Endo- and exo-inulinases: enzyme-substrate interaction and rational immobilization

Insights in inulin binding and inulin oligosaccharide formation by novel multi domain endo-inulinases from Botrytis cinerea

World-wide, pathogenic fungi such as Botrytis cinerea cause tremendous yield losses in terms of food production and post-harvest food decay. Many fungi produce inulin-type oligosaccharides (IOSs) from inulin through endo-inulinases which typically show a two domain structure. B.cinerea lacks a two domain endo-inulinase but contains a three domain structure instead. Genome mining revealed three and four domain (d4) enzymes in the fungal kingdom. Here, three and two domain enzymes were compared in their capacity to produce IOSs from inulin. Hill kinetics were observed in three domain enzymes as compared to Michaelis-Menten kinetics in two domain enzymes, suggesting that the N-terminal extension functions as a carbohydrate binding module. Analysis of the IOS product profiles generated from purified GF6, GF12, GF16 and GF18 inulins and extensive sugar docking approaches led to enhanced insights in the active site functioning, revealing subtle differences between the endo-inulinases from Aspergillus niger and B. cinerea. Improved insights in structure-function relationships in fungal endo-inulinases offer opportunities to develop superior enzymes for the production of specific IOS formulations to improve plant and animal health (priming agents, prebiotics).

Identification and characterization of inulinases by bioinformatics analysis of bacterial glycoside hydrolases family 32 (GH32)

The glycoside hydrolase family contains enzymes that break the glycosidic bonds of carbohydrates by hydrolysis. Inulinase is one of the most important industrial enzymes in the family of Glycoside Hydrolases 32 (GH32). In this study, to identify and classify bacterial inulinases initially, 16,002 protein sequences belonging to the GH32 family were obtained using various databases. The inulin-effective enzymes (endoinulinase and exoinulinase) were identified. Eight endoinulinases (EC 3.2.1.7) and 4318 exoinulinases (EC 3.2.1.80) were found. Then, the localization of endoinulinase and exoinulinase enzymes in the cell was predicted. Among them, two extracellular endoinulinases and 1232 extracellular exoinulinases were found. The biochemical properties of 363 enzymes of the genus Arthrobacter, Bacillus, and Streptomyces (most abundant) showed that exoinulinases have an acid isoelectric point up to the neutral range due to their amino acid length. That is, the smaller the protein (336 aa), the more acidic the pI (4.39), and the larger the protein (1207 aa), the pI is in the neutral range (8.84). Also, a negative gravitational index indicates the hydrophilicity of exoinulinases. Finally, considering the biochemical properties affecting protein stability and post-translational changes studies, one enzyme for endoinulinase and 40 enzymes with desirable characteristics were selected to identify their enzyme production sources. To screen and isolate enzyme-containing strains, now with the expansion of databases and the development of bioinformatics tools, it is possible to classify, review and analyze a lot of data related to different enzyme-producing strains. Although, in laboratory studies, a maximum of 20 to 30 strains can be examined. Therefore, when more strains are examined, finally, strains with more stable and efficient enzymes were selected and introduced for laboratory activities. The findings of this study can help researchers to select the appropriate gene source from introduced strains for cloning and expression heterologous inulinase, or to extract native inulinase from introduced strains.

Development of a sustainable route for the production of high-fructose syrup from the polyfructan inulin

The authors used mesoporous silica microspheres as a support for the immobilization of inulinase from Aspergillus brasiliensis MTCC 1344 by the process of cross-linking. Under optimized operating conditions of pH 6.0, particle/enzyme ratio of 2.0:1.0 and glutaraldehyde concentration of 7 mM, a maximum immobilization yield of 90.7% was obtained after a cross-linking time of 12.25 h. Subsequently, the cross-linked inulinase was utilized for the hydrolysis of 5% inulin, and a maximum fructose concentration of 31.7 g/L was achieved under the optimum conditions of pH 6.0 and temperature 60°C in 3 h. Furthermore, on performing reusability studies during inulin hydrolysis, it was observed that the immobilized inulinase could be reused up to 10 subsequent cycles of hydrolysis, thus providing a facile and commercially attractive process of high-fructose syrup production.

Inulinase immobilization on polyethylene glycol/polypyrrole multiwall carbon nanotubes producing a catalyst with enhanced thermal and operational stability

This paper describes the development of a simple method for mixed non-covalent and covalent bonding of partially purified inulinase on functionalized multiwall carbon nanotubes (f-MWCNTs) with polypyrrole (PPy). The pyrrole (Py) was electrochemically polymerized on MWCNTs in order to fabricate MWCNTs/PPy nanocomposite. Two multiple forms of enzyme were bound to N-H functional groups from PPy and -COO^- from activated MWCNTs to yield a stable MWCNTs/PPy/PEG immobilized preparation with increased thermal stability. Fourier transform infrared (FTIR) spectroscopy and scanning electron microscopy (SEM) were used to confirm functionalization of nanoparticles and immobilization of the enzyme. The immobilization yield of 85% and optimal enzyme load of 345 μg protein onto MWCNTs was obtained. The optimum reaction conditions and kinetic parameters were established using the UV-Vis analytical assay. The best functional performance for prepared heterogeneous catalyst has been observed at pH 3.6 and 10, and at the temperatures of 60 and 80ºC. The half-life (t _1/2) of the immobilized inulinase at 60 and 80ºC was found to be 231 and 99 min, respectively. The reusability of the immobilized formulation was evaluated based on a method in which the enzyme retained 50% of its initial activity, which occurred after the eighteenth operation cycle.

Immobilization of thermostable exo-inulinase from mutant thermophilic Aspergillus tamarii-U4 using kaolin clay and its application in inulin hydrolysis

In this study, attempts were made to immobilize purified exo-inulinase from mutant thermophic Aspergillus tamarii-U4 onto Kaolinite clay by covalent bonding cross-linked with glutaraldehyde with an immobilization yield of 66% achieved. The free and immobilized inulinases were then characterized and characterization of the enzymes revealed that temperature and pH optima for the activity of the free and immobilized enzymes were both 65 °C and pH 4.5 respectively. The free inulinase completely lost its activity after incubation at 65 °C for 6 h while the immobilized inulinase retained 16.4% of its activity under the same condition of temperature and incubation time. The estimated kinetic parameters K_m and V_max for the free inulinase as estimated from Lineweaver-Burk plots were 0.39 mM and 4.21 µmol/min for the free inulinase and 0.37 mM and 4.01 µmol/min for the immobilized inulinase respectively. Inulin at 2.5% (w/v) and a flow rate of 0.1 mL was completely hydrolysed for 10 days at 60 °C in a continuous packed bed column and the operational stability of the system revealed that the half-life of the immobilized inulinase was 51 days. These properties make the immobilized exo-inulinase from Aspergillus tamarii-U4 a potential candidate for the production of fructose from inulin hydrolysis.

Efficient utilisation of hydrogel preparations with encapsulated enzymes - a case study on catalase and hydrogen peroxide degradation

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We present a model for the process of enzyme encapsulation in hydrogels.

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Parameters influencing the process efficiency and substrate conversion rate are selected.

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The diameter of the gel capsule used for enzymatic preparation influences the process efficiency.

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Encapsulated enzymes remain more active than native enzymes and enzymes immobilised on solid supports.

The size of the gel preparation, the concentration of the encapsulated enzyme and the ratio of the preparation volume to the volume of the reaction mixture influence the reaction efficiency with encapsulated biocatalysts. A model of first order enzymatic reaction with substrate diffusion is presented and validated by the decomposition reaction of hydrogen peroxide by catalase. The Thiele modulus (Ф) contains the modified (including the enzyme concentration) enzymatic reaction constant (k′). Based on the model analysis, the Thiele modulus should not exceed a value of 2 (optimally less than 0.5). This value can be controlled by appropriate selection of the enzyme concentration inside and the size of the capsule. A lower Ф value gives a flat substrate concentration profile inside the gel capsule and all the enzyme molecules are involved in the reaction. The optimal diameter of the gel capsule with respect to their separation from the reaction mixture is 1–2 mm.

Asparagine 42 of the conserved endo-inulinase INU2 motif WMNDPN from Aspergillus ficuum plays a role in activity specificity

Endo-inulinase INU2 from Aspergillus ficuum belongs to glycosidase hydrolase family 32 (GH32) that degrades inulin into fructo oligosaccharides consisting mainly of inulotriose and inulotetraose. The 3D structure of INU2 was recently obtained (Pouyez et al., 2012, Biochimie, 94, 2423–2430). An enlarged cavity compared to exo-inulinase formed by the conserved motif W-M(I)-N-D(E)-P-N-G, the so-called loop 1 and the loop 4, was identified. In the present study we have characterized the importance of 12 residues situated around the enlarged cavity. These residues were mutated by site-directed mutagenesis. Comparative activity analysis was done by plate, spectrophotometric and thin-layer chromatography assay. Most of the mutants were less active than the wild-type enzyme. Most interestingly, mutant N42G differed in the size distribution of the FOS synthesized.

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Endo-inulinase INU2 degrades inulin into fructo oligosaccharides.

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12 residues around the catalytic pockets of INU2 enzyme were determined.

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These residues were mutated to either a G or A residue.

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The activity has been tested by plate, spectrophotometric and TLC assays.

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One mutation, N42G, which changes the specificity of activity, has been identified.

Potential applications of carbohydrases immobilization in the food industry

Carbohydrases find a wide application in industrial processes and products, mainly in the food industry. With these enzymes, it is possible to obtain different types of sugar syrups (viz. glucose, fructose and inverted sugar syrups), prebiotics (viz. galactooligossacharides and fructooligossacharides) and isomaltulose, which is an interesting sweetener substitute for sucrose to improve the sensory properties of juices and wines and to reduce lactose in milk. The most important carbohydrases to accomplish these goals are of microbial origin and include amylases (α-amylases and glucoamylases), invertases, inulinases, galactosidases, glucosidases, fructosyltransferases, pectinases and glucosyltransferases. Yet, for all these processes to be cost-effective for industrial application, a very efficient, simple and cheap immobilization technique is required. Immobilization techniques can involve adsorption, entrapment or covalent bonding of the enzyme into an insoluble support, or carrier-free methods, usually based on the formation of cross-linked enzyme aggregates (CLEAs). They include a broad variety of supports, such as magnetic materials, gums, gels, synthetic polymers and ionic resins. All these techniques present advantages and disadvantages and several parameters must be considered. In this work, the most recent and important studies on the immobilization of carbohydrases with potential application in the food industry are reviewed.

Carbohydrate force fields

Carbohydrates present a special set of challenges to the generation of force fields. First, the tertiary structures of monosaccharides are complex merely by virtue of their exceptionally high number of chiral centers. In addition, their electronic characteristics lead to molecular geometries and electrostatic landscapes that can be challenging to predict and model. The monosaccharide units can also interconnect in many ways, resulting in a large number of possible oligosaccharides and polysaccharides, both linear and branched. These larger structures contain a number of rotatable bonds, meaning they potentially sample an enormous conformational space. This article briefly reviews the history of carbohydrate force fields, examining and comparing their challenges, forms, philosophies, and development strategies. Then it presents a survey of recent uses of these force fields, noting trends, strengths, deficiencies, and possible directions for future expansion.

Molecular modeling and docking of microbial inulinases towards perceptive enzyme-substrate interactions

Inulin is emerging as an extremely rare source of sugar, it is having more sweetening capacity than table sugar, has beneficial effect in diabetic patient. Inulinases mainly produced by the microorganism and it degrades inulin into fructose which is a digestible form. There are more than 58 strains of microorganisms which are involved in the production of inulinases. The present report investigates about the selectivity of inulin by inulinase and its action to produce fructose through molecular docking. We have investigated exo-inulinase and endo-inulinases from Penicillium sp. TN-88(BAC16218) and Penicillium sp. TN-88(BAA19132), respectively with different arrangement of amino acids in the active site which detect the substrate. The protein sequences described above were processed to homology modeling by Swiss model and further they were docked with 1-ketose and fructose-6-phosphate as substrate by DOCK6 software package (dock.compbio.ucsf.edu). The results of the present studies represented that fructose-6-phosphate ((2R,3R,4S) fructose-6-phosphate) was having better interaction with exo-inulinase showing grid score of -40.288094 and the conserved amino acid Asp-22, Asp 128, Asp 179 and Ser 84 of exo-inulinase are involved in the bonding. In addition to this it was also seen that 1-ketose ((3S,4R)-ketose 1-phosphate) did not shown any interaction with the conserved part of the endo-inulinase.

Fructose production by inulinase covalently immobilized on sepabeads in batch and fluidized bed bioreactor

The present work is an experimental study of the performance of a recently designed immobilized enzyme: inulinase from Aspergillus sp. covalently immobilized on Sepabeads. The aim of the work is to test the new biocatalyst in conditions of industrial interest and to assess the feasibility of the process in a fluidized bed bioreactor (FBBR). The catalyst was first tested in a batch reactor at standard conditions and in various sets of conditions of interest for the process. Once the response of the catalyst to different operating conditions was tested and the operational stability assessed, one of the sets of conditions tested in batch was chosen for tests in FBBR. Prior to reaction tests, preliminary fluidization tests were realized in order to define an operating range of admissible flow rates. As a result, the FBR was run at different feed flow rates in a closed cycle configuration and its performance was compared to that of the batch system. The FBBR proved to be performing and suitable for scale up to large fructose production.