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  • 1995-1999  (1,940)
  • 1999  (60)
  • 1996  (1,880)
  • Biochemistry and Biotechnology  (1,203)
  • Computational Chemistry and Molecular Modeling  (433)
  • Life Sciences (general)  (304)
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  • 1995-1999  (1,940)
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  • 1
    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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  • 2
    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.
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  • 3
    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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  • 4
    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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  • 5
    Electronic Resource
    Electronic Resource
    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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  • 6
    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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  • 7
    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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  • 8
    Electronic Resource
    Electronic Resource
    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.
    Additional Material: 3 Ill.
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  • 9
    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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  • 10
    Electronic Resource
    Electronic Resource
    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
    Type of Medium: Electronic Resource
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  • 11
    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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  • 12
    Electronic Resource
    Electronic Resource
    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.
    Additional Material: 3 Tab.
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  • 13
    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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  • 14
    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.
    Additional Material: 2 Tab.
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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) 
    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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  • 17
    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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  • 18
    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
    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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  • 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. 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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  • 22
    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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  • 23
    Electronic Resource
    Electronic Resource
    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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  • 24
    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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  • 25
    Electronic Resource
    Electronic Resource
    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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  • 26
    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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  • 27
    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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  • 28
    Electronic Resource
    Electronic Resource
    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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  • 29
    Electronic Resource
    Electronic Resource
    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.
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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
    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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  • 31
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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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  • 32
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    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.
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  • 33
    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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  • 34
    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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  • 35
    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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  • 36
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    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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  • 37
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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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  • 38
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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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  • 39
    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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  • 40
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    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.
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  • 41
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    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.
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  • 42
    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.
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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
    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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  • 45
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    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.
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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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    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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  • 48
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    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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  • 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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    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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  • 51
    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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  • 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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    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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  • 54
    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
    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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  • 56
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    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.
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  • 57
    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.
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  • 58
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    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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  • 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
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    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.
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  • 61
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    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. 115-133 
    ISSN: 0887-3585
    Keywords: receptor proteins ; estrogen receptor ; DNA bending ; DNA unwinding ; DNA recognition ; molecular dynamics ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Molecular dynamics simulations have been conducted to investigate the binding of the glucocorticoid receptor (GR) dimer to DNA. For this purpose simulations of the complex formed by a DNA segment and a dimer of GR-DNA binding domains (GR-DBD) have been carried out, employing an available X-ray structure. A second set of simulations was based on this structure as well, except that the DNA segment was altered to the consensus glucocorticoid response element (GRE). Simulations of a single GR-DBD and of the uncomplexed GRE served as controls. For the simulations, each system was encapsulated in an ellipsoid of water. Protein-DNA interactions, dimer interactions, and DNA structural parameters were analyzed for each system and compared. The consensus GRE is found to yield more favorable and symmetric interactions between the GR-DBDs and the GRE, explaining the ability of the GR dimer to recognize this DNA segment. Further analysis focused on deformations of the DNA that are induced by the binding of GR. The deformations observed involve a 35° bend of the DNA, an unwinding, and a displacement of the helical axis. These deformations are consistent with a mechanism for transcriptional regulation that involves a change of nucleosome packing upon GR binding. Significant protein-protein and protein-DNA interactions, both direct and water mediated, develop due to the deformations of the GRE and are indicative of an increased recognition achieved through DNA deformation. The interactions include direct interactions between the GRE and glycine-458 and serine-459, side groups which differentiate GR from other members of the nuclear hormone receptor family.
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  • 62
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    Proteins: Structure, Function, and Genetics 24 (1996), S. 92-114 
    ISSN: 0887-3585
    Keywords: phospholipid membranes ; permeation ; antibiotics ; computer simulations ; tryptophan ; water ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The microscopic details of lipid-protein interactions are examined using molecular dynamics simulations of the gramicidin A channel embedded in a fully hydrated dimyristoyl phosphatidylcholine (DMPC) bilayer. A novel construction protocol was used to assemble the initial configurations of the membrane protein complex for the simulations. Three hundreds systems were constructed with different initial lipid placement and conformations. Seven systems were simulated with molecular dynamics. One system was simulated for a total of 600 psec, four were simulated for 300 psec, and two for 100 psec. Analysis of the resulting trajectories shows that the bulk solvent-membrane interface region is much broader than traditionally pictured in simplified continuum theories: its width is almost 15 Å. In addition, lipid-protein interactions are far more varied, both structurally and energetically, than is usually assumed: the total interaction energy between the gramicidin A and the individual lipids varies from 0 to -50 kcal/mol. The deuterium quadrupolar splittings of the lipid acyl chains calculated from the trajectories are in good agreement with experimental data. The lipid chains in direct contact with the GA are ordered but the effect is not uniform due to the irregular surface of the protein. Energy decompositions shows that the most energetically favorable interactions between lipid and protein involve nearly equal contributions from van der Waals and electrostatic interactions. The tryptophans, located near the bulk-membrane interface, appear to be particularly important in mediating both hydrogen bonding interactions with the lipid glycerol backbone and water and also in forming favorable van der Waals contacts with the hydrocarbon chains. In contrast, the interactions of the leucine residues with the lipids, also located near the interface, are dominated by van der Waals interactions with the hydrocarbon lipid chains.
    Additional Material: 16 Ill.
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  • 63
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    Proteins: Structure, Function, and Genetics 24 (1996) 
    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 24 (1996), S. iii 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
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  • 65
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    Proteins: Structure, Function, and Genetics 24 (1996), S. 141-142 
    ISSN: 0887-3585
    Keywords: cardiotoxin ; hemolysis ; ion channel toxicology ; mushroom ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Volvatoxin A2, an ion channel disturbed cardiotoxic and hemolytic protein from the edible mushroom, Volvarilla volvacea, has been crystallized by the vapor diffusion method using polyethylene glycol 4000 and ammonium sulfate in sodium acetate buffer pH 4.6. The best crystals belong to the monoclinic space group C2 with unit cell dimensions a = 155.25 Å, b = 58.06 Å, c = 116.92 Å, and β = 119.5°. These crystals diffract to at least 2.2 Å and there are four molecules of molecular weight 24 kDa per asymmetric unit with a solvent content of 48%.
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  • 66
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    Proteins: Structure, Function, and Genetics 24 (1996), S. 145-151 
    ISSN: 0887-3585
    Keywords: protein stability ; protein dynamics ; hydrogen exchange ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: All possible protein folding intermediates exist in equilibrium with the native protein at native as well as non-native conditions, with occupation determined by their free energy level. The study of these forms can illuminate the fundamental principles of protein structure and folding. Hydrogen exchange methods can be used to detect and characterize these partially unfolded forms at native conditions and as a function of mild denaturant and temperature. This information illuminates the requirements that govern the ability of kinetic and equilibrium methods to study folding intermediates.
    Additional Material: 4 Ill.
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  • 67
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    Proteins: Structure, Function, and Genetics 24 (1996), S. 152-157 
    ISSN: 0887-3585
    Keywords: antibody X-ray crystallography ; antibody modeling ; protein structure prediction ; structure comparison ; model evaluation ; prediction accuracy ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A model of the BR96 antibody variable regions is compared to two X-ray structures of a BR96-carbohydrate complex, independently determined after the model was built and analyzed. The comparison illustrates the opportunities and limitations of antibody modeling. Encouraging results were obtained for the prediction of single CDR loop conformations and for the outline of the BR96 antigen binding site. The comparison of CDR loop conformations in the two X-ray structures provides a realistic reference frame for the CDR loop predictions. CDR loop prediction accuracy is lower when not only conformational, but also positional criteria are taken into account.
    Additional Material: 3 Ill.
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  • 68
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    Proteins: Structure, Function, and Genetics 24 (1996), S. 165-177 
    ISSN: 0887-3585
    Keywords: sequence data sets ; similarity screening ; redundancy reduction ; signal peptides ; database errors ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: When preparing data sets of amino acid or nucleotide sequences it is necessary to exclude redundant or homologous sequences in order to avoid overestimating the predictive performance of an algorithm. For some time methods for doing this have been available in the area of protein structure prediction. We have developed a similar procedure based on pair-wise alignments for sequences with functional sites. We show how a correlation coefficient between sequence similarity and functional homology can be used to compare the efficiency of different similarity measures and choose a nonarbitrary threshold value for excluding redundant sequences. The impact of the choice of scoring matrix used in the alignments is examined. We demonstrate that the parameter determining the quality of the correlation is the relative entropy of the matrix, rather than the assumed (PAM or identity) substitution model. Results are presented for the case of prediction of cleavage sites in signal peptides. By inspection of the false positives, several errors in the database were found. The procedure presented may be used as a general outline for finding a problem-specific similarity measure and threshold value for analysis of other functional amino acid or nucleotide sequence patterns.
    Additional Material: 6 Ill.
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  • 69
    ISSN: 0887-3585
    Keywords: NMR ; iron-sulfur proteins ; nuclear Overhauser effect ; paramagnetic relaxation ; relaxation matrix analysis ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We have accounted for the effect of paramagnetism on the intensities of NOEs in a 73-residue paramagnetic metalloprotein, the reduced high-potential iron sulfur protein ISO I from Ectothiorhodospira halophila, whose solution structure had been recently solved by us. The paramagnetic effects were dealt with through a suitably modified complete relaxation matrix approach. We have then recalculated the structure through a distance geometry program by minimizing the difference between the sixth roots of the calculated and experimental NOEs.The average RMSD, calculated on residues 4-71, within the structures constituting the two families decreased from 0.67 to 0.46 Å for backbone atoms and from 1.23 to 1.06 Å for all heavy atoms. The structures in the new family are for the most part within the indetermination of the previous, less resolved, family. A few specific differences are detected and related to the presence of non-negligible paramagnetic effects, which are now properly evaluated.
    Additional Material: 5 Ill.
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  • 70
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    Proteins: Structure, Function, and Genetics 24 (1996), S. 195-208 
    ISSN: 0887-3585
    Keywords: protein evolution ; conserved cysteine ; pyridoxal phosphate ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: It was previously suggested that the conserved Cys-191 of aspartate aminotransferases (AATases) is conserved, not because it is essential, but because it is frozen in the sequence, with no neutral corridor to traverse to the similar phenotype of Ala-191 (Gloss et al., Biochemistry 31:32-39, 1992). This hypothesis has now been tested by additional mutations. All possible one-base mutations from Cys were made at position 191. All of these variants display kinetic parameters (kcat and kcat/KM values) that differ from the wild-type enzyme by 30% or more. The non-conserved cysteines that are predominantly Ala in other AATase sequences (Cys-82, Cys-192, and Cys-401) were mutated to Ser to test the corollary that a neutral Cys → Ala corridor does exist for these positions. These Cys → Ser mutations yielded enzymes with wild-type-like kinetic parameters. The pKa values of the internal aldimines of the mutants, Cys-191 → Ser, Phe, Tyr, and Trp are higher than that of wild type by 0.6-0.8 pH units. The stabilities to urea denaturation of the Cys-191 mutants are similar to that of wild type, while those of the non-conserved cysteines show greater variation. Examination of the three-dimensional environment of the five cysteines showed that the van der Waals contacts of Cys-191 are more conserved than are those of the non-conserved cysteines. These data provide further support for the above hypothesis.
    Additional Material: 5 Ill.
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  • 71
    ISSN: 0887-3585
    Keywords: scorpion venom ; neurotoxin ; NMR ; structure-activity relationships ; calcium activated-potassium channel ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The venom of the North African scorpion Androctonus mauretanicus mauretanicus possesses numerous highly active neurotoxins that specifically bind to various ion channels. One of these, P05, has been found to bind specifically to calcium-activated potassium channels and also to compete with apamin, a toxin extracted from bee venom. Besides the highly potent ones, several of these peptides (including that of P01) have been purified and been found to possess only a very weak, although significant, activity in competition with apamin. The amino acid sequence of P01 shows that it is shorter than P05 by two residues. This deletion occurs within an α-helix stretch (residues 5-12). This α-helix has been shown to be involved in the interaction of P05 with its receptor via two arginine residues. These two arginines are absent in the P01 sequence. Furthermore, a proline residue in position 7 of the P01 sequence may act as an α-helix breaker. We have determined the solution structure of P01 by conventional two-dimensional 1H nuclear magnetic resonance and show that 1) the proline residue does not disturb the α-helix running from residues 5 to 12; 2) the two arginines are topologically replaced by two acidic residues, which explains the drop in activity; 3) the residual binding activity may be due to the histidine residue in position 9; and 4) the overall secondary structure is conserved, i.e., an α-helix running from residues 5 to 12, two antiparallel stretches of β-sheet (residues 15-20 and 23-27) connected by a type I′ β-turn, and three disulfide bridges connecting the α-helix to the β-sheet.
    Additional Material: 10 Ill.
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  • 72
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    Proteins: Structure, Function, and Genetics 24 (1996), S. 379-387 
    ISSN: 0887-3585
    Keywords: infrared spectroscopy ; protein structure ; unfolding ; RNase T1 ; RNase A ; histone-like protein HBsu ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Fourier-transform infrared (FTIR) spectroscopy has been used to study the thermally induced exchange characteristics of those backbone amide protons which persist H-D exchange at ambient conditions in ribonuclease A, in wild type ribonuclease T1 and some of its variants, and in the histone-like protein HBsu. The H-D exchange processes were induced by increasing the thermal energy of the protein solutions in two ways: (i) by linearly increasing the temperature, and (ii) by a temperature jump. To trace the H-D exchange in the proteins, various infrared absorption bands known to be sensitive to H-D exchange were used as specific monitors. Characteristic H-D exchange curves were obtained from which the endpoints (TH/D) of H-D exchange could be determined. The H-D exchange curves, the TH/D-values and the phase transition temperatures Tm were used to estimate the structural flexibility and stability of the given proteins. It is suggested that time-resolved FTIR spectroscopy can be used to determine global stability parameters of proteins.
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  • 73
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    Proteins: Structure, Function, and Genetics 24 (1996), S. 394-401 
    ISSN: 0887-3585
    Keywords: cytokines ; homology modeling ; erythropoietin ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A model of the structure of erythropoietin (Epo) is presented based on structural homology to other hemopoietic cytokines. A model of the erythropoietin receptor complex was made based on evidence that this includes a homodimer of the receptor chain with known sequence. Key interactions are noted which explain data from mutation experiments, although at not all residues believed to be important to binding of Epo are at the interface. This is consistent with the hypothesis that the Epo receptor complex includes proteins in addition to the cloned receptor chain that have been cross-linked to Epo (Todokoro et al., Proc. Natl. Acad. Sci. USA 84:4126-4130, 1987; Mayeux et al., J. Biol. Chem. 266:23380-23385, 1991) but not isolated.
    Additional Material: 5 Ill.
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  • 74
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    Proteins: Structure, Function, and Genetics 24 (1996), S. 402-403 
    ISSN: 0887-3585
    Keywords: Tus ; terminus site ; protein-DNA interaction ; replication arrest ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Crystals of the Escherichia coli replication terminator protein (Tus) complexed with its binding site DNA were obtained by a microdialysis method using PEG 4000. They belong to the tetragonal space group P41212 or P43212 with the unit cell parameter: a = 68.1 Å, c = 230.7 Å and contain one protein-DNA complex in an asymmetric unit. The native data set has been collected to 2.7 Å resolution.
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  • 75
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    Proteins: Structure, Function, and Genetics 24 (1996), S. 404-406 
    ISSN: 0887-3585
    Keywords: DAHP synthase ; metalloenzyme ; shikimate pathway ; KDOP synthase ; affinity chromatography ; protein crystallography ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The phenylalanine-regulated isozyme of 3-deoxy-D-arabino-heptulosonate-7-phosphate- synthase (DAHPS) from Escherichia coli, its binary complexes with either substrate, phosphoenolpyruvate (PEP), or feedback inhibitor, Phe, and its ternary complexes with either PEP or Phe plus metal cofactor (either Mn2+, Cd2+, or Pb2+) were crystallized from polyethylglycol (PEG) solutions. All crystals of the DAHPS without Phe belong to space group C2, with cell parameters a = 213.5 Å, b = 54.3 Å, c = 149.0 Å, β = 116.6°. All crystals of the enzyme with Phe also belong to space group C2, but with cell parameters a = 297.1 Å, b = 91.4 Å, c = 256.5 Å, and β = 148.2°.
    Additional Material: 1 Tab.
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  • 76
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    Proteins: Structure, Function, and Genetics 24 (1996) 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
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  • 77
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    Proteins: Structure, Function, and Genetics 24 (1996), S. 1-1 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
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  • 78
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
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  • 79
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    Proteins: Structure, Function, and Genetics 24 (1996), S. 410-410 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
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  • 80
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    Proteins: Structure, Function, and Genetics 24 (1996), S. 427-432 
    ISSN: 0887-3585
    Keywords: GCN4 ; protein folding ; folding kinetics ; helix formation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: To determine when secondary structure forms as two chains coalesce to form an α-helical dimer, the folding rates of variants of the coiled coil region of GCN4 were compared. Residues at non-perturbing positions along the exterior length of the helices were substituted one at a time with alanine and glycine to vary helix propensity and therefore dimer stability. For all variants, the bimolecular folding rate remains largely unchanged; the unfolding rate changes to largely account for the change in stability. Thus, contrary to most folding models, widespread helix is not yet formed at the rate-limiting step in the folding pathway. The high-energy transition state is a collapsed form that contains little if any secondary structure, as suggested for the globular protein cytochrome c (Sosnick et al., Proteins 24:413-426, 1996).
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  • 81
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    Proteins: Structure, Function, and Genetics 24 (1996), S. 433-438 
    ISSN: 0887-3585
    Keywords: structure refinement ; buried water ; free energy calculation ; molecular dynamics simulation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Water molecules inside cavities in proteins constitute integral parts of the structure. We have sought a quantitative measure of the hydrophilicity of the cavities by calculating energies and free energies of introducing a water molecule into these cavities. A threshold value of the water-protein interaction energy at -12 kcal/mol was found to be able to distinguish hydrated from empty cavities. It follows that buried waters have entropy comparable to that of liquid water or ice. A simple consistent picture of the energetics of the buried waters provided by this study enabled us to address the reliability of buried waters assigned in experiments.
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  • 82
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    Proteins: Structure, Function, and Genetics 24 (1996), S. 413-426 
    ISSN: 0887-3585
    Keywords: protein folding ; folding kinetics ; folding barriers ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Experiments with cytochrome c (cyt c) show that an initial folding event, molecular collapse, is not an energetically downhill continuum as commonly presumed but represents a large-scale, time-consuming, cooperative barrier-crossing process. In the absence of later misfold-reorganization barriers, the early collapse barrier limits cyt c folding to a time scale of milliseconds. The collapse process itself appears to be limited by an uphill search for some coarsely determined transition state structure that can nucleate subsequent energetically downhill folding events. An earlier “burst phase” event at strongly native conditions appears to be a non-specific response of the unfolded chain to reduced denaturant concentration. The molecular collapse process may or may not require the co-formation of the amino- and carboxyl-terminal helices, which are present in an initial metastable intermediate directly following the rate-limiting collapse. After the collapse-nucleation event, folding can proceed rapidly in an apparent two-state manner, probably by way of a predetermined sequence of metastable intermediates that leads to the native protein structure (Bai et al., Science 269:192-197, 1995).
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  • 83
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    Proteins: Structure, Function, and Genetics 24 (1996), S. i 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
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  • 84
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    Proteins: Structure, Function, and Genetics 25 (1996), S. 12-27 
    ISSN: 0887-3585
    Keywords: protein-membrane interaction ; free energy perturbation ; lipid desolvation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The desolvation of lipid molecules in a complex of the enzyme human synovial phospholipase A2 with a lipid membrane is investigated as a mechanism that enhances the overall activity of the enzyme. For this purpose the interaction of the enzyme phospholipase A2 with a dilauryl-phosphatityl-ethanolamin (DLPE) membrane monolayer surface has been studied by means of molecular dynamics simulations. Two enzyme-membrane complexes, a loose and a tight complex, are considered. For comparison, simulations are also carried out for the enzyme in aqueous solution. The conformation, dynamics, and energetics of the three systems are compared, and the interactions between the protein and lipid molecules are analyzed. Free energies of solvation are calculated for the lipid molecules in the enzyme-membrane interface. Along with the calculated dielectric susceptibility at this interface, the results show the desolvation of lipids in a tightly bound, but not in a loosely bound protein-membrane complex. The desolvated lipids are found to interact mainly with hydrophobic protein residues, Including Leu-2, Val-3, Ala-18, Leu-19, Phe-24, Val-31, and Phe-70. The results also explain why the turnover rate of phospholipase A2 complexed to a membrane is enhanced after a critical amount of negatively charged reaction product is accumulated. © 1996 Wiley-Liss, Inc.
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  • 85
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    Proteins: Structure, Function, and Genetics 25 (1996), S. 38-47 
    ISSN: 0887-3585
    Keywords: protein structure prediction ; Bayesian statistics ; amino acid substitution ; information theory ; solvent accessibility ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We introduce a novel Bayesian probabilistic method for predicting the solvent accessibilities of amino acid residues in globular proteins. Using single sequence data, this method achieves prediction accuracies higher than previously published methods. Substantially improved predictions - comparable to the highest accuracies reported in the literature to date - are obtained by representing alignments of the example proteins and their homologs as strings of residue substitution classes, depending on the side chain types observed at each alignment position. These results demonstrate the applicability of this relatively simple Bayesian approach to structure prediction and illustrate the utility of the classification methodology previously developed to extract information from aligned sets of structurally related proteins. © 1996 Wiley-Liss, Inc.
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  • 86
    ISSN: 0887-3585
    Keywords: computer simulation ; force-field analysis ; molecular dynamics of proteins ; water solvation properties ; van der Waals interactions ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A critical evaluation is presented of the sensitivity of the results of molecular dynamics simulations of proteins to changes in the parameters describing water-protein and protein-protein van der Waals interactions in the GROMOS force field. The origin of the van der Waals and electrostatic parameters of the GROMOS standard force field is reviewed, and possible weaknesses are discussed. Four alternate sets of van der Waals parameters for the oxygen types of the GROMOS force field that have been suggested by different authors are then tested against the original force field. Six 500 ps molecular dynamics simulations of the potato carboxypeptidase inhibitor (PCI) in solution using the different parameter sets are analyzed and the results compared with the available X-ray and NMR data. It is shown that the behavior of the molecular system is very sensitive to changes in the van der Waals parameters of the oxygens, especially when affecting the interactions between water and aliphatic or aromatic groups. It is also shown that correction of just the repulsive van der Waals parameter of the water oxygen for its interactions with nonpolar groups is sufficient to correct the main deficiency of the original GROMOS parameter set. Nevertheless, the present study suggests that further refinement of the current parameters is still needed for a proper representation of nonbonded interactions. © 1996 Wiley-Liss, Inc.
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  • 87
    ISSN: 0887-3585
    Keywords: de novo design ; protein structure ; inverse folding ; genetic algorithms ; 1H NMR ; CD ; peptide ; protein folding ; methanol ; ethylene glycol ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: In response to the Paracelsus Challenge (Rose and Creamer, Proteins, 19:1-3, 1994), we present here the design, synthesis, and characterization of a helical protein, whose sequence is 50% identical to that of an all-β protein. The new sequence was derived by applying an inverse protein folding approach, in which the sequence was optimized to “fit” the new helical structure, but constrained to retain 50% of the original amino acid residues. The program utilizes a genetic algorithm to optimize the sequence, together with empirical potentials of mean force to evaluate the sequence-structure compatibility. Although the designed sequence has little ordered (secondary) structure in water, circular dichroism and nuclear magnetic resonance data show clear evidence for significant helical content in water/ethylene glycol and in water/methanol mixtures at low temperatures, as well as melting behavior indicative of cooperative folding. We believe that this represents a significant step toward meeting the Paracelsus Challenge.
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  • 88
    ISSN: 0887-3585
    Keywords: dehalogenase ; hydrolase ; Pseudomonas ; crystallization ; X-ray diffraction ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The dimeric L-2-haloacid dehalogenase from Pseudomonas sp. YL, (subunit mass, 26179 Da), has been crystallized by vapor diffusion, supplemented by repetitive seeding, against a 50 mM potassium dihydrogenphosphate solution (pH 4.5) containing 15% (w/v) polyethylene glycol 8,000 and 1% (v/v) n-propanol. The crystals belong to the monoclinic space group C2 with unit cell dimensions of a = 92.21 Å, b = 62.78 Angst; c = 50.84 Å, and β = 122.4°, and contain two dehalogenase dimers in the unit cell. They are of good quality and diffract up to 1.5 Å resolution.
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  • 89
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    Proteins: Structure, Function, and Genetics 25 (1996), S. 143-156 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The magnitude of the conformational entropy change experienced by the peptide backbone upon protein folding was investigated experimentally and by computational analysis. Experimentally, two different pairs of mutants of a 33 amino acid peptide corresponding to the leucine zipper region of GCN4 were used for high-sensitivity microcalorimetric analysis. Each pair of mutants differed only by having alanine or glycine at a specific solvent-exposed position under conditions in which the differences in stability could be attributed to differences in the conformational entropy of the unfolded state. The mutants studied were characterized by different stabilities but had identical heat capacity changes of unfolding (ΔCp), identical solvent-related entropies of unfolding (ΔSsolv), and identical enthalpies of unfolding (ΔH) at equivalent temperatures. Accordingly, the differences in stability between the different mutants could be attributed to differences in conformational entropy. The computational studies were aimed at generating the energy profile of backbone conformations as a function of the main chain dihedral angles φ and ϱ. The energy profiles permit a direct calculation of the probability distribution of different conformers and therefore of the conformational entropy of the backbone. The experimental results presented in this paper indicate that the presence of the methyl group in alanine reduces the conformational entropy of the peptide backbone by 2.46 ± 0.2 cal/K · mol with respect to that of glycine, consistent with a 3.4-fold reduction in the number of allowed conformations in the alanine-containing peptides. Similar results were obtained from the energy profiles. The computational analysis also indicates that the addition of further carbon atoms to the side chain had only a small effect as long as the side chains were unbranched at position β. A further reduction with respect to Ala of only 0.61 and 0.81 cal/K · mol in the backbone entropy was obtained for leucine and lysine, respectively. β-branching (Val) produces the largest decrease in conformational entropy (1.92 cal/K · mol less than Ala). Finally, the backbone entropy change associated with the unfolding of an α-helix is 6.51 cal/K · mol for glycine. These and previous results have allowed a complete estimation of the conformational entropy changes associated with protein folding. © 1996 Wiley-Liss, Inc.
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  • 90
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    Proteins: Structure, Function, and Genetics 25 (1996), S. 169-179 
    ISSN: 0887-3585
    Keywords: protein structure prediction ; prediction of secondary structural class ; prediction of folding type ; amino acid composition ; jackknife analysis ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The success rates reported for secondary structural class prediction with different methods are contradictory. On one side, the problem of recognizing the secondary structural class of a protein knowing only its amino acid composition appears completely solved by simply applying jury decision with an elliptically scaled distance function. Chou and coworkers repeatedly (see Crit. Rev. Biochem. Mol. Biol. 30:275-349, 1995) published prediction accuracies near 100%. On the other hand, traditional secondary structure prediction techniques achieve success rates of about 70% for the secondary structural state per residue and about 75% for structural class only with extensive input information (full sequence of the query protein, its amino acid composition and length, multiple alignments with homologous sequences).In this article, we resolve the paradox and consider (1) the question of the secondary structural class definition, (2) the role of the representativity of the test set of protein tertiary structure for the current state of the Protein Data Bank (PDB); and (3) we estimate the real impact of amino acid composition on secondary structural class. We formulate three objective criteria for a reasonable definition of secondary structural classes and show that only the criterion of Nakashima et al. (J. Biochem. 99:153-162, 1986) complies with all of them. Only this definition matches the distribution of secondary structural content in representative PDB subsets, whereas other criteria leave many proteins (up to 65% of all PDB entries) simply unassigned.We review critically specialized secondary-structural class prediction methods, especially those of Chou and coworkers, which claim almost 100% accuracy using only amino acid composition, and resolve the paradox that these prediction accuracies are better than those from secondary structure predictions from multiple alignments. We show (i) that these techniques rely on a preselection of test sets which removes irregular proteins and other proteins without any class assignment (about 35% of all PDB entries); and (ii) that even for preselected representative test sets, the success rate drops to 60% and lower for a 4-type classification (α, β, α + β, α/β). The prediction accuracies fall to about 50% if the secondary structural class definition of Nakashima et al. is applied and only few irregular proteins are preselected and removed from automatically generated, representative subsets of the PDB.We have applied two new vector decomposition methods for secondary structural content prediction from amino acid composition alone, with and without consideration of amino acid compositional coupling in the learning set of tertiary structures respectively, to the problem of class prediction and achieve about 60% correct assignment among four classes (α, β, mixed, irregular) as well as single sequence-based secondary structure prediction methods like GORIII and COMBI. Our results demonstrate that 60% correctness is the upper limit for a 4-type class prediction from amino acid composition alone for an unknown query protein and that consideration of compositional coupling does not improve the prediction success. The prediction program SSCP offering secondary structural class assignment for query compositions and sequences has been made available as a World Wide Web and E-mail service. © 1996 Wiley-Liss, Inc.
    Additional Material: 3 Ill.
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  • 91
    ISSN: 0887-3585
    Keywords: proteinase K ; complex ; hexapeptide ; mercury ; ternary complex ; inhibitor ; structure ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The crystal structure of a ternary complex of proteinase K, Hg(II) and a hexapeptide N-Ac-Pro-Ala-Pro-Phe-Pro-Ala-NH2 has been determined at 2.2 Å resolution and refined to an R factor of 0.172 for 12,910 reflections. The mercury atom occupies two alternate sites, each of which was assigned an occupancy of 0.45. These two sites are bridged by Cys-73 Sγ which forms covalent bonds to both. Both mercury sites form regular polyhedrons involving atoms from residues Asp-39, His-69, Cys-73, His-72, Met-225, and Wat-324. The complex formation with mercury seems to disturb the stereochemistry of the residues of the catalytic triad Asp-39, His-69, and Ser-224 appreciably, thus reducing the enzymatic activity of proteinase K to 15%. The electron density in the difference Fourier map shows that the hexapeptide occupies the S1 subsite predominantly and the standard recognition site constituted by Ser-132 to Gly-136 and Gly-100 to Tyr-104 segments is virtually empty. The hexapeptide is held firmly through a series of hydrogen bonds involving protein atoms and water molecules. As a result of complex formation, Asp-39, His-69, Met-225, Ile-220, Ser-219, Thr-223, and Ser-224 residues move appreciably to accommodate the mercury atoms and the hexapeptide. The largest movement is observed for Met-225 which is involved in multiple interactions with both mercury and the hexapeptide. The activity results indicate an inhibition rate of 95%, as a result of the combined effect of mercury and hexapeptide. © 1996 Wiley-Liss, Inc.
    Additional Material: 6 Ill.
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  • 92
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    Proteins: Structure, Function, and Genetics 25 (1996), S. 225-236 
    ISSN: 0887-3585
    Keywords: enzyme reaction ; ab initio quantum mechanical ; semiempirical quantum mechanical ; continuum electrostatics ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The catalytic mechanism of triosephosphate isomerase (TIM) was investigated with ab initio quantum mechanical calculations. Electrostatic interactions between the quantum mechanical active site and the protein and solvent environment were modeled using the finite difference Poission-Boltzman method. The complexes of TIM with the substrate dihydroxyacetone phosphate (DHAP), five possible intermediates and the product glyceraldehyde-3-phosphate (GAP) were optimized in the active-site model at the 3-21G(*) level and energy profile for the proton abstraction from DHAP by the active-site Glu167 was calculated at the MP2/3-21G(*)//3-21G(*) level. Calculated energetics of the enzyme reaction were found to be in reasonable agreement with the experimental findings. Calculations revealed that an enediol of the substrate is a probable intermediate in the enzyme reaction. It was suggested that the proton abstracted from the substrate by the active-site glutamate goes to the carbonyl oxygen of the substrate producing enediol intermediate either directly or after it is exchanged with solvent. © 1996 Wiley-Liss, Inc.
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  • 93
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    Proteins: Structure, Function, and Genetics 25 (1996), S. 253-260 
    ISSN: 0887-3585
    Keywords: protein structure ; protein folding ; chaperone ; folding path ; amphiphilic sequences ; β-sheet proteins ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A major bottleneck in the field of biochemistry is our limited understanding of the processes by which a protein folds into its native conformation. Much of the work on this issue has focused on the conserved core of the folded protein. However, one might imagine that a ubiquitous motif for unaided folding or for the recognition of chaperones may involve regions on the surface of the native structure. We explore this possibility by an analysis of the spatial distribution of regions with amphiphilic α-helical potential on the surface of β-sheet proteins.All proteins, Including β-sheet proteins, contain regions with amphiphilic α-helical potential. That is, any α-helix formed by that region would be amphiphilic, having both hydrophobic and hydrophilic surfaces. In the three-dimensional structure of all β-sheet proteins analyzed, we have found a distinct pattern in the spatial distribution of sequences with amphiphilic α-helical potential. The amphiphilic regions occur in ring shaped clusters approximately 20 to 30 Å in diameter on the surface of the protein. In addition, these regions have a strong preference for positively charged amino acids and a lower preference for residues not favorable to α-helix formation. Although the purpose of these amphiphilic regions which are not associated with naturally occurring α-helix is unknown, they may play a critical role in highly conserved processes such as protein folding. © 1996 Wiley-Liss, Inc.
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  • 94
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    Proteins: Structure, Function, and Genetics 25 (1996), S. 267-285 
    ISSN: 0887-3585
    Keywords: myoglobin ; histidine ; hydrophobic core ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Proton nuclear magnetic resonance spectroscopy was applied to sperm whale apomyoglobin to describe the conformation adopted by the protein under native conditions. The study focused on the A-B-G-H interface, a region known to form a compact subdomain in the apoprotein (Hughson and Baldwin, Biochemistry 28:4415-4422, 1989). Two histidine residues located in this subdomain, His24 and His119, interact and are thought to play a role in the acid denaturation process (Barrick et al., J. Mol. Biol. 237:588-601, 1994). A stable double mutant at these positions (His24Va1/His119Phe sperm whale apomyoglobin) was compared with wild-type apomyoglobin. The amino acid replacements result in chemical shift perturbations near the mutations, in particular in the AB interhelical region, and in a deceleration of backbone amide hydrogen exchange in the B helix from position 27 to position 33. The double mutant data were used to expand and confirm the wild-type spectral analysis. Signals from the D helix were identified that demonstrate the formation of holoprotein-like structure. The assigned wild-type nuclear Overhauser effects, although in small number, were sufficient to construct a model of the compact subdomain of the apoprotein. This was achieved by using the structure of the holoprotein and restraining it with the geometrical information on the apoprotein in a simulated annealing procedure. The experimental restraints define a low-resolution model of the A-B-G-H interface in apomyoglobin. © 1996 Wiley-Liss, Inc.
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  • 95
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    Proteins: Structure, Function, and Genetics 25 (1996), S. 300-314 
    ISSN: 0887-3585
    Keywords: electrostatic modeling ; Poisson-Boltzmann equation ; finite difference ; multigrid ; allosteric regulation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: While ion pairs are readily identified in crystal structures, longer range electrostatic interactions cannot be identified from the three-dimensional structure alone. These interactions are likely to be important in large, multisubunit proteins that are regulated by allosteric interactions. In this paper, we show that these interactions are readily detected by electrostatic modeling, using, as an example, unliganded Escherichia coli aspartate transcarbamylase, a widely studied allosteric enzyme with 12 subunits and a molecular weight of 310 kD. The Born, dipolar, and site-site interaction terms of the free energy of protonation of the 810 titratable sites in the holoenzyme were calculated using the multigrid solution of the nonlinear Poisson-Boltzmann equation. Calculated titration curves are in good agreement with experimental titration curves, and the structural asymmetry observed in the crystal structure is readily apparent in the calculated free energies and pK1/2 values. Most of the residues with pK1/2 values that differ substantially from those of model compounds are buried in the low dielectric medium of the protein, particularly at the intersubunit interfaces. The dependence of the site-site interaction free energies on distance is complex, with a steep dependence at distances less than 5 Å and a more shallow dependence at longer distances. Interactions over distances of 6 to 15 Å require a bridging residue and are often not apparent in the structure. The network of interactions between ionizable groups extends across and between subunits and provides a potential mechanism for transmitting long-range structural effects and allosteric signals. © 1996 Wiley-Liss, Inc.
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  • 96
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    Proteins: Structure, Function, and Genetics 25 (1996), S. 335-341 
    ISSN: 0887-3585
    Keywords: solution X-ray scattering ; calcium-dependent conformational change ; calmodulin-melittin complex ; deviation from crystal structure ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The solution structure of a mutant calmodulin (des84) lacking Glu84 in the central helix linking the two calmodulin lobes is substantially different from its crystal structure. As determined by small-angle X-ray scattering, the radius of gyration and the maximum linear dimension of des84 in the presence of 0.1 mM calcium are 20.8 Å and 62.5 Å, respectively. These respective dimensions are larger than those expected from the crystal structure of des84, 18.5 Å and 55.0 Å, and smaller than those expected from the crystal structure of wild type, 22.8 Å and 67.5 Å. The distance distribution function of des84 indicates that it assumes an elongated, dumbbell shape in solution. The solution scattering profile of des84 is indistinguishable from that of wild-type calmodulin. The calcium-dependent binding of melittin to des84 causes a change in its shape from elongated to spherical, as seen with other calmodulins. In comparison with calcium-saturated des84, calcium-free des84 is slightly elongated; a slight compaction is observed with native calmodulin. The observed differences between the averaged solution structure and the crystal structure of des84 suggests that an ensemble of structures is available to calmodulin in solution and that its target need not induce a change in its conformation. These results support the theory that the linker region of the central helix of calmodulin functions as a flexible tether. © 1996 Wiley-Liss, Inc.
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  • 97
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    Proteins: Structure, Function, and Genetics 25 (1996), S. 354-365 
    ISSN: 0887-3585
    Keywords: classification of protein structures ; method for structural comparison ; porin ; bacteriochlorophyll α protein ; sequence-structure relationship ; WWW ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We have developed a new method and program, SARF2, for fast comparison of protein structures, which can detect topological as well as nontopological similarities. The method searches for large ensembles of secondary structure elements, which are mutually compatible in two proteins. These ensembles consist of small fragments of Cα-trace, similarly arranged in three-dimensional space in two proteins, but not necessarily equally-ordered along the polypeptide chains. The program SARF2 is available for everyone through the World-Wide Web (WWW). We have performed an exhaustive pairwise comparison of all the entries from a recent issue of the Protein Data Bank (PDB) and report here on the results of an automated hierarchical cluster analysis. In addition, we report on several new cases of significant structural resemblance between proteins. To this end, a new definition of the significance of structural similarity is introduced, which effectively distinguishes the biologically meaningful equivalences from those occurring by chance. Analyzing the distribution of sequence similarity in significant structural matches, we show that sequence similarity as low as 20% in structurally-prealigned proteins can be a strong indication for the biological relevance of structural similarity. © 1996 Wiley-Liss, Inc.
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  • 98
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    Proteins: Structure, Function, and Genetics 25 (1996), S. 398-400 
    ISSN: 0887-3585
    Keywords: procathepsin L ; proenzyme ; cysteine protease ; crystallization ; purification ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Human procathepsin L has been expressed in the yeast Pichia pastoris and its inactive (Cys25Ser) and unglycosylated (Thr110Ala) mutant purified, concentrated to 4 mg/ml, and crystallized by vapor diffusion against solution containing 1.4 M (Na, K)PO4 buffer, pH 7.8. Crystal size was Increased by multiple macroseeding. The crystals are orthorhombic, of space group P212121, with cell dimensions of a = 40.2 Å, b = 88.4 Å, and c = 94.9 Å. A 2.2 Å native data set was collected using synchrotron radiation. Although molecular replacement solution for the mature portion of the enzyme was easily found, the resulting maps could not be interpreted in the proregion. Heavy-atom derivative search is in progress. © 1996 Wiley-Liss, Inc.
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  • 99
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    Proteins: Structure, Function, and Genetics 25 (1996), S. 389-397 
    ISSN: 0887-3585
    Keywords: molecular recognition ; molecular surface ; lipophilicity ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A survey of hydrophobic patches on the surface of 112 soluble, monomeric proteins is presented. The largest patch on each individual protein averages around 400 Å2 but can range from 200 to 1,200 Å2. These areas are not correlated to the sizes of the proteins and only weakly to their apolar surface fraction. Ala, Lys, and Pro have dominating contributions to the apolar surface for smaller patches, while those of the hydrophobic amino acids become more important as the patch size Increases. The hydrophilic amino acids expose an approximately constant fraction of their apolar area independent of patch size; the hydrophobic residue types reach similar exposure only in the larger patches. Though the mobility of residues on the surface is generally higher, it decreases for hydrophilic residues with Increasing patch size. Several characteristics of hydrophobic patches catalogued here should prove useful in the design and engineering of proteins. © 1996 Wiley-Liss, Inc.
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  • 100
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    Proteins: Structure, Function, and Genetics 25 (1996), S. i 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
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