Changes in Functionality of Germinated and Non-Germinated Brown Rice Fermented by Bacillus natto.

Germinated brown rice (GBR) is brown rice (BR) that has been germinated. GBR accumulates more nutrients and has a softer texture than BR. The aim of this study was to ferment GBR and BR using Bacillus natto and to investigate the functionality of the fermented products compared with white rice (WR) as a control. After fermentation with B. natto, the crude ash, total essential amino acids, and fat contents of each sample increased, while the crude protein content decreased. Moreover, the γ-aminobutyric acid and γ-oryzanol contents decreased, while the 2,2-diphenyl-1-picrylhydrazyl (DPPH) free radical scavenging increased significantly in all fermented samples. The nattokinase activity (FU/g) of the fermented products was highest for GBR (43.11), followed by BR (19.62), and lowest for WR (12.24). Collectively, these results indicate that GBR fermented with B. natto yields better nutritional value and functional properties than fermented BR or WR.

Effective hybrid approach for protein structure prediction in a two-dimensional Hydrophobic-Polar model.

Hydrophobic-polar (HP) models are widely used to predict protein folding and hydrophobic interactions. Numerous optimization algorithms have been proposed to predict protein folding using the two-dimensional (2D) HP model. However, to obtain an optimal protein structure from the 2D HP model remains challenging. In this study, an algorithm integrating particle swarm optimization (PSO) and Tabu search (TS), named PSO-TS, was proposed to predict protein structures based on the 2D HP model. TS can help PSO to avoid getting trapped in a local optima and thus to remove the limitation of PSO in predicting protein folding by the 2D HP model. In this study, a total of 28 protein sequences were used to evaluate the accuracy of PSO-TS in protein folding prediction. The proposed PSO-TS method was compared with 15 other approaches for predicting short and long protein sequences. Experimental results demonstrated that PSO-TS provides a highly accurate, reproducible, and stabile prediction ability for the protein folding by the 2D HP model.

Protein folding prediction in the HP model using ions motion optimization with a greedy algorithm.

BACKGROUND: The function of a protein is determined by its native protein structure. Among many protein prediction methods, the Hydrophobic-Polar (HP) model, an ab initio method, simplifies the protein folding prediction process in order to reduce the prediction complexity. RESULTS: In this study, the ions motion optimization (IMO) algorithm was combined with the greedy algorithm (namely IMOG) and implemented to the HP model for the protein folding prediction based on the 2D-triangular-lattice model. Prediction results showed that the integration method IMOG provided a better prediction efficiency in a HP model. Compared to others, our proposed method turned out as superior in its prediction ability and resilience for most of the test sequences. The efficiency of the proposed method was verified by the prediction results. The global search capability and the ability to escape from the local best solution of IMO combined with a local search (greedy algorithm) to the new algorithm IMOG greatly improve the search for the best solution with reliable protein folding prediction. CONCLUSION: Overall, the HP model integrated with IMO and a greedy algorithm as IMOG provides an improved way of protein structure prediction of high stability, high efficiency, and outstanding performance.

A Particle Swarm Optimization-Based Approach with Local Search for Predicting Protein Folding.

The hydrophobic-polar (HP) model is commonly used for predicting protein folding structures and hydrophobic interactions. This study developed a particle swarm optimization (PSO)-based algorithm combined with local search algorithms; specifically, the high exploration PSO (HEPSO) algorithm (which can execute global search processes) was combined with three local search algorithms (hill-climbing algorithm, greedy algorithm, and Tabu table), yielding the proposed HE-L-PSO algorithm. By using 20 known protein structures, we evaluated the performance of the HE-L-PSO algorithm in predicting protein folding in the HP model. The proposed HE-L-PSO algorithm exhibited favorable performance in predicting both short and long amino acid sequences with high reproducibility and stability, compared with seven reported algorithms. The HE-L-PSO algorithm yielded optimal solutions for all predicted protein folding structures. All HE-L-PSO-predicted protein folding structures possessed a hydrophobic core that is similar to normal protein folding.

Engineering of dual-functional hybrid glucanases.

1,3-1,4-ß-D-Glucanase (lichenase) and 1,3-ß-D-glucanase (laminarinase) are fibrolytic enzymes which play an important role in the hydrolysis of polysaccharide components. Both of these glucanases have been employed in a number of industrial applications. This study aims to improve or combine the novel properties of both glucanases in an attempt to create desirable hybrid enzymes with economic benefits for industrial applications. A truncated and mutated 1,3-1,4-ß-D-glucanase gene (TFs(W203F)) from Fibrobacter succinogenes, and a 1,3-ß-D-glucanase gene (TmLam) from hyperthermophilic Thermotoga maritima were used as target enzymes. The substrate-binding domains (TmB1 and TmB2) and the catalytic domain (TmLam(CD)) of TmLam were ligated to the N- or C-terminus of TFsW203F to create four hybrid enzymes, TmB1-TFs(W203F), TFs(W203F)-TmB2, TmB1-TFs(W203F)-TmB2 and TFs(W203F)-TmLam(CD). The results obtained from kinetic studies show that increased specific activities and turnover rate for lichenan and laminarin were observed in TmB1-TFs(W203F)-TmB2 and TFs(W203F)-TmLam(CD), respectively. Furthermore, fluorescence and circular dichroism spectrometric analyses indicated that the hybrid TFs(W203F)-TmLam(CD) was structurally more stable than the parental TFs(W203F), which was attributed to an improved thermal tolerance of the hybrid enzyme. This study has been successful in creating bifunctional hybrid glucanases with dual substrate catalytic functions which warrant further evaluation of their possible use in industrial applications.

Structural and catalytic roles of residues located in beta13 strand and the following beta-turn loop in Fibrobacter succinogenes 1,3-1,4-beta-D-glucanase.

BACKGROUND: Fibrobacter succinogenes 1,3-1,4-beta-D-glucanase (Fsbeta-glucanase) is the only naturally occurring circularly permuted beta-glucanase among bacterial glucanases with reverse protein domains. We characterized the functional and structural significance of residues 200-209 located in the domain B of Fsbeta-glucanase, corresponding to the major surface loop in the domain A region of Bacillus licheniformis glucanase. METHODS: Rational design approaches including site-directed mutagenesis, initial-rate kinetics, and structural modeling analysis were used in this study. RESULTS: Our kinetic data showed that D202N and D206N exhibited a 1.8- and 1.5-fold increase but G207N, G207-, F205L, N208G and T204F showed a 7.0- to 2.2-fold decrease, in catalytic efficiency (k(cat)/K(M)) compared to the wild-type enzyme. The comparative energy DeltaDeltaG(b) value in individual mutant enzymes was well correlated to their catalytic efficiency. D206R mutant enzyme exhibited the highest relative activity at 50 degrees C over 10 min, whereas K200F was the most heat-sensitive enzyme. CONCLUSIONS: This study demonstrates that Phe205, Gly207, and Asn208 in the Type II turn of the connecting loop may play a role in the catalytic function of Fsbeta-glucanase. GENERAL SIGNIFICANCE: Residues 200-209 in Fsbeta-glucanase resided at the similar structural topology to that of Bacillus enzyme were found to play some similar catalytic function in glucanase.

Mutational and structural studies of the active-site residues in truncated Fibrobacter succinogenes1,3-1,4-beta-D-glucanase.

1,3-1,4-beta-D-Glucanases (EC 3.2.1.73) specifically hydrolyze beta-1,4-glycosidic bonds located prior to beta-1,3-glycosidic linkages in lichenan or beta-D-glucans. It has been suggested that truncated Fibrobacter succinogenes 1,3-1,4-beta-D-glucanase (TFsbeta-glucanase) can accommodate five glucose rings in its active site upon enzyme-substrate interaction. In this study, 12 mutant enzymes were created by mutating the conserved residues Gln70, Asn72, Gln81 and Glu85 proposed to bind to substrate subsites +1 and +2 and the catalytic properties of these mutants were determined. The most significant change in catalytic activity was observed on mutation of Gln70, with a 299-fold and 498-fold lower k(cat)/K(m) for the mutants Q70A and Q70I, respectively, compared with the wild-type enzyme. Mutagenesis, kinetic and structural studies revealed that the conserved residues surrounding the active site of TFsbeta-glucanase at substrate subsites +1 and +2 play an important role in its catalytic function, with the following order of importance: Gln70 > Asn72 > Glu85 > Gln81. The crystal structure of mutant E85I was determined at 2.2 A resolution. Further analysis of the E85I mutant structure revealed that the loop located at the concave site moved approximately 2 A from its position in the native enzyme complex without changing the core structure.

The effect of centaurein on interferon-gamma expression and Listeria infection in mice.

We previously found that centaurein enhanced IFN-gamma transcription in T cells. Here, we demonstrate that centaurein increased the IFN-gamma expression in T and NK cells and the serum IFN-gamma level in mice. Centaurein elevated the transcription of T-bet but not GATA-3, which is consistent with its effect on that of IFN-gamma but not IL-4. Additionally, centaurein effectively protected mice against Listeria infection. Moreover, centaurein per se or in combination with antibiotics could treat Listeria infection. Our mechanistic studies suggest that centaurein augments IFN-gamma expression via a transcriptional up-regulation of T-bet and that centaurein protects against or treats Listeria infection via a modulation of IFN-gamma expression.