Computer-aided subsite mapping of α-amylases

Subsite mapping is a crucial procedure in the characterization of α-amylases (EC 3.2.1.1), which are extensively used in starch-based industries and in diagnosis of pancreatic and salivary glands disorders. A computer-aided method has been developed for subsite mapping of α-amylases, which substitutes the difficult, expensive, and time-consuming experimental determination of action patterns to crystal structures based energy calculations. Interaction energies between enzymes and carbohydrate substrates were calculated after short energy minimization by a molecular mechanics program. A training set of wild type and mutant amylases with known experimental action patterns of 13 enzymes of wide range of origin was used to set up the procedure. Calculations for training set resulted in good correlation in case of subsite binding energies (r² = 0.827–0.929) and bond cleavage frequencies (r² = 0.727–0.835). A set of eight novel barley amylase 1 mutants was used to test our model. Subsite binding energies were predicted with r² = 0.502 correlation coefficient, while bond cleavage frequency prediction resulted in r² = 0.538. Our computer-aided procedure may supplement the experimental subsite mapping methods to predict and understand characteristic features of α-amylases.     

Characterization of α-amylase inhibitor from rice bean with inhibitory activity against midgut α-amylases from Spodoptera litura

The α-amylase inhibitor (α-AI) activity varied from 7.529 to 10.766 (IU/g) in 13 rice bean with different genotypes. BRS-2 exhibited the highest α-AI activity (55.3%). Rice bean α-AI was purified to homogeneity by 80% ammonium sulfate precipitation, dialysis, ion exchange chromatography on DEAE-Sepharose and gel filtration through Superdex-75. Its homogeneity was confirmed by SDS-PAGE under reducing conditions showing a single band protein of molecular weight 25 kDa. The inhibitor was purified to 75.9 fold with final yield of 28.0% with specific activity of 660.2 IU. Inhibition studies carried out at pH from 2.2 to 9.0 revealed pH optimum at pH 6.9 (69.3%). The maximum α-AI activity was found at 37°C (68.8 %) and the lowest was revealed at 100°C (37.0%). Optimum inhibitory activity was expressed during pre-incubation of enzyme with inhibitor at pH 6.9 and 37°C. Isoelectric focusing of purified inhibitor showed a single band near pH 4.7. The first 6 amino acids in the N-terminus were recorded as Ala-Ser-Ser-Arg-Phe-Cys (ASSRFC). The purified inhibitor inhibited the α-amylase from the larval midgut of Spodoptera litura up to 86.6%. The α-amylase inhibitors are important seed storage proteins because of their potentiality for exploitation in pest control and crop defense against insect infestation. Their expression at high levels can confer resistance in transgenic legumes, which could be exploited for crop improvement.     

Characterization of cDNA clones for rye endosperm β-amylase and analysis of β-amylase deficiency in rye mutant lines

Summary In order to characterize a -amylase deficiency in the endosperm of mutant rye lines, homologous cDNA probes were prepared. A rye cDNA library was constructed from a normal line and screened with a barley -amylase probe. Three partial cDNA clones specific for endosperm -amylase in rye were isolated and characterized. The largest of these clones was used to investigate the expression of endosperm -amylase in mutant and normal lines by Northern hybridization. These experiments, as well as in vitro translation experiments, demonstrate the absence of endosperm -amylase mRNA in mutant lines. Sequencing of three different cDNA clones revealed a single nucleotide difference, which suggests that two genes encoding endosperm -amylase genes might exist in rye. From Southern blots we anticipate that these two genes are tightly linked. Results of these experiments and previous data indicating that the mutation was located within the -amylase locus on chromosome 5 are consistent with the hypothesis that the mutation results from a deletion simultaneously affecting the two genes. However, due to extensive polymorphism within normal lines used as control, additional experiments will be required to further substantiate this conclusion. The deduced amino acid sequence reveals the occurrence of three short glycine-rich repeats containing 11 or 12 residues close to the carboxyl terminus of the protein. A comparison of the nucleotide sequence between rye and previously described barley cDNA clones revealed ca. 90% homology at the amino acid level, except in this C-terminal repeated part, where it drops to 45%.     

Microbial α-amylases from pond larvae attached to starch-plastic films

Summary Starch-containing plastic films exposed to a natural freshwater environment were shown previously to undergo significant depletion of the starch components. The culture media from a number of starch-hydrolyzing bacteria that had been collected from larvae attached to these films were found to have -amylase activity. Levels of amylase activity increased with culture age. Most of the activity was found to be cell-associated, and correlated on starch zymograms with an activity at about 55 kDa, in the >50% ammonium sulfate fractionation sample. The pH optimum for these amylases was just at or slightly above neutral, with a temperature optimum of about 65°C.     

Properties of a major α-globulin of rice endosperm

Globulin was isolated from milled rice (Oryza sativa, line IR480-5-9) by 5% NACl extraction and was precipitated by (NH₄)₂SO₂ or by dialysis against water. The extract was purified by repeated isoelectric precipitation at pH 4.5. The major globulin fraction (40%) exhibited one band by electrophoresis at pH 4.5 but two bands at pH 8.3. Similarly, one sharp peak was shown by sedimentation corresponding to 1.41S (α-globulin) in acetic acid (pH 2) and NaOH (pH 11.7) but a broad asymmetric peak was obtained at pH 6.7, 8.3 and 8.9. Gel filtration of the α-globulin at pH 6.5 exhibited 2 proteins with MW 20 000 and 98 000. The results suggest a pH dependent aggregation phenomenon. The two proteins could not be separated by DEAE-cellulose chromatography. SDS-polyacrylamide electrophoresis of α-globulin revealed one subunit with MW 18 000. This α-globulin is poorer in lysine and histidine but richer in cystine, methionine, arginine, tyrosine and glutamic acid than whole milled rice proteinfa]Taken part from the M.S. thesis of AAP from the University of the Philippine at Los Baños (1977).     

Thermal adaptation of α-amylases: a review

The temperature adaptation of α-amylase can be gained by different adjustments in protein structure with consecutive effects on the stability and flexibility of the protein. In this review, meso, thermo and cold-active α-amylases have been compared with respect to their structure and intramolecular interactions. With decrease in temperature, the number of ionic interactions also decreases, leading to greater flexibility of proteins. It has also been observed that the proline and arginine content is higher in thermophilic amylases as compared to meso and psychrophilic amylases, increasing the rigidity and structural stability of protein molecule.     

Development of new α-amylases for raw starch hydrolysis

This paper describes the discovery of a new 4 domain α-amylase from Anoxybacillus contaminans which very efficiently hydrolyses raw starch granules. Compared to traditional starch liquefying α-amylases, this new 4 domain α-amylase contains a starch binding domain. The presence of this starch-binding domain enables the enzyme to efficiently hydrolyse starch at a temperature below the gelatinisation temperature. At a reaction temperature of 60°C and in combination with a glucoamylase from Aspergillusniger it was possible to liquefy 99% of the starch obtaining a DX value of 95%.

Furthermore, we describe how the current HFCS process can be turned into a low temperature simultaneous liquefaction and saccharification process by using this new 4 domain α-amylase in combination with a glucoamylase.     

Comparison of amino acid sequences of eleven different α-amylases

Summary A comparison was made of the amino acid sequences of 11 different -amylases. The 6 animal -amylases tested were found to be highly homologous (about 80 to 90%, depending on the species compared). Amino acid sequence of Bacillus stearothermophilus -amylase was fairly homologous (about 60%) with that of a thermostable -amylase from Bacillus amyloliquefaciens. Homology was least among the thermolabile amylases from Bacillus subtilis, Aspergillus oryzae, plants and animals. Nevertheless, four highly homologous regions were found in the amino acid sequences of all the enzymes, despite their widely different origins. It was inferred that these four homologous regions were likely to be the active and/or substrate-binding sites.     

Myoinositol hexaphosphate as a potential inhibitor of α-amylases

Myoinositol hexaphosphate (MHP) strongly inhibited α-amylases of different origins. The inhibition of wheat α-amylase is noncompetitive with an apparent K_i value of 1 mM, pH dependent and markedly increased by the preincubation of enzyme with MHP before the addition of substrate. Addition of Ca²⁺ did not reverse the inhibition of α-amylase indicating that its inhibition was not due to the binding of Ca²⁺ by MHP.     

Characterization of recombinant β-amylases from Oryza sativa

Four putative β-amylase genes found in the Oryza sativa cDNA sequence database (KOME) were expressed in Escherichia coli. Recombinant proteins from two of these genes showed β-amylase activity. Similarly to β-amylases from other plants, the optimum pH of the recombinant rice β-amylases was about 5.5-6.0, but they exhibited inferior heat stability to soybean β-amylase.     

Purification of secreted α-amylases by immunoaffinity chromatography with cross-reactive antibody

Two isozymes of rice -amylases expressed and secreted by recombinant yeast were purified by immunoaffinity chromatography by using cross-reactive antibody. Antibodies raised against partially purified barley -amylase adsorbed rice -amylases in fermentation broth by a cross-reaction. By use of these antibodies as ligands, rice -amylases were concentrated and purified to a high degree in one-step immunoaffinity chromatography. Because of the differences in the contaminating impurities between the barley -amylase (antigen) from barley malt and rice -amylases (target protein) secreted from yeast, the high purity of eluted -amylases was attained without the use of highly purified antigen for immunization. Utilization of cross-reactive antibodies in immunoaffinity chromatography is useful for the purification of recombinant proteins in the absence of a sufficient amount and high enough purity of the target proteins to be purified.     

A hemicellulosic β-D-glucan from the endosperm of sorghum grain

A hemicellulosic β-D-glucan of $\text{d.p.}$ ≈26 has been isolated from the endosperm of sorghum grain. Methylation analysis, partial hydrolysis with acid, and periodateoxidation studies showed that the glucan is linear and has both (1 → 3)- and (1 → 4)-linked D-glucopyranose residues in the ratio of 3:2. The low, positive, specific rotation and chromium trioxide oxidation studies indicated that the D-glucose residues are β-linked.     

Some properties of A β-1,3-glucanase from rye

Molecular-sieve chromatography of an extract from ungerminated rye indicated the presence of enzymes which hydrolysed cellobiose, laminaribiose and the β-glucans cellodextrin, laminarin and barley β-glucan. A purified endo-β-1,3-glucanase was prepared from the extract by ammonium sulphate fractionation and molecular-sieve chromatography on Biogel P60. The substrate specificity and some properties of the enzyme are reported and the in vivo role of the enzyme is discussed.     

Immobilization of anaerobic thermophilic bacteria for the production of cell-free thermostable α-amylases and pullulanases

Summary For the production of cell-free thermostable -amylases and pullulanases various anaerobic thermophilic bacteria that belong to the genera Clostridium and Thermoanaerobacter were immobilized in calcium alginate gel beads. The entrapment of bacteria was performed in full as well as in hollow spheres. An optimal limited medium, which avoided bacterial outgrowth, was developed for the cultivation of immobilized organisms at 60° C using 0.4% starch as substrate. Compared to non-immobilized cells these techniques allowed a significant increase (up to 5.6-fold) in the specific activities of the extracellular enzymes formed. An increase in the productivity of extracellular enzymes was observed after immobilization of bacteria in full spheres. In the case of C. thermosaccharolyticum, for instance, the productivity was raised from 90 units (U)/ 10¹² cells up to 700 U/10¹² cells. Electrophoretic analysis of the secreted proteins showed that in all cases most of the amylolytic enzymes formed were released into the culture medium. Proteins that had a molecular mass of less than 450 000 daltons could easily diffuse through the gel matrix. Cultivation of immobilized bacteria in semi-continuous and fed-batch cultures was also accompanied by an elevation in the concentration of cell-free enzymes. Offprint requests to: G. Antranikian     

Mathematical modeling of maize starch liquefaction catalyzed by α-amylases from Bacillus licheniformis: effect of calcium, pH and temperature

The first step of starch hydrolysis, i.e. liquefaction has been studied in this work. Two commercial α-amylases from Bacilllus licheniformis, known as Termamyl and Liquozyme have been used for this purpose. Using starch as the substrate, kinetics of both enzymes has been determined at optimal pH and temperature (pH 7, T = 80 °C) and at 65 °C and pH 5.5. Michaelis–Menten model with uncompetitive product inhibition was used to describe enzyme kinetics. Mathematical models were developed and validated in the repetitive batch and fed-batch reactor. Enzyme inactivation was described by the two-step inactivation model. All experiments were performed with and without calcium ions. The activities of both tested amylases are approximately one hundred times higher at 80 °C than at 65 °C. Lower inactivation rates of enzymes were noticed in the experiments performed at 65 °C without the addition of calcium than in the experiments at 80 °C. Calcium ions in the reaction medium significantly enhance amylase stability at 80 °C and pH 7. At other process conditions (65 °C and pH 5.5) a weaker calcium stabilizing effect was detected.     

Production and characterization of extracellular α-amylases from the thermophilic fungus Thermomyces lanuginosus (wild and mutant strains)

-Amylases from the thermophilic fungus, Thermomyces lanuginosus ATCC 34626 (wild and mutant strains), were purified to homogeneity by a simple procedure including, consecutively, precipitation with ice-cold 2-propanol, anion-exchange and molecular-sieve chromatographic methods. The molecular masses of the purified -amylases (both with pI values of 3.0) were 58 kDa by SDS-PAGE. The optimal pH of -amylase activity was 5.0 for the wild enzyme and 4.5 for the mutant one. 1-Cyclohexyl-3-(2-morpholinyl-4-ethyl)-carbodiimide (40–100 mM) and N-bromosuccinimide (0.1–1 mM) inhibited the enzymes, suggesting the involvement of carboxylic groups and tryptophan residues in the catalytic process.     

Saponin-like substances inhibit α-galactosidase production in the endosperm of fenugreek seeds

When fenugreek (Trigonella foenum-graecum L.) endosperms plus testa (endosperms), which had been isolated from 5-h-imbibed seeds, were incubated for at least 2 h under germination conditions, they leaked substances which, like exogenous abscisic acid (ABA), inhibited the production of fenugreek endosperm -galactosidase. However, unlike ABA, 8 h treatment with these inhibitors had no effect on fenugreek endosperms which had been isolated from 15-h-imbibed seeds and leached for 2 h. This indicated that either their inhibitory action was on processes which were related to the production of -galactosidase and had been completed by this time, or that there might be factors present which inactivate these inhibitors. It was also concluded that the action of the endosperm leachate could not be attributed to the presence of ABA. The activity of the leachate decreased when it originated from endosperms imbibed for periods longer than 25 h and thin-layer chromatography (TLC) of extracts from these endosperms showed decreased contents of the leachable inhibitors as imbibition proceeded. From the seed leachate, which had a TLC pattern and inhibitory action similar to that of the endosperm, were isolated three substances which, when applied to endosperms, inhibited the production of -galactosidase activity. According to their chromatographic behaviour and their reaction with specific reagents, there are strong indications that these substances are saponins. These diffusible saponin-like substances were located in both endosperm and perisperm and their physiological role is discussed.Abbreviations ABA abscisic acid - PEG polyethylenglycol - TLC thin-layer chromatography We wish to thank the Alexander S. Onasis Public Benefit Foundation for a grant to K.Z. and Dr. J.S.G. Reid (University of Stirling, Scotland) for a kind gift of fenugreek seeds.