Low-resolution SAXS and comparative modeling based structure analysis of endo-β-1,4-xylanase a family 10 glycoside hydrolase from Pseudopedobacter saltans comb. nov

Mn2+-induced structural flexibility enhances the entire catalytic cycle and the cleavage of mismatches in prokaryotic argonaute proteins

Prokaryotic Argonaute (pAgo) proteins, a class of DNA/RNA-guided programmable endonucleases, have been extensively utilized in nucleic acid-based biosensors. The specific binding and cleavage of nucleic acids by pAgo proteins, which are crucial processes for their applications, are dependent on the presence of Mn2+ bound in the pockets, as verified through X-ray crystallography. However, a comprehensive understanding of how dissociated Mn2+ in the solvent affects the catalytic cycle, and its underlying regulatory role in this structure-function relationship, remains underdetermined. By combining experimental and computational methods, this study reveals that unbound Mn2+ in solution enhances the flexibility of diverse pAgo proteins. This increase in flexibility through decreasing the number of hydrogen bonds, induced by Mn2+, leads to higher affinity for substrates, thus facilitating cleavage. More importantly, Mn2+-induced structural flexibility increases the mismatch tolerance between guide-target pairs by increasing the conformational states, thereby enhancing the cleavage of mismatches. Further simulations indicate that the enhanced flexibility in linkers triggers conformational changes in the PAZ domain for recognizing various lengths of nucleic acids. Additionally, Mn2+-induced dynamic alterations of the protein cause a conformational shift in the N domain and catalytic sites towards their functional form, resulting in a decreased energy penalty for target release and cleavage. These findings demonstrate that the dynamic conformations of pAgo proteins, resulting from the presence of the unbound Mn2+ in solution, significantly promote the catalytic cycle of endonucleases and the tolerance of cleavage to mismatches. This flexibility enhancement mechanism serves as a general strategy employed by Ago proteins from diverse prokaryotes to accomplish their catalytic functions and provide useful information for Ago-based precise molecular diagnostics.

Interaction between a Commercial Mannoprotein and Cyanidin-3-O-glucoside-4-vinylphenol and Its Stability and Antioxidative Properties as a Novel Functional Pigment

Hydroxyphenyl-pyranoanthocyanins, which are derived from anthocyanins and phenolic acids during the fermentation and aging of red wine, are prone to polymerization and precipitation, which largely limits their application and bioactivity research. In the present study, cyanidin-3-O-glucoside-4-vinylphenol (C3GVP), a hydroxyphenyl-pyranoanthocaynin, was prepared from C3G and p-coumaric acid, and mannoprotein (MP) was employed to improve its stability in various complex solvents by forming a stable anthocyanin-MP complex. We used scanning electron microscopy, ultraviolet-visible spectroscopy, Fourier-transform infrared spectroscopy, and circular dichroism spectroscopy to observe structural changes in C3GVP and MP. The results demonstrated that the intermolecular polymerization of C3GVP was mitigated and the secondary conformation of MP was changed slightly. Fluorescence spectroscopy and molecular docking indicated that C3GVP and MP interacted via hydrogen bonds and hydrophobic interactions. Importantly, the C3GVP-MP complex exhibited better thermal stability and antioxidant capacity than C3G.

Molecular dynamics-based structural insights of the first putative endoglucanase, PsGH5A of glycoside hydrolase family 5 from Pseudopedobacter saltans

CONTEXT

The putative endoglucanase, PsGH5A, from Pseudopedobacter saltans of family GH5 contains a catalytic module, PsGH5 (β/α)₈-TIM barrel), at N-terminal followed by a family 6 carbohydrate-binding module (CBM6, β-sandwich). Superposition of PsGH5A with PDB homologs revealed Glu220 and Glu318 as evolutionarily conserved and catalytic residues performing the hydrolysis through retaining-type mechanism, a canonical property of GH5 family. PsGH5A showed higher affinity for longer cellooligosaccharides, as long as cellodecaose with binding free energy (∆G) of - 13.72 kcal/mol upon the molecular docking, thereby indicating the endo-mode of hydrolysis. The radius of gyration, Rg (2.7 nm), and solvent accessible surface area, SASA (229.6 nm²), of PsGH5A-Cellotetraose complex were determined by MD simulation which was lower than that of PsGH5A (Rg, 2.8 nm, SASA, 267 nm²) demonstrating the compactness and affinity of PsGH5A with the cellulosic ligands. Cellulose compatibility of PsGH5A was further confirmed by MMPBSA and per-residue decomposition analysis, where notable ∆G of - 54.38 kcal/mol for PsGH5A-Cellotetraose complex was observed. Thus, PsGH5A could be potentially an efficient endoglucanase as it accommodated larger cellooligosaccharides at its active-site. PsGH5A is the first putative endoglucanase studied here from P. saltans which could be genome-mined for lignocellulosic biomass saccharification in the renewable energy sector.

METHODS

The 3-D structure of PsGH5A generated by AlphaFold2, RaptorX, SwissModel, Phyre2 and Robetta tool; YASARA was used for energy minimization of built models. UCLA SAVES-v6 was used for quality assessment of models. Molecular Docking was performed using SWISS-DOCK server and Chimera software. Molecular Dynamics simulations and MMPBSA analysis of PsGH5A and PsGH5A-Cellotetraose complex were performed on GROMACS 2019.6.

Computational and SAXS-based structure insights of pectin acetyl esterase (CtPae12B) of family 12 carbohydrate esterase from Clostridium thermocellum ATCC 27405

Pectin is a complex form of polysaccharide and is composed of several structural components that require the concerted action of several pectinases for its complete degradation. In this study, in silico and solution structure of a pectin acetyl esterase (CtPae12B) of family 12 carbohydrate esterase (CE12) from Clostridium thermocellum was determined. The CtPae12B modelled structure, showed a new α/β hydrolase fold, similar to the fold found in the crystal structures of its nearest homologues from CE12 family, which differed from α/β hydrolase fold found in glycoside hydrolases. In the active site of CtPae12B, two loops (loop1 and loop6) play an important role in the formation of a catalytic triad Ser15-Asp187-His190, where Ser15 acts as a nucleophile. The structural stability of CtPae12B and its catalytic site was detected by performing molecular dynamic (MD) simulation which showed stable and compact conformation of the structure. Molecular docking method was employed to analyse the conformations of various suitable ligands docked at the active site of CtPae12B. The stability and structural specificity of the catalytic residues with the ligand, 4-nitrophenyl acetate (4-NPA) was confirmed by MD simulation of CtPae12B-4NPA docked complex. Moreover, it was found that the nucleophile Ser15, forms hydrophobic interaction with 4-NPA in the active site to complete covalent catalysis. Small angle X-ray scattering analysis of CtPae12B at 3 mg/mL displayed elongated, compact and monodispersed nature in solution. The ab initio derived dummy model showed that CtPae12B exists as a homotrimer at 3 mg/mL which was also confirmed by dynamic light scattering.Communicated by Ramaswamy H. Sarma.

Biomphalaria glabrata infected with Angiostrongylus cantonensis: Proteomic changes in the snail host

Angiostrongylus cantonensis is the main cause of human eosinophilic meningitis. Humans are accidental hosts, becoming infected due to ingestion of raw intermediate (snails and slugs) or paratenic hosts. Once ingested, the larvae migrate towards the brain where they die, causing the disease. To develop better mollusk control strategies, it is important to first understand what happens in the snail during infection, therefore our purpose was to characterize proteomic, metabolic and immunologic changes in Biomphalaria glabrata 24 h after infection with A. cantonensis. For this purpose, proteins were extracted from infected and uninfected snails and analyzed through mass spectrometry. Hemolymph was also collected, the number of hemocytes was counted and urea, nitric oxide, calcium, glycogen levels as well as alanine and aspartate aminotransferases activities were assessed. The cephalopodal region and gonad-digestive gland complex were dissected and their glycogen content was measured. After infection with A. cantonensis, we observed an increase of hemocytes and granulocytes as well as an increase in hemoglobin type 2 proteins. Temptin-like protein was also found up-regulated in infected snails. Several proteins with structural function (such as myosin heavy chain - striated muscle - like and protein LOC106059779 with ADAM/reprosolin domain) were also differentially expressed, suggesting loss/damage of internal tissues. Increase in phosphoglycerate mutase indicates an increase in glycolysis, possible to compensate the increase in energetic needs. Consequently, there is a decrease in glycogen reserves, particularly in the gonad - digestive gland complex.

In silico modelling and characterization of eight blast resistance proteins in resistant and susceptible rice cultivars

Background

Nucleotide-binding site-leucine-rich repeat (NBS-LRR) resistance genes are the largest class of plant resistance genes which play an important role in the plant defense response. These genes are better conserved than others and function as a recognition-based immune system in plants through their encoded proteins.

Results

Here, we report the effect of Magnaporthe oryzae, the rice blast pathogen inoculation in resistant BR2655 and susceptible HR12 rice cultivars. Transcriptomic profiling was carried out to analyze differential gene expression in these two cultivars. A total of eight NBS-LRR uncharacterized resistance proteins (RP1, RP2, RP3, RP4, RP5, RP6, RP7, and RP8) were selected in these two cultivars for in silico modeling. Modeller 9.22 and SWISS-MODEL servers were used for the homology modeling of eight RPs. ProFunc server was utilized for the prediction of secondary structure and function. The CDvist Web server and Interpro scan server detected the motif and domains in eight RPs. Ramachandran plot of eight RPs confirmed that the modeled structures occupied favorable positions.

Conclusions

From the present study, computational analysis of these eight RPs may afford insights into their role, function, and valuable resource for studying the intricate details of the plant defense mechanism. Furthermore, the identification of resistance proteins is useful for the development of molecular markers linked to resistance genes.

Supplementary Information

The online version contains supplementary material available at 10.1186/s43141-020-00076-0.

Computational modeling and small-angle X-ray scattering based structure analysis and identifying ligand cleavage mechanism by processive endocellulase of family 9 glycoside hydrolase (HtGH9) from Hungateiclostridium thermocellum ATCC 27405

The cellulases of family 9 glycoside hydrolase with subtle difference in amino acid sequence have shown different types of catalytic activities such as endo-, exo- or processive endocellulase. However, the reason behind the different types of catalytic activities still unclear. In this study, the processive endocellulase, HtGH9 of family 9 GH from Hungateiclostridium thermocellum was modeled by homology modeling. The catalytic module (HtGH9t) of HtGH9 modeled structure displayed the (α/α)₆ barrel topology and associated family 3 carbohydrate binding module (HtCBM3c) displayed β-sandwich fold. Ramachandran plot of HtGH9 modeled structure displayed all the amino acid residues in allowed region except Asn225 and Asp317. Secondary structure analysis of modeled HtGH9 showed the presence of 41.3% α-helices and 11.0% β-strands which was validated through circular dichroism analysis that showed the presence of 42.6% α-helices and 14.5% β-strands. Molecular Dynamic (MD) simulation of HtGH9 structure for 50 ns showed Root Mean Square Deviation (RMSD), 0.84 nm and radius of gyration (Rg) 3.1 nm. The Small-angle X-ray scattering of HtGH9 confirmed the monodisperse state. The radius of gyration for globular shape (Rg) was 5.50 ± 0.15 nm and for rod shape (Rc) by Guinier plot was 2.0 nm. The loop formed by amino acid residues, 264-276 towards one end of the catalytic site of HtGH9 forms a barrier, that blocks the non-reducing end of the cellulose chain causing the processive cleavage resulting in the release of cellotetraose. The position of the corresponding loop in cellulases of family 9 GH is responsible for different types of cleavage patterns.

Combined SAXS and computational approaches for structure determination and binding characteristics of Chimera (CtGH1-L1-CtGH5-F194A) generated by assembling β-glucosidase (CtGH1) and a mutant endoglucanase (CtGH5-F194A) from Clostridium thermocellum

Chimera (CtGH1-L1-CtGH5-F194A) developed by fusing β-glucosidase (CtGH1) at N-terminal and endoglucanase (CtGH5-F194A) at C-terminal was structurally characterized. Its secondary structure analysis by CD showed 38% α-helix, 9.3% β-sheets and 52.7% random coils corroborating with prediction. In-silico modeled structure of Chimera comprised two modules, CtGH1 and CtGH5-F194A displaying (α/β)8 fold. Ramachandran plot of Chimera showed 99.9% residues in allowed region. Binding interaction of Chimera with cello-oligosaccharides suggested active forms of CtGH1 and CtGH5-F194A and their involvement in catalysis. MD simulation of cellohexaose bound endoglucanase module of Chimera showed favourable flexibility in loops, LA with H-bond formation with Asn510 and in loop LC relocation of Tyr687 away from active site efficiently releasing the product after catalysis. Higher short range interaction energy of Chimera, -383 kJ/mol than the individual endoglucanase, 254 kJ/mol against cellohexaose suggested higher efficient catalysis by Chimera. β-Glucosidase module of Chimera showed fluctuations in outer loops suggesting conformational changes that might be contributing to improved hydrolysis. SAXS analysis of Chimera displayed monodispersed state. Guinier analysis of Chimera showed globular shape (Rg= 3.15 ± 0.10 nm). Kratky plot confirmed fully folded and flexible behaviour in solution. Gasbor modeled structure of Chimera displayed an elongated structure with two modules having shape similar to bean-bag contour.

Small-angle X-ray scattering based structure, modeling and molecular dynamics analyses of a family 5 glycoside hydrolase first endo-mannanase named as RfGH5_7 from Ruminococcus flavefaciens

Endo-β-1,4-mannanase named as RfGH5_7 from Ruminococcus flavefaciens cloned, expressed and purified earlier was structurally characterized in present study. The RaptorX modeled structure of RfGH5_7 showed a (β/α)₈ Triose-phosphate Isomerase (TIM) barrel fold. The Ramachandran plot assessment of RfGH5_7 showed that all amino acids fall in allowed region except one, Asn22 in the disallowed region. The superposition of RfGH5_7 modeled structure with its nearest homologues revealed that Glu154 acts as proton donor while Glu249 acts as nucleophile. Secondary structure of RfGH5_7 through Circular Dichroism (CD) analysis revealed 33.5% α-helices, 17% β-strands and 49.5% random coils. Molecular Dynamic (MD) simulation showed Root Mean Square Deviation (RMSD), 0.67 nm and radius of gyration (Rg) between 1.9 nm and 1.85 nm. The binding interaction of mannotetraose on the surface of RfGH5_7 structure displayed polar interactions with His219, Tyr221, Trp278, Ser279 and Gly282 residues. Small-angle X-ray scattering (SAXS) analysis displayed the intact and monodispersed nature of the enzyme RfGH5_7. The radius of gyration (Rg) by Guinier analysis for globular shape was found to be 2.29 ± 0.09 nm and for rod-shape it was 0.95 ± 0.02 nm. Kratky plot confirmed that RfGH5_7 structure is compact and folded in solution. The ab initio derived dummy model of RfGH5_7 displayed single domain structure of yellow humped fish like shape. The RfGH5_7 modeled structure was well fitted with ab initio derived model from SAXS data. Communicated by Ramaswamy H. Sarma.

Structure and biochemical characterization of glucose tolerant β-1,4 glucosidase (HtBgl) of family 1 glycoside hydrolase from Hungateiclostridium thermocellum

β-1,4-glucosidase (HtBgl) of family 1 glycoside hydrolase from Hungateiclostridium thermocellum was cloned in pET28a(+) vector, expressed, biochemically and structurally characterized. HtBgl displayed 67 U/mg activity against 4-nitrophenyl-β-d-glucopyranoside, followed by 180 U/mg against cellobiose and 42 U/mg activity against 4-nitrophenyl-β-d-galactopyranoside. HtBgl displayed an optimum temperature of 65 °C and an optimum pH of 6.0. HtBgl was stable in the pH range, 4.0-8.0 and displayed the thermostability up to 60 °C for 1 h. HtBgl displayed the glucose tolerance up to 750 mM and retained ~70% activity after 20 h. HtBgl crystal structure submitted (PDB id 5OGZ) by others exhibited a classical Triosephosphate Isomerase, (β/α)₈-barrel fold. Protein melting analysis of HtBgl exhibited a single peak at 78 °C and the addition of 5 mM Mg²⁺ shifted the peak to 82 °C. Molecular dynamics studies showed that the amino acid residues from 351 to 375 exhibit the flexibility due to the presence of the catalytic acid residue. The structure comparison of HtBgl with homologous proteins and its docking analysis with probable ligands revealed that the residues, E166 and E355 are involved in the catalysis. The SAXS analysis of HtBgl showed that the protein is monomeric and present in a fully folded state. The radius of gyration (Rg) found was 2.15-2.26 nm. The bell-shaped curve obtained by Kratky plot analysis displayed the globular shape and fully folded state with flexibility in the N-terminal region. The HtBgl crystal structure superposed well with the SAXS derived dummy atom model.

Enzymatic Properties of endo-1,4-β-xylanase from Wheat Malt

BACKGROUND

Arabinoxylan (AX) is the main non-starch polysaccharide in wheat. Wheat malts are traditional raw materials for beer brewing. AX is divided into water-soluble arabinoxylan (WEAX) and waterinsoluble arabinoxylan (WUAX). In the mashing stage of beer production, WUAX in malt is degraded by arabinoxylanase to WEAX, which is further degraded to smaller molecules and retained in the final beer. The viscosity of WEAX is related to its molecular weight. WEAX with higher molecular weight and viscosity can increase viscosity and turbidity and reduce filtration speed of wort and beer; WEAX with moderate molecular weight and viscosity contributes to the foaming characteristics and foam stability, and promotes the taste and texture of a beer; WEAX with small molecular weight has the functions of anti-tumor and lowering blood pressure and is regarded as a prebiotic. Because WEAXs with different molecular weight and properties have different impacts on the beer brewing process and qualities of the final beer, it becomes more important to control the degradation of AX during the brewing process of a beer. Endo-1,4-β-xylanase (EC 3.2.1.8) is the most important AX degrading enzyme, which cleaves the β -xylosidic bond between two d-xylopyranosyl residues linked in β-(1,4). The study of enzymatic properties of endo-1,4-β-xylanase from wheat malt is very important for the rational formulation of the content and molecular weight of WEAX in wort and beer during the mashing procedure when using wheat malt as the main raw materials.

OBJECTIVE

In this article, our motivation is to study the enzymatic properties (including optimum pH and temperature, pH and temperature stability, the effect of inhibitors) of wheat malt endo-1,4-β-xylanase.

METHODS

In this article, we prepared crude enzyme according to the method of Guo with minor modifications. The endo-1,4-β-xylanase activity was determined according to the method of Biely in the previous report with minor modifications. The 0.5 mL crude enzyme sample was mixed with 0.5 mL 1 mg/mL 4-O-methyl-dglucurono- d-xylan dyed with Remazol Brilliant Blue R (RBBR-Xylan) solution, intensively mixed, and incubated at 40 °C for exactly 90 min. The reaction was stopped by precipitation using 2 mL absolute ethanol, and the reaction mixture was stirred acutely and placed at room temperature for 30 min. Then, the mixture was mixed again and centrifuged at 6000 g for 10 min. The supernatant was collected and the absorbance was measured at 590 nm. Absolute ethanol and RBBR-Xylan were added to the control tubes first, and after the reaction was completed, the crude enzyme sample was added. One unit of endo-1,4-β-xylanase was defined as at pH 5.5 and 40 °C liberate 1 μmol xylose equivalents in 1 min per g dry wheat malt.

RESULTS

The results showed that the optimal activity of endo-1,4-β-xylanase was achieved at pH 5.5-6.0, and the enzyme was extremely stable at pH 4.5, 5.5 and 6.5 after incubation for 30, 50 and 60 min, respectively. The optimal temperature was 40-45 °C and the deactivation temperature was 75 °C. Endo-1,4-β-xylanase was stable at 20 °C and 40 °C; the stability was slightly decreased at 50 °C and rapidly decreased at 55 °C. The enzyme activity was mildly inhibited by K+, Na+, and Pb2+, moderately inhibited by Ca2+, Mg2+ and Mn2+ and severely inhibited by Cu2+, Ag+ and EDTA.

CONCLUSION

We have got the enzymatic properties of endo-1,4-β-xylanase from wheat malt, so during wort mashing, we could apply this research result to carry out the rational formulation of the content and molecular weight of WEAX in wort and beer during the mashing procedure when using wheat malt as the main raw materials. Expected to solve the technical problems such as high viscosity, slow filtration speed and so on, but also highlight the typical flavors of WEAX such as rich and persistent foam and mellow texture during the brewing process of a beer.