinase calmodulin binding peptide (Persechini and Kretsinger: Journal of Cardiovascular Pharmacology 12:501-512, 1988). Not only are the hydrophobic interactions important in this model, but there are several favorable electrostatic interactions that are predicted as a result of the molecular modeling. The regions of troponin-C and calmodulin to which amphiphilic helices bind are similar to the regions to which the neuroleptic drugs such as trifluoperazine have been predicted to bind (Strynadka and James: Proteins 3:1-17, 1988).
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  • 67
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    Proteins: Structure, Function, and Genetics 7 (1990), S. 249-256 
    ISSN: 0887-3585
    Keywords: β-barrels ; β-strand ; scaffold design ; molecular modeling ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The 8-old parallel α/β-barrel topology is encountered in proteins that display an impressive variety of functions, suggesting that this topology may be a rather nonspecific and stable folding motif. Consequently, this motif can be considered as an interesting framework to design novel proteins. It has been shown that the shape of the β-sheet portion of the barrel can be approximated by a hyperboloid. This geometric object may therefore be used as a scaffold to construct an idealized eight-standard β-barrel. To facilitate the de novo design of such structures, a collection of modelling tools has been developed allowing secondary structure elements to be mapped onto the scaffold surface and rotation and translation operations to be performed about user defined axes while evaluating their contribution to the conformational energy of the system. These tools have been applied in a systematic study assessing the φ, ψ requirements to design symmetric eight standard β barrels with optimal hydrogen bonding between adjacent β-strands. It is observed that: (a) the β-sheet structure can be closed without introducing irregular stagger between β-strands and (b) the region of φ, ψ dihedral angle space compatible with the formation of regular symmetric eight standard β-barrels coincides with the φ, ψ region corresponding to average β-strands in known protein structures, suggesting that barrel closure does not impose gross constraints on β-strand geometry.
    Additional Material: 3 Ill.
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  • 68
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    Proteins: Structure, Function, and Genetics 7 (1990), S. 280-290 
    ISSN: 0887-3585
    Keywords: proteases ; protein turnover ; post-translational processing ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A system has been developed or the expression in E. coli of 12 of the 14 expressed mouse submandibular gland kallikreins as cassettes subcloned directly from cDNA. Using the epidermal growth factor binding protein (mGK-9) and the γ-subunit of nerve growth factor (nGK)-3, as test cases, mature processed forms, obtained as functionally active proteins, as well as various precursor forms, were isolated. The expression system described allows rapid isolation of kallikrein protein from corresponding cDNA with yields of approximately 1.0 mg of purified protein from 10 g of initial cell paste. This expression system will facilitate structure/function studies of the mouse glandular kallikrein gene family and help elucidate the regions of the mature proteins responsible for the diverse catalytic behavior and growth factors interactions observed in this family of proteins.
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  • 69
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    Proteins: Structure, Function, and Genetics 8 (1990), S. 203-212 
    ISSN: 0887-3585
    Keywords: hydrogen bonding diagram ; motifs ; helical wheel ; helical net ; protein structure ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A program is described which generates hydrogen bonding diagrams of protein structures and optionally helical wheels and helical nets. The program can also be used simply to calculate the connectivities of β-strands and to automatically extract simple structural motifs such as hairpins or Greek keys. The program greatly reduces the effort required to produce these diagrams and offers considerable flexibility in the information which can be represented. The usefulness of the program is illustrated by several examples including comparing homologous families, correlating protein structure with attributes of individual residues, and extracting all examples of the ψ-loop motif from the Brookhaven Data Bank.
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  • 70
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    Proteins: Structure, Function, and Genetics 8 (1990), S. 251-257 
    ISSN: 0887-3585
    Keywords: peroxidase ; active site ; structure conservation ; hydrophobic cluster analysis ; sequence comparison ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A number of peroxidase amino acid sequences show limited homology to short regions comprising the known active site cleft of yeast cytochrome c peroxidase. Otherwise no clear homology is visible in linear alignments between this enzyme and other peroxidases. We have subjected eight peroxidase sequences to hydrophobic cluster analysis. Our results suggest that these peroxidases are evolutionary related and that they share many folding characteristics.
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  • 71
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    Proteins: Structure, Function, and Genetics 7 (1990), S. 257-264 
    ISSN: 0887-3585
    Keywords: protein families ; structure prediction ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Hydrophobic side chains often are buried in the interior of a protein, and evolutionarily related proteins usually maintain the hydrophobic character of buried position. In this paper we shown that a pattern of hydrophobicity values derived from a set of related protein sequences is well correlated with the linear pattern of side-chain solvent accessibility values, calculated from a known protein structure representative of the sequences. In several cases, information from aligned sequences can be used to select the correct tertiary fold from a large database of protein structures.
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  • 72
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    Proteins: Structure, Function, and Genetics 7 (1990), S. 291-295 
    ISSN: 0887-3585
    Keywords: full screen editor ; consensus calculation ; secondary structure ; automatic alignment ; alignment merging ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A dedicated sequence editor ALMA, was developed for aligning many sequences of proteins or RNA molecules or longer DNA fragments. Like previously published editors, ALMA is menu directed, screen oriented, and offers similarity and consensus display. ALMA has the additional features of collective movement of sequences, acceptance of input from many sources including structure files and databases, secondary structure display, and easy merging of alignments. In order to maintain sequence integrity and save disk space, gaps and sequences are stored separately. Automatic recovery of a session is possible. Finally, The program allows interaction between manual and automatic alignment.
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  • 73
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    Proteins: Structure, Function, and Genetics 7 (1990), S. 317-334 
    ISSN: 0887-3585
    Keywords: protein structure ; computer modeling ; structure prediction ; sequence homology ; structure homology ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Comparative modeling methods are described that can be used to construct a three-dimensional model structure of a new protein from knowledge of its sequence and of the experimental structure and sequences of other members of its homology family. The methods are illustrated with the mammalian serine protease family, for which seven experimental structures have been reported in the literature, and the sequence for over 35 different protein members of the family are available. The strategy for modeling these proteins is presented, and criteria are developed for determining and assigning the reliability of the modeled structure. Criteria are described that are specially designed to help detect cases in which it is likely that the local structure diverges significantly from the usual conformation of the family.
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  • 74
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    Proteins: Structure, Function, and Genetics 7 (1990), S. 366-377 
    ISSN: 0887-3585
    Keywords: computer modeling ; protein ; structure ; α-carbons ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A procedure for the construction of complete protein structures from only αcarbon coordinates is described. This involves building the backbone by sequential addition of Pro, Gly, or Ala residues. This main chain structure is then refined using molecular dynamics. Side chains are constructed by sequential addition of atoms with intermediate molecular dynamics refinement. For α lytic protease (a structure that is mostly β sheet) a backbone root mean square deviation (RMSD) of 0.19 Å and an overall RMSD of 1.24 Å from the crystallographic coordinates are attained. For troponin C (67% β-helix), where the coordinates are available only for the α-carbons, a backbone RMSD of 0.41 Å and an overall RMSD of 1.68 Å are attained (fits kindly provided by Dr. Michael James and Natalie Strynadka). For flavodoxin a backbone RMSD of 0.49 Å and an overall RMSD of 1.64 Å were attained.
    Additional Material: 1 Ill.
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  • 75
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    Proteins: Structure, Function, and Genetics 7 (1990), S. 378-402 
    ISSN: 0887-3585
    Keywords: conformational distance ; conformational comparison ; generalized bond matrix representation ; structure space ; evolution ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We address herein the problem of delineating the relationships between the known protein structures. In order to study this problem, methods have been developed to represent arbitrarily sized fragments of biopolymer backbone, and to compare distributions of such fragments. These methods are applied to a classification of 123 structures representing the entire set of known x-ray structures. The resulting data are analyzed (on the four-Cα length scale) to determine both the large-scale organization of the set of known structures (i.e., the relationships between large groups of structures, each comprised of proteins that are structurally related) and its local structure (i.e., the quantitative degree of similarity between any two specific structures). It is shown that the set of structures from a continuum of structural types, ranging from allhelical to all-sheet/barrel proteins. It is further demonstrated that the density of protein structures is not uniform across this continuum, but rather that structures cluster in certain regions, separated by regions of lower population. The properties of the various regions of the structural space are determined. The existence is demonstrated of strong quantitative correlations between the contents of different types of four-Cα fragments within protein structures, which imply significant constraints on the types of architecture that can occur in proteins. Analysis of the distribution of structures demonstrates some hitherto unsuspected similarities and suggests that, in some circumstances, neither structural similarity no sequence homology may be necessary conditions for evolutionary relationship between proteins. It is also suggested that these unsuspected similarities may imply similar folding mechanisms for structures of apparently different global architecture. Cases are also noted in which apparently similar structures may fold by different mechanisms. The connection between structure and dynamic properties is discussed, and a possible role of dynamics in the evolution of protein structures is suggested. The sensitivity of the methods presented herein to anomalies of structure refinement is demonstrated. It is suggested that present results provide a frame-work for analyzing experimental results on structural similarity obtained using vibrational circular dichroism spectra, which are sensitive to local backbone structure.
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  • 76
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    Proteins: Structure, Function, and Genetics 8 (1990), S. 173-178 
    ISSN: 0887-3585
    Keywords: mitochondria ; amino acid composition ; hydrophobicity ; composition space ; membrane protein ; transmembrane region ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A compact mitochondrial gene contains all essential information about the synthesis of mitochondrial proteins which play their roles in a small compartment of the mitochondrium. Almost no noncoding regions have been found through the gene, but a necessary set of tRNAs for the 20 amino acids is provided for biosynthesis, some of them coding different amino acids from those in a usual cell. Since the gene is so compact that the produced proteins would have some characteristic aspects for the mitrochondrium, amino acid compositions of mitochondrial proteins (mt-proteins) were examined in the 20-dimensional composition space. The results show that compositions of proteins translated from the mitochondrial genes have a distinct character having more hydrophobic content than others, which is illustrated by a clustered distribution in the multidimensional composition space. The cluster is located at the tail edge of the global distribution pattern of a Gaussian shape for other various kinds of proteins in the space. The mt-proteins are rich in hydrophobic amino acids as is a membrane protein, but are different from other membrane proteins in a lesser content of Val. A good correlation found between the base and amino acid compositions for the mitochondria was examined in comparison to those of organisms such as thermophilic bacterium having an extreme G-C-rich base composition.
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  • 77
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    Proteins: Structure, Function, and Genetics 8 (1990), S. 213-225 
    ISSN: 0887-3585
    Keywords: molecular modeling ; energy calculations ; δ-hemolysin ; melittin ; crystal packing ; raft ; bilayer ; membrane insertion ; channel formation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Molecular modeling and energy calculations have been used to study how δ-hemolysin and melittin helices may aggregate on membrane surfaces and insert through membranes to form channels. In these models adjacent antiparallel amphipathic helices form planar “raft” structures, in which one surface is hydrophobic and the other hydrophilic. Models of δ-hemolysin crystal structure were developed using these “rafts.” These models are based on the unit cell constants and the crystal symmetry obtained from the preliminary crystal data. Energy calculations favor channel models of δ-hemolysin with six or eight monomers per channel.
    Additional Material: 7 Ill.
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  • 78
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    Proteins: Structure, Function, and Genetics 8 (1990), S. 280-286 
    ISSN: 0887-3585
    Keywords: circular dichroism ; secondary structure ; insulin ; insulin analogs ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Vacuum UV circular dichroism spectra measured down to 178 nm for hexameric 2-zinc human insulin, zinc-free human insulin, and the two engineered and biologically active monomeric mutants, [B/S9D] and [BS9D, T27E] human insulin, show significant differences. The secondary structure analysis of the 2-zinc human insulin (T6) in neutral solution was determined: 57% helix, 1% β-strand, 18% turn, and 24% random coil. This is very close to the corresponding crystal structure showing that the solution and solid structures are similar. The secondary structure of the monomer shows a 10-15% increase in antiparallel β-structure and a corresponding reduction in random coil structure. These structural changes are consistent with an independent analysis of the corresponding difference spectra. The advantage of secondary structure analyses of difference spectra is that the contribution of odd spectral features stemming mainly from side chain chromophores is minimized and the sensitivity of the analyses improved. Analysis of the CD spectra of T6 2-zinc, zinc-free human insulin and monomeric mutant insulin by singular value decomposition indicates that the secondary structure changes following the dissociation of hexamers into dimers and monomers are two-state processes.
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  • 79
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    Proteins: Structure, Function, and Genetics 8 (1990), S. 334-340 
    ISSN: 0887-3585
    Keywords: protein structure ; structural comparison ; α-β barrels ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: By exhaustive structural comparisons, we have found that about one-third of the α-helix-turn-β-strand polypeptides in α-β barrel domains share a common structural motif. The chief characteristics of this motif are that first, the geometry of the turn between the α-helix and the β-strand is somewhat constrained, and second, the β-strand contains a hydrophobic patch that fits into a hydrophobic pocket on the α-helix. The geometry of the turn does not seem to be a major determinant of the α-β unit, because the turns vary in length from four to six residues. However, the motif does not occur when there are few constraints on the geometry of the turn-for instance, when the turns between the α-helix and the β-strands are very long. It also occurs much less frequently in flat-sheet α-β proteins, where the topology is much less regular and the amount of twist on the sheet varies considerably more than in the barrel proteins. The motif may be one of the basic building blocks from which α-β barrels are constructed.
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  • 80
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    Proteins: Structure, Function, and Genetics 8 (1990), S. 341-351 
    ISSN: 0887-3585
    Keywords: conserved sequence ; diagnostic peptide ; superfamily classificaiton ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: From protein sequence comparison data found in the literature, a library was organized using peptide fragment sequences which are common to related proteins. Each of the fragments was then examined for its occurrence in all the protein superfamilies defined by the NBRF-PIR data base. We have selected those fragment peptides that appear exclusively in one or a few superfamilies, and thus made a library of fragment peptides that characterize specific superfamilies. Such characteristic peptides are, in general, five to seven residues long and contain unusually high proportions of glycine and cysteine. This collection is a useful resource for the classification and functional prediction of protein molecules.
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  • 81
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    Proteins: Structure, Function, and Genetics 8 (1990), S. 352-364 
    ISSN: 0887-3585
    Keywords: crystallography ; refinement ; structure comparison ; molecular replacement ; precision ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The structure of a small rubredoxin from the bacterium Desulfovibrio desulfuricans has been determined and refined at 1.5 Å resolution. The hairpin loop containing seven residues in other rubredoxins is missing in this 45 residue molecule, and once that fact was determined by amino acid sequencing studies, refinement progressed smoothly to an R value of 0.093 for all reflections from 5 to 1.5 Å resolution. Nearly all of the water molecules in the well-ordered triclinic unit cell have been added to the crystallographic model. As in the other refined rubredoxin models, the Fe-S4 complex is slightly distorted from ideal tetrahedral coordination.
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  • 82
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    Proteins: Structure, Function, and Genetics 7 (1990), S. 1-15 
    ISSN: 0887-3585
    Keywords: α-fibrous proteins ; 4-α-helix bundle ; membrane-spanning proteins ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Additional Material: 5 Ill.
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    Proteins: Structure, Function, and Genetics 7 (1990), S. 52-61 
    ISSN: 0887-3585
    Keywords: molecular dynamics ; protein simulations ; dihydrofolate reductase ; trimethoprim ; drug binding ; solvation ; binding free energies ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Structural and thermodynamic interactions for the binding of trimethoprim and related congeners to the binary complex of diphydrofolate reductase (from chicken) and NADPH are explored using free energy simulation methods. Good agreement between structures from experimental X-ray refinement and molecular dynamics simulations is found for the complexes. Agreement with thermodyanmic measurements is found as well. Our thermodynamic calculations suggest that entropic contributions and desolvation thermodynamics can play a crucial role in overall bindings, and that extreme care must be taken in the use of simple model building to rationalize or predict protein-drug binding.
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  • 84
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    Proteins: Structure, Function, and Genetics 7 (1990), S. 172-184 
    ISSN: 0887-3585
    Keywords: aspartic proteases ; retroviral proteases ; sequence homology ; related structures ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The model of human immuno-deficiency virus (HIV-1) protease which was based on the crystal structure of Rous sarcoma virus (RSV) protease has been compared to the recently determined crystal structure of chemically synthesized HIV-1 protease. The overall difference between the model and crystal structure was 1.4 Å root mean square (rms) deviation for 86 superimposed Cα atoms. The position of the flexible flap differs in the model and six residues at the amino terminus were incorrectly placed. With these exceptions, all atoms of the model and crystal structure agree to 2.11 Å runs deviation. The conformation of some surface bends in the model agrees less well with the crystal structure. Identical amino acids in RSV and HIV proteases were modeled more reliably than different types of amino acids. The amino acids which form the substrate binding site were modeled most accurately to 1.2 Å rms deviation for all atoms compared to the crystal structure. This suggests that functionally significant regions of related proteins can be modeled with high accuracy. The model gave correct predictions for residues making interactions with the substrate, and thereof could be used to design inhibitors, The model based on the RSV protease structure is more similar to the experimental structure than are previous models based on the structures of non-viral aspartic proteases.
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  • 85
    ISSN: 0887-3585
    Keywords: phosphorylation ; tyrosine ; cis-peptide ; exocytosis ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Seven proteins each contain 8 to 52 tandem repeats of a unique class of oligopeptide. The consensus peptide for each is rhodopsin Tyr Pro Pro Gln Glysynapto-physin Tyr Gly Pro Gln Glysynexin Tyr Pro Pro Pro Pro Glygliadin Tyr Pro Pro Pro Gln ProRNA polymerase II Tyr Ser Pro Thr Ser Pro Serhordein Phe Pro Gln Gln Pro Gln Gln Progluten Tyr Pro Thr Ser Pro Gln Gn Gly TyrAlthough there is obvious variations of sequence and of length, the penta-to nonapeptides share an initial Tyr(or Phe) and have high Pro contents and abundant Gly, Gln, and Ser. We have evaluated helical models that both recognize the uniqueness of these sequence repeats and accommodate variations on the basic theme.We have developed a group of related heical model for these proteins with about three oligopeptide repeats per turn of 10-20 Å. These models share several common features: Most of the φ dihedral angels are -54°, to accommodate Pro at all positions expect the first (Tyr). Except for the β-turns, most ψ dihedral angles are near +140° as found in polyproline. Each oligopeptide has at least one β-turn; several have two. Some contains a cis-Tyr, Pro peptide bond; a few have a cis-bond plus one β-turn. Tyr side chains vary from totally exposed to buried within the helices and could mode to accommodate either external hydrophobic interactions or phosphorylation. The several related structures seem to be readily interconverted without major change in the overall helical parameters, and therein may lie the key to their functions.
    Additional Material: 10 Ill.
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  • 86
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    Proteins: Structure, Function, and Genetics 7 (1990), S. 156-171 
    ISSN: 0887-3585
    Keywords: β-lactamase ; penicillinase ; penicillin-binding protein ; penicillin antibiotics ; X-ray diffraction ; protein structure prediction ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Two crystal (A and B) of the 29,500 Da Class A β-lactamase (penicillinase) from Bacillus licheniformis 749/C have been examined crystallographically. The structure of B-form crystals has been solved to 2 Å resolution, the starting model for which was a 3.5 Å structure obtained from A-form crystals. The β-lactamase has an α + β structure with 11 helices and 5 β-strands seen also in a peinicilin target DD-peptidase of Streptomyces R61.1 Atomic parameters of the two molecules in the asymmetric unit were refined by simulated annealing at 2.0 Å resolution. The R factor is 0.208 for the 27,330 data greater than 3 (F), with water molecules excluded from the model. The catalytic Ser-70 is at the N-terminus of a helix and is within hydrogen bonding distance of conversed Lys-73. Also interacting with the Lys-73 are Asn-132 and the conserved Glu-166, which is on a potentially flexible helix-containing loop. The structure suggests the binding of β-lactam substrates is facilitated by interactions with Lys-234, Tyhr-235, and Ala-237 in a conserved β-strand peptide, which is antiparallel to the β-lactam's acylamido linkage; an exposed cavity near Asn-170 exits for acylamido Substituent. The reactive double bond of clavulanate-type inhibitors may interact with Arg-244 on the fourth β-strand. A very similar binding site architecture is seen in the DD-peptidase.
    Additional Material: 8 Ill.
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  • 87
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    Proteins: Structure, Function, and Genetics 7 (1990), S. 198-204 
    ISSN: 0887-3585
    Keywords: protein stability ; protein design ; strain ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: An attempt has been made to identify residues in T4 phage lyoszyme that may have strained conformations and, by appropriate site-directed replacements, to reduce this strain and thus increase the thermostability of the protein. Valine 131, within α-helix 126-134, was identified as a potential candidate. Its side-chain rotational as a potential candidate. Its side-chain rotation angle, χ1, differs by approximately 18° from the low-energy trans configuration. In addition, it is largely solvent exposed, yet is held in a rigid conformation. The mutant protein with Val 131 replaced by alanine temperature 0.9°C higher than that of wildtype lyoszyme at pH 2.8. As a control, The mutant Val 131 → Thr was also constructed and its melting temperature was found to be marginally lower than wild type. Higher-resolution crystal structure determination of the mutant lysozymes show that their structure are virtually identical with that of wild-type lyoszyme, except for the Val → Ala or Val → Thr replacement. Analysis of the different structures suggests that the design of the Val→Ala substitution was, in principle, successful, although the apparent gain in stability caused by reduction in strain is modest and is somewhat offset by the loss of hydrophobic interactions and by entrophic effects. The results also help to provide a structural retionalization that alanine has a higher helix propensity than valine or theronine.
    Additional Material: 2 Ill.
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  • 88
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    Proteins: Structure, Function, and Genetics 7 (1990), S. 265-279 
    ISSN: 0887-3585
    Keywords: potential of means force ; motions of helices ; correlated fluctuations ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The concept of secondary structure motions is examined in a molecular dynamics simulation of the protein myohemerythrin. We extracted from the simulation a corresponding trajectory of helices and demonstrated that the fluctuations of the protein are dominated by a rigid shift of these secondary structure elements. The relative motions of the helices are regular, with no clear periodicity. They are bounded by ∼2 for the center of mass motions and by 20° for the relative orientations. The potential of mean force for the interactions of the helices was calculated, and the correlations between the different extended motions were investigated. It shown that the one-dimensional mean force potentials are close to quadratic for most of the helices coordinates. The anharmonicity is reflected by changes in the direction of the normal modes as a function of the energy and by the existence of multiple free energy minima for the helices packing. The multiple conformations are associated with a single type of secondary structure coordinate: the angle that describes the relative orientation of the helices in a plane perpendicular to the line connecting their center of mass.
    Additional Material: 12 Ill.
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  • 89
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    Proteins: Structure, Function, and Genetics 7 (1990), S. 299-305 
    ISSN: 0887-3585
    Keywords: protein stability ; guanidine hydrochloride denaturation ; conformational changes ; polypeptide backbone ; alanine insertion ; glycine insertion ; circular dichroism spectra ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Single alanine and glycine insertions were introduced at 20 randomly selected positions in staphylococcal nuclease. The resulting changes in catalytic activity and in stability to guanidine hydrochloride denaturation indicate that the native state structure is frequently able to accommodate the extra residue without great difficulty, even insertions within secondary structural elements such as alpha helices and beta sheets. On average, an inserted residue reduces the free energy of denaturation (ΔGH2O) by an amount roughly comparable to an alanine or glycine substitution for one of the residues flanking the site of insertion. Several positions outside of the enzyme active site were found where insertions, but not substitutions, lead to structural changes that modify catalytic activity and the circular dichroism spectrum. Amino acid insertions represent a virtually unexplored class of genetic mutation that may prove complementary to amino acid substitutions for engineering proteins with altered functional and structural properties.
    Additional Material: 3 Ill.
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  • 90
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    Proteins: Structure, Function, and Genetics 7 (1990), S. 358-365 
    ISSN: 0887-3585
    Keywords: synthetic myoglobins ; X-ray crystallography ; protein engineering ; heme proteins ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Crystal have been grown of myoglobin produced in Escherichia coli from a synthetic gene, and the structure has been solved to 1.9 Å resolution. The space group of the crystals is P6, which is different from previously solved myoglobin crystal forms. The synthetic myoglobin is essentially identical to myoglobin isolated from sperm whale tissue, except for the retention of the initiator methionine at the N-terminus and the substitution of asparagine for aspartic acid at position 122. Superposition of the coordinates of native and synthetic sperm whale myoglobins reveals only minor changes in the positions of main chain atoms and roeientation of some surface side chains. Crystals of variant of the “synthetic” myoglobin have also been grown for structural analysis of the role of key amino acid residues in ligand and specificity.
    Additional Material: 5 Ill.
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  • 91
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    Proteins: Structure, Function, and Genetics 8 (1990), S. i 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
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  • 92
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    Proteins: Structure, Function, and Genetics 8 (1990), S. 14-22 
    ISSN: 0887-3585
    Keywords: computation ; conformational energy ; interactions in proteins ; protein folding ; twisted β-sheets ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The preferred structural pattern of antiparallel β-barrels in proteins, described as the right-handed tilting of the peptide strands with respect to the axis of the barrel, is accounted for in terms of intra- and interchain interaction energies. It is related to the preference of β-sheets for right-handed twisting. Conformational energy computations have been carried out on three eight-stranded antiparallel β-barrels composed of six-residue strands, in which L-Val and Gly alternate, and having a right-handed, a left-handed, or no tilt. After energy minimization, the relative energies of these structures were 0.0, 8.6, and 46.1 kcal/mol, respectively; i.e., the right-tilted β-barrel is favored energetically, in agreement with anti-parallel β-barrels observed in proteins. Tilting of the barrel is favored, relative to the nontilted structure, by both intra- and interstrand interactions, because tilting allows better packing of the bulky side chains. On the other hand, the energy difference between the left- and right-tilted barrels arises essentially from intrachain interactions. This is a consequence of the preference of β-sheets for a right-handed twist. Space limitations inside the barrel are satisfied if there is an alternation of bulky residues and residues with small or no side chain (preferably Gly) in neighboring positions on adjacent strands. Such a pattern is seen frequently in antiparallel β-barrels of globular proteins. The computations indicate that a structure with Val…Gly pairs can be accommodated in a β-barrel with no distortion.
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  • 93
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    Proteins: Structure, Function, and Genetics 8 (1990) 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
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  • 94
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    Proteins: Structure, Function, and Genetics 8 (1990), S. 133-155 
    ISSN: 0887-3585
    Keywords: evolution ; alignment ; globins ; phycocyanin ; helix interfaces ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Globins and phycocyanins are two classes of proteins with different function, different ligands, and no substantial sequence similarity, yet the conformations of their polypeptide chains show very similar folding patterns. Does this arise from a genuine, albeit very distant, evolutionary relationship, or does it represent a common solution of a structural problem? We address this question by a very detailed comparison of the structures of the two protein families. An analysis of the helices and their interactions shows many features common to globins and phycocyanins, including some exceptional features of the globins such as a 3-10 C helix and the unusual “crossed-ridge” packing pattern at the B/E helix interfaces. We conclude that the evidence supports the hypothesis of distant evolutionary relationship between globins and phycocyanins.
    Additional Material: 12 Ill.
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  • 95
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    Proteins: Structure, Function, and Genetics 7 (1990), S. 41-51 
    ISSN: 0887-3585
    Keywords: DNA binding proteins ; maximum likelihood ; CRP ; finite mixtures ; transcription regulation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Statistical methodology for the identification and characterization of protein binding sites in a set of unaligned DNA fragments is presented. Each sequence must contain at least one common site. No alignment of the sites is required. Instead, the uncertainty in the location of the sites is handled by employing the missing information principle to develop an “expectation maximization” (EM) algorithm. This approach allows for the simultaneous identification of the sites and characterization of the binding motifs. The reliability of the algorithm increases with the number of fragments, but the computations increase only linearly. The method is illustrated with an example, using known cyclic adenosine monophophate receptor protein (CRP) binding sites. The final motif is utilized in a search for undiscovered CRP binding sites.
    Additional Material: 3 Ill.
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  • 96
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    Proteins: Structure, Function, and Genetics 7 (1990), S. 99-111 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Additional Material: 7 Ill.
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  • 97
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    Proteins: Structure, Function, and Genetics 7 (1990), S. 205-214 
    ISSN: 0887-3585
    Keywords: protein secondary structures ; circular dichroism ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Additional Material: 8 Ill.
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  • 98
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    Proteins: Structure, Function, and Genetics 7 (1990), S. 227-233 
    ISSN: 0887-3585
    Keywords: rhinovirus receptor ; ICAM-1 ; structure prediction ; immunoglobulin superfamily ; docking receptor to virus ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A model has been built of the amino-terminal domain of the intercellular adhesion molecule-1 (ICAM-1), the receptor for most human rhinovirus serotypes. The model was based on sequence and presumed structural homology to immunoglobulin constant domains. It fits well into the putative receptors attachment site, the canyon, on the human rhinovirus-14 (HRV14) surface in a manner consistent with most of the mutational data for ICMA-1 (Staunton, D. E., Dustin, M. L., Erickson, H. P., Springer, T. A. Cell, in press, 1989) and HRV14 (Colonno, R. J., Condra, J. H., Mizutani, S., Callahan, P. L., Davies, M. E., Murcko, M. A. Proc. Natl. Acad. Sci. U.S.A. 85: 5449-5453, 1988).
    Additional Material: 6 Ill.
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  • 99
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    Proteins: Structure, Function, and Genetics 8 (1990), S. 30-43 
    ISSN: 0887-3585
    Keywords: molecular mechanics ; solvation energy ; trypsin ; energy minimization ; side chains ; protein crystallography ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A “knowledge-based” method of predicting the unknown structure of a protein from a homologous known structure using energetics to determine a sidechain conformation is proposed. The method consists of exchangin the residues in the known structure for the sequence of the unknown protein. Then a conformational search with molecular mechanics energy minimization is done on the exchanged residues. The lowest energy conformer is the one picked to be the predicted structure. In the structure of bovine trypsin, the importance of including a solvation energy term in the search is demonstrated for solvent accessible residues, while molecular mechanics alone is enough to correctly predict the conformation of internal residues. The correctness of the model is assessed by a volume error overlap of the predicted structure compared to the crystal structure. Finally, the structure of rat trypsin is predicted from the crystal structure of bovine trypsin. The sequences of these two proteins are 74% identical and all of the significant changes between them are on external residues. Thus, the inclusion of solvation energy in the conformational search is necessary to accurately predict the structure of the exchanged residues.
    Additional Material: 13 Ill.
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  • 100
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    Proteins: Structure, Function, and Genetics 8 (1990), S. 386-397 
    ISSN: 0887-3585
    Keywords: LGIC superfamily ; proto-binding site ; cys-loop motif ; docking model ; anionic site ; specificity residue ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A generalized model is presented of agonist binding to ligand-gated ion channels (LGICs). Broad similarity in the structure of agonists suggests that the binding sites of LGICs may have evolved from a protobinding site. Aligned sequence data identified as a candidate for such a site a highly conserved 15 residue stretch of primary structure in the N-terminal extracellular region of all known LGIC subunits. We modeled this subregion, termed the cys-loop, as a rigid, amphiphilic β-hairpin and propose that it may form a major determinant of a conserved structural binding cleft.In the model of the binding complex (1) an invariant aspartate residue at position 11 of the cys-loop is the anionic site interacting with the positively charged amine group of agonists, (2) a local dipole within the π-electron system of agonists is favorably oriented in the electrostatic field of the invariant aspartate, (3) the ε ring-proton of a conserved aromatic residue at the turn of the cys-loop interacts orthogonally with the agonist α-electron density at its electronegative center, and (4) selective recognition is partly a result of the type of amino acid residue at position 6 of the cys-loop. Additionally, the formation of a hydrogen bond between the electronegative atom of the π-electron system of agonist and a complementary group in the receptor may be important in the high-affinity binding of agonists.
    Additional Material: 5 Ill.
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