Crystallographic structure and molecular dynamics simulations of the major endoglucanase from Xanthomonas campestris pv. campestris shed light on its oligosaccharide products release pattern

Biochemical characterization of the catalytic domain from a novel hyperthermophilic β-glucanase and its application for KOS production

Konjac oligosaccharide (KOS) exhibits various biological activities, and hyperthermophilic β-glucanases offer many advantages for KOS production from konjac glucanmannan (KGM). In this study, a novel β-glucanase, EG003, belonging to the glycosyl hydrolase (GH) subfamily 5_1, was predicted from the genome of the a Thermus strain. The recombinant EG003 and its catalytic domain, EG003A, were successfully expressed and characterized. EG003A displayed maximum activity at 95 °C and pH 8.0, with a specific activity of 1047.6 U/mg and retained approximately 50 % activity after 6 h at 90 °C. The enzyme exhibited both β-1,4-glucanase and β-1,3-1,4-glucanase activity with KGM and sodium carboxymethylcellulose (CMC), lichenan and oat β-glucan as substrates. Degree of polymerization (DP) 3 was the major oligosaccharide from the hydrolysis of KGM, while DP3 and DP4 were predominant products from the hydrolysis of oat β-glucan. Molecular docking analyses revealed that the catalytic mechanism of EG003A is consistent with those of other reported GH5_1 β-glucanases. Additionally, the viscosity of 500 mL solution of 1 % KGM decreased rapidly from 31,193 mPa.s to 4.50 mPa.s in 3 min with 30 U EG003A. This study provides an efficient hyperthermophilic β-glucanase with promising application for KOS production.

Exploring the partial degradation of polysaccharides: Structure, mechanism, bioactivities, and perspectives

Polysaccharides are promising biomolecules with lowtoxicity and diverse bioactivities in food processing and clinical drug development. However, an essential prerequisite for their applications is the fine structure characterization. Due to the complexity of polysaccharide structure, partial degradation is a powerful tool for fine structure analysis, which can effectively provide valid information on the structure of backbone and branching glycosidic fragments of complex polysaccharides. This review aims to conclude current methods of partial degradation employed for polysaccharide structural characterization, discuss the molecular mechanisms, and describe the molecular structure and solution properties of degraded polysaccharides. In addition, the effects of polysaccharide degradation on the conformational relationships between the molecular structure and bioactivities, such as antioxidant, antitumor, and immunomodulatory activities, are also discussed. Finally, we summarize the prospects and current challenges for the partial degradation of polysaccharides. This review will be of great value for the scientific elucidation of polysaccharide fine structures and potential applications.

Computer Simulation to Rationalize “Rational” Engineering of Glycoside Hydrolases and Glycosyltransferases

Glycoside hydrolases and glycosyltransferases are the main classes of enzymes that synthesize and degrade carbohydrates, molecules essential to life that are a challenge for classical chemistry. As such, considerable efforts have been made to engineer these enzymes and make them pliable to human needs, ranging from directed evolution to rational design, including mechanism engineering. Such endeavors fall short and are unreported in numerous cases, while even success is a necessary but not sufficient proof that the chemical rationale behind the design is correct. Here we review some of the recent work in CAZyme mechanism engineering, showing that computational simulations are instrumental to rationalize experimental data, providing mechanistic insight into how native and engineered CAZymes catalyze chemical reactions. We illustrate this with two recent studies in which (i) a glycoside hydrolase is converted into a glycoside phosphorylase and (ii) substrate specificity of a glycosyltransferase is engineered toward forming O-, N-, or S-glycosidic bonds.

Synthetic Biology and Biocomputational Approaches for Improving Microbial Endoglucanases toward Their Innovative Applications

Microbial endoglucanases belonging to the β-1-4 glycosyl hydrolase family are useful enzymes due to their vast industrial applications in pulp and paper industries and biorefinery. They convert lignocellulosic substrates to soluble sugars and help in the biodegradation process. Various biocomputational tools can be utilized to understand the catalytic activity, reaction kinetics, complexity of active sites, and chemical behavior of enzyme complexes in reactions. This might be helpful in increasing productivity and cost reduction in industries. The present review gives an overview of some interesting aspects of enzyme design, including computational techniques such as molecular dynamics simulation, homology modeling, mutational analysis, etc., toward enhancing the quality of these enzymes. Moreover, the review also covers the aspects of synthetic biology, which could be helpful in faster and reliable development of useful enzymes with desired characteristics and applications. Finally, the review also deciphers the utilization of endoglucanases in biodegradation and emphasizes the use of diversified protein engineering tools and the modification of metabolic pathways for enzyme engineering.

A linker of the proline-threonine repeating motif sequence is bimodal

The linker of the endoglucanase from Xanthomonas campestris pv. campestris ((PT)₁₂) has a specific sequence, a repeating proline-threonine motif. In order to understand its role, it has been compared to a regular sequence linker, in this work-the cellobiohydrolase 2 from Trichoderma reesei (CBH2). Elastic properties of the two linkers have been estimated by calculating free energy profile along the linker length from an enhanced sampling molecular dynamics simulation. The (PT)₁₂ exhibits more pronounced elastic behaviour than CBH2. The PT repeating motif results in a two-mode energy profile which could be very useful in the enzyme motions along the substrate during hydrolytic catalysis.