Structure and functional investigation of ligand binding by a family 35 carbohydrate binding module (CtCBM35) of ß-mannanase of family 26 glycoside hydrolase from Clostridium thermocellum.

Functional attributes of recombinant CtCBM35 (family 35 carbohydrate binding module) of ß-mannanase of family 26 Glycoside Hydrolase from Clostridium thermocellum were deduced by biochemical and in silico approaches. Ligand-binding analysis of expressed CtCBM35 analyzed by affinity-gel electrophoresis and fluorescence spectroscopy exhibited association constants Ka ~ 1.2·10(5) and 3.0·10(5) M(-1) with locust bean galactomannan and mannotriose, respectively. However, CtCBM35 showed low ligand-binding affinity with insoluble ivory nut mannan with Ka of 5.0·10(-5) M(-1). Unfolding transition analysis by fluorescence spectroscopy explained the conformational changes of CtCBM35 in the presence of guanidine hydrochloride (5 M) and urea (6.25 M). This explained that CtCBM35 has good conformational stability and requires higher free energy of denaturation to invoke unfolding. The three-dimensional (3-D) model of CtCBM35 from C. thermocellum generated by Modeller9v8 displayed predominance of ß-sheets arranged as ß-jelly-roll fold. The secondary structure of CtCBM35 by PredictProtein showed the presence of two α-helices (3%), 12 ß-sheets (45%), and 15 random coils (52%). Secondary structural element analysis of cloned, expressed, and purified recombinant CtCBM35 by circular dichroism also corroborated the in silico predicted secondary structure. Multiple sequence alignment of CtCBM35 showed conserved residues (Tyr123, Gly124, and Phe125), which are commonly observed in mannan specific CBMs. Docking analysis of CtCBM35 with manno-oligosaccharide displayed the involvement of Tyr26, Gln29, Asn43, Trp66, Tyr68, Leu69, Arg76, and Leu127 residues, making polar contact with the ligand molecules. Ligand docking analysis of CtCBM35 exhibiting higher binding affinity with mannotriose and galactomannan (Man-Gal-Man moiety) substantiated the affinity binding and fluorescence results, displaying similar values of Ka.

Major antifungal activity from the bulbs of Indian squill Urginea indica is a chitinase.

We have identified a chitinase with antifungal activity in the bulbs of the plant Urginea indica(Indian squill) and purified it about 26-fold. The purified preparation contained a Mr 29 kDa protein that was an active growth inhibitor of the fungal pathogens Fusarium oxysporum and Rhizoctonia solani in an in vitro assay. Amino acid sequence analysis of the Mr 29 kDa protein revealed it to be highly homologous to the family 19 glycoside hydrolases, which are known to possess chitinase activity. The U. indica chitinase lacked a cysteine-rich N-terminal domain (characteristic of class I chitinases) and contained a conserved motif indicative of the signature 1 of family 19 glycoside hydrolases. It shared a approximately 70% sequence identity with the 26 kDa endochitinase of Hordeum vulgare, a typical class II chitinase of family 19. The five cysteines in the partial sequence of the Mr 29 kDa chitinase were found to be identical in location to five of the seven cysteines present in the catalytic domain of the H. vulgare enzyme. The molecular weight, the lack of an N-terminal cysteine-rich sequence, and the striking identity to the H. vulgare endochitinase suggest that the Mr 29 kDa U. indica protein is a putative class II chitinase. The antifungal activity is presumably mediated through the chitinolytic activity of the Mr 29 kDa protein.

Ultrasonic pre-irradiation effect upon aqueous enzymatic oil extraction from almond and apricot seeds.

The present work evaluates the benefit of using ultrasonic pre-irradiation before extracting oil from almond and apricot seeds by aqueous enzymatic oil extraction (AEOE) process. The use of a commercial preparation which is a mixture of three proteases in AEOE gave 75% w/w oil yield from almonds at pH 4.0 in 18 h at 40 degrees C. The ultrasonic pre-irradiation at 70 W for 2 min increased the yield to 95%, w/w and reduced the extraction time to 6 h. The effect of ultrasonic pre-irradiation on meal morphology could be visually seen by scanning electron micrographs. It indicates development of of microfractures and disruption of cell walls in almond powder. With apricot, also, ultrasonic pre-irradiation also marginally increased the oil yield obtained by AEOE to 77% w/w and reduced the extraction time to 6 h. Thus, ultrasonic pre-irradiation step may reduce time required to extract oil from edible oils from plant sources and hence can improve through put in commercial oil production process.

A solvent tolerant isolate of Enterobacter aerogenes.

A solvent tolerant strain of Enterobacter aerogenes was isolated from soil by cyclohexane enrichment. Presence of cyclohexane (20%) in culture media prolonged the lag phase and caused reduction in biomass. Transmission electron micrographs showed convoluted cell membrane and accumulation of solvent in case of the cells grown in cyclohexane. The Enterobacter isolate was able to grow in the range of organic solvents having log P above 3.2 and also in presence of mercury, thus showing potential for treatment of solvent rich wastes.

Purification and characterization of a solvent stable protease from Pseudomonas aeruginosa PseA.

A solvent tolerant Pseudomonas aeruginosa PseA strain was isolated from soil. It secreted a novel alkaline protease, which was stable and active in the presence of range of organic solvents, thus potentially useful for catalysis in non-aqueous media. The protease was purified 11.6-fold with 60% recovery by combination of ion exchange and hydrophobic interaction chromatography using Q-Sepharose and Phenyl Sepharose 6 Fast Flow matrix, respectively. The apparent molecular mass based on the sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE) was estimated to be 35,000 Da. The enzyme was stable in the pH range of 6.0-9.0, the optimum being 8.0. The Km and Vmax towards caseinolytic activity were found to be 2.7 mg/ml and 3 micromol/min, respectively. The protease was most active at 60 degrees C and characterized as a metalloprotease because of its sensitivity to EDTA and 1,10-phenanthroline. It was tested positive for elastase activity towards elastin-orcein, thus appears to be an elastase, which is known as pseudolysin in other strains of P. aeruginosa. The protease withstands range of detergents, surfactants and solvents. It is stable and active in all the solvents having log P above 3.2, at least up to 72 h. These two properties make it an ideal choice for applications in detergent formulations and enzymatic peptide synthesis.

One-step purification and characterization of an alkaline protease from haloalkaliphilic Bacillus sp.

An alkaline protease producer haloalkaliphilic bacteria (isolate Vel) was isolated from west coast of India. It was related to Bacillus pseudofirmus on the basis of 16S r RNA gene sequencing, lipid profile and other biochemical properties. The protease secreted by this bacteria was purified 10-fold with 82% yield by a single step method on Phenyl Sepharose 6 Fast Flow column. The apparent molecular mass based on the sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE) was estimated to be 29 000 Da. The Km and Vmax towards caseinolytic activity were found to be 2 mg ml(-1) and 289.8 microg min(-1), respectively. The enzyme was active over the pH range of 8.5-12.0, the optimum being 10-11.0. The purified enzyme when kept at 45 degrees C and 50 degrees C for 40 min retained 92% and 85% protease activity, respectively. Effect of NaCl concentration on protease activity showed that the enzyme was slightly inhibited with high concentration of salt. The proteolytic activity was inhibited by PMSF, suggesting that the enzyme may belong to serine type protease. Interestingly, the activity was slightly enhanced with SDS (0.1%) and Triton X-100 (0.1%) but remained unaffected by Tween 80 (0.1%). The activity was affected by metal ions to varying extent. While Mn2+, Zn2+ and Mg2+ had no significant effect on protease activity, the enzyme was activated with Ca2+ (1 mM) and Cu2+ (5 mM). The stability of the enzyme in the presence of detergent components and surfactants is particularly attractive for its application in detergent industries.

Extraction of oil from Jatropha curcas L. seed kernels by combination of ultrasonication and aqueous enzymatic oil extraction.

Use of ultrasonication as a pretreatment before aqueous oil extraction and aqueous enzymatic oil extraction was found to be useful in the case of extraction of oil from the seeds of Jatropha curcas L. The use of ultrasonication for 10 min at pH 9.0 followed by aqueous oil extraction gave a yield of 67%. However, the maximum yield of 74% was obtained by ultrasonication for 5 min followed by aqueous enzymatic oil extraction using an alkaline protease at pH 9.0. Use of ultrasonication also resulted in reducing the process time from 18 to 6 h.

An integrated process for separation of major and minor proteins from goat serum.

Analysis of minor proteins in animal sera is of considerable clinical significance. To be able to detect these proteins, depletion of major proteins (albumin and immunoglobulin G [IgG]) is necessary. Many of these proteins are also required in pure form for a variety of biochemical applications. The present work uses goat serum as the system and describes the separation and purification of both major and several minor proteins. This was carried out by judicious adaptation and combination of separation technologies such as immobilized metal ion affinity chromatography (on a somewhat novel matrix), dye affinity chromatography, and lectin affinity chromatography. Albumin, IgG, alpha2-macroglobulin, alpha1-proteinase inhibitor, and transferrin were obtained from the serum. The purified preparations were found to be homogeneous on sodium dodecyl sulfate polyacrylamide gel electrophoresis.

Magnetite-alginate beads for purification of some starch degrading enzymes.

Starch degrading enzymes, viz., beta-amylase, glucoamylase, and pullulanase, were purified using magnetite-alginate beads. In each case, the enzyme activity was eluted by using 1.0 M maltose. beta-Amylase (sweet potato), glucoamylase (Aspergillus niger), and pullulanase (Bacillus acidopullulyticus) from their crude preparations were purified 37-, 31-, and 49-fold with 86, 87, and 95% activity recovery, respectively. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis showed single band in each case.

An assessment of nonspecific adsorption to Eudragit S-100 during affinity precipitation.

The problem of nonspecific adsorption to the reversibly soluble-insoluble polymers is of considerable importance in the design of an affinity precipitation protocol. It was seen that activation and coupling of the affinity ligand to the polymer changes the nature of the polymer surface in a significant fashion. The results with pure trypsin, partially purified trypsin preparation, and crude protein extract-containing protein inhibitors of trypsin and alpha-amylase and the reversibly soluble-insoluble polymer Eudragit S-100, show that nonspecific adsorption may not be a severe limitation in such systems.

Affinity precipitation of trypsin with soybean trypsin inhibitor linked Eudragit S-100.

Soybean trypsin inhibitor linked to Eudragit S-100 was used for the affinity precipitation of trypsin. Polymer and ligand concentrations used in conjugate preparation showed remarkable effect on the trypsin recovery. Trypsin precipitation efficiency amounted to 89% and recovery was 74%. The final purification of relatively crude commercial trypsin resulted in 1.85-fold purification. The SDS-PAGE analysis indicated significant purification. The precipitated enzyme activity was around 96% and recovered enzyme activity was 83%.

Magnetic alginate microparticles for purification of alpha-amylases.

Spherical magnetic alginate microparticles (25-60 microm in diameter) were prepared using the microemulsion system, with water-saturated 1-pentanol as the organic phase. The limited solubility of 1-pentanol in water enabled simple removal of the organic solvent from the prepared beads with water solution. The prepared alginate microparticles were used as magnetic affinity adsorbents for specific purification of alpha-amylases. Enzyme activity was eluted by 1.0 M maltose. alpha-Amylases from Bacillus amyloliquefaciens and porcine pancreatic acetone powder were purified 9- and 12-fold with 88 and 96% activity recovery, respectively.

Purification of phospholipase D by two-phase affinity extraction.

An aqueous two-phase system of polyethylene glycol (PEG)-salt was used for purification of phospholipase D (PLD) from peanuts and carrots. Alginate, a known macroaffinity ligand for PLD, was incorporated in the PEG phase and resulted in 91 and 93% of the enzyme activity (from peanuts and carrots, respectively) getting partitioned in the PEG phase. The elution of the enzyme from alginate was facilitated by exploiting the fact that the latter can be reversibly precipitated in the presence of Ca2+. The enzyme was eluted from the polymer by using 0.5 M NaCl. Peanuts and carrots PLD could be purified 78- and 17-fold with 82 and 85% activity recovery, respectively. The purified enzyme from both sources gave a single band on sodium dodecyl sulfate-polyacrylamide gel (SDS-PAGE) electrophoresis.

Reversibly soluble macroaffinity ligand in aqueous two-phase separation of enzymes.

Use of alginate as a free bioligand incorporated in an aqueous two-phase system of polyethylene glycol 6000-salt resulted in considerable purification of wheat germ alpha-amylase and sweet potato beta-amylase from their crude extracts. The elution of the enzyme from the free bioligand was facilitated by exploiting the fact that alginate can be reversibly precipitated in the presence of Ca2+. alpha-Amylase could be purified 42-fold with 92% activity recovery. beta-Amylase on the other hand could be purified 43-fold with 90% recovery. Both purified enzymes showed a single band on sodium dodecylsulfate-polyacrylamide gel electrophoresis.

Chitosan as a macroaffinity ligand purification of chitinases by affinity precipitation and aqueous two-phase extractions.

(1) Chitosan was found to be a suitable macroaffinity ligand for affinity precipitation of chitinase from Neurospora crassa, cabbage and puffballs. (2) The activity recoveries of 85, 82 and 90% with concomitant fold purifications in terms of specific activities were 27, 15 and 30 with N. crassa, cabbage and puffballs and were obtained with affinity precipitation. These results were obtained with clarified extracts/homogenates as the starting materials. (3) The incorporation of chitosan in poly(ethylene glycol) (PEG)-salt aqueous two-phase system allowed purification of chitinases from these sources directly from unclarified extracts/homogenates. (4) The 96% (w/v) chitosan (of initially introduced into the aqueous two-phase system) partitioned into PEG-phase and this enhanced the partitioning of chitinases into PEG-phase. The chitosan, free as well as bound to chitinases, could be separated from PEG-phase by increasing the pH to 7. (5) By the process of desorption with 2.0 M MgCl2, 86, 80 and 88% activity recoveries (% expressed in terms of total units of enzyme activities in the crude extract) were obtained in the case of N. crassa, cabbage and puffballs, respectively. The corresponding fold purifications in terms of specific activities were 34, 20 and 38. (6) The purified preparations gave single bands on sodium dodecyl sulfate-polyacrylamide gel electrophoresis and the estimated molecular masses agreed with the reported values in the literature.

Purification of recombinant green fluorescent protein by three-phase partitioning.

The technique of three-phase partitioning (TPP) was used to purify the green fluorescent protein (GFP) in a single step. TPP uses a combination of ammonium sulphate and tert-butanol to precipitate proteins from their crude extracts. In the first round of TPP with 20% ammonium sulphate saturation at the ratio of crude to tert-butanol 1:1 (v/v), most of the GFP remains in the lower aqueous phase. When subjected to a second round of TPP with 60% ammonium sulphate saturation at the ratio of crude to tert-butanol 1:2 (v/v) gives 78% recovery of GFP with a 20-fold purification. The sodium dodecyl sulphate-polyacrylamide gel electrophoretic (SDS-PAGE) analysis of purified preparation shows single band. The fluorescence excitation and emission spectra agreed with values reported in literature.

Hydrolysis of rice hull by crosslinked Aspergillus niger cellulase.

A. niger cellulase was crosslinked by glutaraldehyde to obtain a heat-stable enzyme preparation for rice hull cellulose hydrolysis. Under optimized crosslinking conditions of 0.12 M glutaraldehyde, pH 7.0, temperature 40 degrees C and at 45 min of crosslinking, a preparation having 15% more activity than free enzyme was obtained which also had considerable improvement in heat stability at 65 degrees C and 70 degrees C. Whereas the free enzyme lost 80% of its activity in 4 h at 65 degrees C, the crosslinked preparation lost only 30% activity. The crosslinked preparation hydrolyzed cellulosic biomass more effectively giving 2.2 mg/ml glucose and 52% corresponding saccharification in 4 h at 65 degrees C as compared to 14% saccharification by free enzyme under similar conditions.

Purification of alpha-amylases using magnetic alginate beads.

Magnetic alginate beads were used to purify alpha-amylases from porcine pancreas, starchzyme, BAN 240L (a commercial purification from Bacillus subtilis), and wheat germ. The beads bound a significant level of alpha-amylase activity from porcine pancreas, BAN 240L, and wheat germ. In each case, the enzyme activity could be eluted by using 1.0 M maltose, a known competitive inhibitor of alpha-amylase. In the case of BAN 240L, 3.6-fold purification with 72% recovery of activity was observed. In the case of wheat germ enzyme, starting from the crude extract, 48-fold purification with 70% activity recovery was observed. Sodium dodecyl sulfate polyacrylamide gel electrophoresis analysis also indicated considerable purification in the latter case.

A crosslinked preparation of E. coli beta-D-galactosidase.

beta-D-Galactosidase from E. Coli was crosslinked using glutaraldehyde and two bisimidoesters. With glutaraldehyde and dimethyl adipimidate (DMA), it is possible to obtain preparations having higher activity than the native enzyme. Glutaraldehyde and DMA gave preparations showing enhanced thermal stability. The preparation crosslinked with DMA, when used for continuous hydrolysis of lactose in milk, was found to be significantly better than the native enzyme.