Conformational Switch of the 250s Loop Enables the Efficient Transglycosylation in GH Family 77.

Amylomaltases (AMs) play important roles in glycogen and maltose metabolism. However, the molecular mechanism is elusive. Here, we investigated the conformational dynamics of the 250s loop and catalytic mechanism of Thermus aquaticus TaAM using path-metadynamics and QM/MM MD simulations. The results demonstrate that the transition of the 250s loop from an open to closed conformation promotes polysaccharide sliding, leading to the ideal positioning of the acid/base. Furthermore, the conformational dynamics can also modulate the selectivity of hydrolysis and transglycosylation. The closed conformation of the 250s loop enables the tight packing of the active site for transglycosylation, reducing the energy penalty and efficiently preventing the penetration of water into the active site. Conversely, the partially closed conformation for hydrolysis results in a loosely packed active site, destabilizing the transition state. These computational findings guide mutation experiments and enable the identification of mutants with an improved disproportionation/hydrolysis ratio. The present mechanism is in line with experimental data, highlighting the critical role of conformational dynamics in regulating the catalytic reactivity of GHs.

Enhancing 2-O-α-D-glucopyranosyl-L-ascorbic acid synthesis by weakening the acceptor specificity of CGTase toward glucose and maltose.

2-O-α-D-glucopyranosyl-L-ascorbic acid (AA-2G) is a stable derivative of L-ascorbic acid (L-AA), which has been widely used in food and cosmetics industries. Sugar molecules, such as glucose and maltose produced by cyclodextrin glycosyltransferase (CGTase) during AA-2G synthesis may compete with L-AA as the acceptors, resulting in low AA-2G yield. Multiple sequence alignment combined with structural simulation analysis indicated that residues at positions 191 and 255 of CGTase may be responsible for the difference in substrate specificity. To investigate the effect of these two residues on the acceptor preference and the AA-2G yield, five single mutants Bs F191Y, Bs F255Y, Bc Y195F, Pm Y195F and Pm Y260F of three CGTases from Bacillus stearothermophilus NO2 (Bs), Bacillus circulans 251 (Bc) and Paenibacillus macerans (Pm) were designed for AA-2G synthesis. Under optimal conditions, the AA-2G yields of the mutants Bs F191Y and Bs F255Y AA-2G were 34.3% and 7.9% lower than that of Bs CGTase, respectively. The AA-2G yields of mutant Bc Y195F, Pm Y195F and Pm Y260F were 45.8%, 36.9% and 12.6% higher than those of wild-type CGTases, respectively. Kinetic studies revealed that the residues at positions 191 and 255 of the three CGTases were F, which decreased glucose and maltose specificity and increased L-AA specificity. This study not only proposes for the first time that the AA-2G yield can be improved by weakening the acceptor specificity of CGTase toward sugar byproducts, but also provides new insight on the modification of CGTase that catalyze the double-substrate transglycosylation reaction.

Effect of point defects on acetylene hydrogenation reaction over Ni(111) surface: a density functional theory study.

Density functional theory (DFT) calculations are carried out to investigate the effect of point defects on acetylene hydrogenation reaction over Ni(111) surface with three different defect concentrations (DC = 0.0500, 0.0625, and 0.0833), compared with the perfect Ni(111) surface. The adsorptions of C2 species and H atoms and the mechanism of acetylene hydrogenation via the ethylene pathway are systematically analyzed. The results indicate that the existence of defects will make C2 species and H atoms more inclined to adsorb near the defects. Introducing an appropriate amount of point defect concentration can enhance the catalytic activity and ethylene selectivity of Ni. In this work, DC = 0.0625 Ni(111) surface has the highest catalytic activity and selectivity of ethylene. This work provides useful theoretical information on the effect of defects on acetylene hydrogenation and is helpful for the design of Ni and related metal catalysts with defects.

Theoretical study on the reaction mechanism and selectivity of acetylene semi-hydrogenation on Ni-Sn intermetallic catalysts.

Recently, Ni-Sn intermetallic compounds (IMCs) with unique geometric structures have been proved to be selective catalysts for acetylene hydrogenation to ethylene, but the origin of the selectivity remains unclear. In this work, a density functional theory (DFT) study has been carried out to investigate the mechanism of acetylene hydrogenation on six surfaces of Ni-Sn IMCs, and the geometric effects towards ethylene selectivity were revealed. Two key parameters (adsorption energy and the hydrogenation barrier of ethylene), which determine the ethylene selectivity, were studied quantitatively. The adsorption sites for C2Hy (y = 2, 3, 4) can be classified into three types: Type 1 (Ni3Sn(111) and Ni3Sn2(101)-2) with Ni trimers, Type 2 (Ni3Sn(001) and Ni3Sn2(001)) with Ni monomers, and Type 3 (Ni3Sn2(101) and Ni3Sn2(001)-2) with reconstructed metal trimers. The adsorption energy (Ead) decreases following the order: Type 1 > Type 3 > Type 2, which indicates that the adsorption strength depends significantly on site ensemble: a more isolated Ni site would facilitate the desorption of ethylene. However, the surface roughness mainly dominates the hydrogenation barrier of ethylene. Either low or high roughness decreases the interactions between H and C2H4 (Eint), resulting in an enhanced energy barrier for over-hydrogenation of C2H4 (Ea,hydr); while moderate roughness benefits Eint and lowers Ea,hydr. The selectivity to ethylene is denoted as ΔEa = Ea,hydr - |Ead|, thus depending on the interplay of site ensemble effects and surface roughness. From this point of view, Ni3Sn(001) and Ni3Sn2(101) surfaces with well-isolated Ni ensembles and low (or high) surface roughness exhibit decreased |Ead| and increased Ea,hydr, giving rise to excellent selectivity to ethylene. This work provides significant understanding of the origin of ethylene selectivity in terms of geometric effects, which gives helpful instruction for the design and preparation of intermetallic catalysts for acetylene semi-hydrogenation.

Simultaneously improving the activity and thermostability of a new proline 4-hydroxylase by loop grafting and site-directed mutagenesis.

trans-Proline 4-hydroxylases (trans-P4Hs) hydroxylate free L-proline to trans-4-hydroxy-L-proline (trans-4-Hyp) is a valuable chiral synthon for important pharmaceuticals such as carbapenem antibiotics. However, merely few microbial trans-P4Hs have been identified, and trans-4-Hyp fermentations using engineered Escherichia coli strains expressing trans-P4Hs are usually performed at temperatures below 37 °C, which is likely due to poor stability and low activities. In the present study, a new trans-P4H from uncultured bacterium esnapd13 (UbP4H) with potential in the fermentative production of trans-4-Hyp at 37 °C was reported. In order to enhance the activity and thermostability of UbP4H, the replacement of its putative "lid" loop in combination with site-directed mutagenesis was performed. Consequently, four loop hybrids were designed by substituting a loop of UbP4H (A162-K178) with the corresponding sequences of four other known trans-P4Hs, respectively. Among them, UbP4H-Da exhibited a doubled activity when compared to the wild type (81.6 ± 1.9 vs. 40.4 ± 4.6 U/mg) but with reduced thermostability (t1/2, 11 vs. 47 min). Meanwhile, 10 single variants were designed through sequence alignments and folding free energy calculations. Three best point substitutions were respectively combined with UbP4H-Da, resulting in UbP4H-Da-R90G, UbP4H-Da-E112P, and UbP4H-Da-A260P. UbP4H-Da-E112P exhibited a 1.8-fold higher activity (85.2 ± 0.6 vs. 46.6 ± 4.0 U/mg), a 7.6-fold increase in t1/2 (359 vs. 47 min), and a 3 °C rise in Tm (46 vs. 43 °C) when compared to UbP4H. The fed-batch fermentations of trans-4-Hyp at 37 °C using trans-4-Hyp producing chassis cells expressing UbP4H or its variants were evaluated, and a 3.3-fold increase in trans-4-Hyp titer was obtained for UbP4H-Da-E112P (12.9 ± 0.1 vs. 3.9 ± 0.0 g/L for UbP4H). These results demonstrate the potential application of UbP4H-Da-E112P in the industrial production of trans-4-Hyp.

Enhancing thermostability and removing hemin inhibition of Rhodopseudomonas palustris 5-aminolevulinic acid synthase by computer-aided rational design.

OBJECTIVE: To enhance the thermostability and deregulate the hemin inhibition of 5-aminolevulinic acid (ALA) synthase from Rhodopseudomonas palustris (RP-ALAS) by a computer-aided rational design strategy. RESULTS: Eighteen RP-ALAS single variants were rationally designed and screened by measuring their residual activities upon heating. Among them, H29R and H15K exhibited a 2.3 °C and 6.0 °C higher melting temperature than wild-type, respectively. A 6.7-fold and 10.3-fold increase in specific activity after 1 h incubation at 37 °C was obtained for H29R (2.0 U/mg) and H15K (3.1 U/mg) compared to wild-type (0.3 U/mg). Additionally, higher residual activities in the presence of hemin were obtained for H29R and H15K (e.g., 64% and 76% at 10 µM hemin vs. 27% for wild-type). The ALA titer was increased by 6% and 22% in fermentation using Corynebacterium glutamicum ATCC 13032 expressing H29R and H15K, respectively. CONCLUSION: H29R and H15K showed high thermostability, reduced hemin inhibition and slightly high activity, indicating that these two variants are good candidates for bioproduction of ALA.

Metabolic engineering of Corynebacterium glutamicum by synthetic small regulatory RNAs.

Corynebacterium glutamicum is an important platform strain that is wildly used in industrial production of amino acids and various other biochemicals. However, due to good genomic stability, C. glutamicum is more difficult to engineer than genetically tractable hosts. Herein, a synthetic small regulatory RNA (sRNA)-based gene knockdown strategy was developed for C. glutamicum. The RNA chaperone Hfq from Escherichia coli and a rationally designed sRNA consisting of the E. coli MicC scaffold and a target binding site were proven to be indispensable for repressing green fluorescent protein expression in C. glutamicum. The synthetic sRNA system was applied to improve glutamate production through knockdown of pyk, ldhA, and odhA, resulting almost a threefold increase in glutamate titer and yield. Gene transcription and enzyme activity were down-regulated by up to 80%. The synthetic sRNA system developed holds promise to accelerate C. glutamicum metabolic engineering for producing valuable chemicals and fuels.

Insights into Interfacial Synergistic Catalysis over Ni@TiO2- x Catalyst toward Water-Gas Shift Reaction.

The mechanism on interfacial synergistic catalysis for supported metal catalysts has long been explored and investigated in several important heterogeneous catalytic processes (e.g., water-gas shift (WGS) reaction). The modulation of metal-support interactions imposes a substantial influence on activity and selectivity of catalytic reaction, as a result of the geometric/electronic structure of interfacial sites. Although great efforts have validated the key role of interfacial sites in WGS over metal catalysts supported on reducible oxides, direct evidence at the atomic level is lacking and the mechanism of interfacial synergistic catalysis is still ambiguous. Herein, Ni nanoparticles supported on TiO2- x (denoted as Ni@TiO2- x) were fabricated via a structure topotactic transformation of NiTi-layered double hydroxide (NiTi-LDHs) precursor, which showed excellent catalytic performance for WGS reaction. In situ microscopy was carried out to reveal the partially encapsulated structure of Ni@TiO2- x catalyst. A combination study including in situ and operando EXAFS, in situ DRIFTS spectra combined with TPSR measurements substantiates a new redox mechanism based on interfacial synergistic catalysis. Notably, interfacial Ni species (electron-enriched Niδ- site) participates in the dissociation of H2O molecule to generate H2, accompanied by the oxidation of Niδ--O v-Ti3+ (O v: oxygen vacancy) to Niδ+-O-Ti4+ structure. Density functional theory calculations further verify that the interfacial sites of Ni@TiO2- x catalyst serve as the optimal active site with the lowest activation energy barrier (∼0.35 eV) for water dissociation. This work provides a fundamental understanding on interfacial synergistic catalysis toward WGS reaction, which is constructive for the rational design and fabrication of high activity heterogeneous catalysts.

Molecular Mechanism of Double-Displacement Retaining ß-Kdo Glycosyltransferase WbbB.

Glycosyltransferases (GTs) are pivotal enzymes involved in glycosidic bond synthesis, which can lead to either retention or inversion of the glycosyl moiety's anomeric configuration. However, the catalytic mechanism for retaining GTs remains a subject of controversy. In this study, we employ MD and QM/MM metadynamics to investigate the double-displacement catalytic mechanism of the retaining ß-Kdo transferase WbbB. Our findings demonstrate that the nucleophile Asp232 initiates the reaction by attacking the sugar ring containing a carboxylate at the anomeric position, forming a covalent adduct. Subsequently, the adduct undergoes a rotational rearrangement, ensuring proper orientation of the anomeric carbon for the acceptor substrate. In the second step, Glu158 acts as the catalytic base to abstract the proton of the acceptor substrate to complete the transglycosylation reaction. Notably, His265 does not function as the anticipated catalytic acid; instead, it stabilizes the phosphate group through H-bonding interactions. Our simulations support the double-displacement mechanism implicated from the crystallographic studies of WbbB. This mechanism deviates from the common SNi-type and retaining glycoside hydrolase mechanisms, thereby expanding our understanding of GT catalytic mechanisms.

Enhancing the heterologous expression of latex clearing protein from Streptomyces sp. strain K30 in Escherichia coli through fermentation condition optimization and molecular modification.

Latex clearing protein from Streptomyces sp. strain K30 (LcpK30) is a natural oxidoreductase that can catalyse the cleavage of rubber through dioxygenation. It has significant potential applications in polymer degradation. However, its limited expression in engineered strains restricts its utility. This study aimed to enhance the soluble expression and enzyme activity of LcpK30 in E. coli BL21 (DE3) by optimizing fermentation conditions and making molecular modifications. The enzyme activity reached 5.05 U·mL-1 by optimizing the induction conditions, adding cofactors, and using chemical chaperones, which was 237.1 % of the initial case. Further enhancements in soluble expression were achieved through site mutations guided by the PROSS server, resulting in 8 out of 13 mutants with increased protein expression, a high positive mutation rate of 61.5 %. Subsequently, combined mutants were created by merging single mutants with enhanced protein expression and enzyme activity. The top three double mutants, G91D/S149A, G91D/A210H, and G91D/H296P, displayed expression levels at 173.3 %, 173.3 %, and 153.3 % of the wild-type LcpK30, respectively. These mutants also exhibited enhanced fermentation enzyme activity, reaching 149.5 %, 250.0 %, and 420.2 % compared to the wild-type, along with improved specific activities. This study provides insights for the efficient production of LcpK30 and a practical foundation for its application.

Mechanistic Insights into How the Protonation State of D234 Dictates the Reactivity in Streptomyces coelicolor ß-N-Acetylhexosaminidase.

ß-N-Acetylhexosaminidases (HEXs) play important roles in human diseases and the biosynthesis of human milk oligosaccharides. Despite extensive research, the catalytic mechanism of these enzymes remains largely unexplored. In this study, we employed quantum mechanics/molecular mechanics metadynamics to investigate the molecular mechanism of Streptomyces coelicolor HEX (ScHEX), which has shed light on the transition state structures and conformational pathways of this enzyme. Our simulations revealed that Asp242, located near the assisting residue, can switch the reaction intermediate to an oxazolinium ion or a neutral oxazoline, depending on the protonation state of the residue. Moreover, our findings indicated that the free energy barrier of the second-step reaction starting from the neutral oxazoline increases steeply due to the reduction in the anomeric carbon positive charge and the shortening of the C1-O2N bond. Our results provide valuable insights into the mechanism of substrate-assisted catalysis and could facilitate the design of inhibitors and the engineering of analogous glycosidases for biosynthesis.

Multiple approaches of loop region modification for thermostability improvement of 4,6-α-glucanotransferase from Limosilactobacillus fermentum NCC 3057.

4,6-α-glucanotransferase (4,6-α-GT), as a member of the glycoside hydrolase 70 (GH70) family, converts starch/maltooligosaccharides into α,1-6 bond-containing α-glucan and possesses potential applications in food, medical and related industries but does not satisfy the high-temperature requirement due to its poor thermostability. In this study, a 4,6-α-GT (ΔGtfB) from Limosilactobacillus fermentum NCC 3057 was used as a model enzyme to improve its thermostability. The loops of ΔGtfB as the target region were optimized using directed evolution, sequence alignment, and computer-aided design. A total of 11 positive mutants were obtained and iteratively combined to obtain a combined mutant CM9, with high resistance to temperature (50 °C). The activity of mutant CM9 was 2.08-fold the activity of the wild type, accompanied by a 5 °C higher optimal temperature, a 5.76 °C higher melting point (Tm, 59.46 °C), and an 11.95-fold longer half-life time (t1/2). The results showed that most of the polar residues in the loop region of ΔGtfB are mutated into rigid proline residues. Molecular dynamics simulation demonstrated that the root mean square fluctuation of CM9 significantly decreased by "Breathing" movement reduction of the loop region. This study provides a new strategy for improving the thermostability of 4,6-α-GT through rational loop region modification.

Diverse prebiotic effects of isomaltodextrins with different glycosidic linkages and molecular weights on human gut bacteria in vitro.

Isomaltodextrin (IMD) is a novel dietary fiber enzymatically produced by reconstructing the molecular chain structure of starch using glycosyltransferases. In this study, the specific prebiotic effects of α-1,6 linear and α-1,2 or α-1,3 branched IMDs with different molecular weights (Mw) on human intestinal bacteria were investigated by pure culture of single strains and mixed fermentation of human fecal microflora in vitro. The results showed that α-1,6 linear IMDs markedly promoted beneficial Bifidobacterium and Lactobacillus in both pure culture and mixed fermentation. α-1,3 branching exhibited similar selectivity with α-1,6 linkage but yielded more butyrate in pure cultures. In contrast, IMDs containing α-1,2 branches were utilized efficiently only during mixed fermentation, which was speculated to result from metabolic cross-feeding. Regarding Mw, IMDs with lower Mw showed better prebiotic effects in pure cultures but no differences in mixed culture. These findings provide a theoretical basis for their application as functional foods.

Trehalose promotes high-level heterologous expression of 4,6-α-glucanotransferase GtfR2 in Escherichia coli and mechanistic analysis.

4,6-α-Glucanotransferases (4,6-α-GTs) hold great potential for applications in the food and medical industries because of their efficient transglycosylation ability. However, it is relatively difficult to achieve high soluble expression because of their high molecular weight and multidomain nature. In this study, 4,6-α-GT of Burkholderia sp. (GtfR2) was successfully expressed in E. coli, and the activity attained 1.55 × 104 U/mL by traditional fermentation optimization. However, a large number of inactive inclusion bodies of GtfR2 were still present due to aggregation and precipitation. The trehalose-mediated strategy was first proposed and applied in the fermentation process of GtfR2. Trehalose addition significantly reduced inclusion bodies, resulting in an increase in GtfR2 activity (6.48 × 104 U/mL), which was 4.20 times higher than that of the control group. Our molecular dynamics simulations revealed that trehalose could spontaneously stabilize the conformational dynamics of GtfR2 by binding to the groove, loop, α-helix and N-terminal unstable regions on the surface. This strategy was also available to enhance the soluble expression of other 4,6/4,3-α-GTs, which were increased by 3.03-77.19 times. This study is the first to observe that trehalose can inhibit the aggregation and precipitation of GtfR2, which provides a new perspective for the recombinant expression of 4,6/4,3-α-GTs.

Directional-path modification strategy enhances PET hydrolase catalysis of plastic degradation.

Poly (ethylene terephthalate) (PET) is a widely used type of general plastic that produces a significant amount of waste due to its non-degradable properties. We propose a novel directional-path modification (DPM) strategy, involving positive charge amino acid introduction and binding groove remodeling, and apply it to Thermobifida fusca cutinase to enhance PET degradation. The highest value of PET degradation (90%) was achieved in variant 4Mz (H184S/Q92G/F209I/I213K), exhibiting values almost 30-fold that of the wild-type. We employed molecular docking, molecular dynamics simulations, and QM/MM MD for the degradation process of PET, accompanied by acylation and deacylation. We found that the distance of nucleophilic attack was reduced from about 4.6 Å in the wild type to 3.8 Å in 4Mz, and the free energy barrier of 4Mz dropped from 14.3 kcal/mol to 7.1 kcal/mol at the acylation which was the rate-limiting step. Subsequently, the high efficiency and universality of the DPM strategy were successfully demonstrated in LCC, Est119, and BhrPETase enhancing the degradation activity of PET. Finally, the highest degradation rate of the pretreated commercial plastic bottles had reached to 73%. The present study provides insight into the molecular binding mechanism of PET into the PET hydrolases structure and proposes a novel DPM strategy that will be useful for the engineering of more efficient enzymes for PET degradation.

Efficient bioproduction of 5-aminolevulinic acid, a promising biostimulant and nutrient, from renewable bioresources by engineered Corynebacterium glutamicum.

BACKGROUND: 5-Aminolevulinic acid (5-ALA) is a promising biostimulant, feed nutrient, and photodynamic drug with wide applications in modern agriculture and therapy. Considering the complexity and low yield of chemical synthesis methods, bioproduction of 5-ALA has drawn intensive attention recently. However, the present bioproduction processes use refined glucose as the main carbon source and the production level still needs further enhancement. RESULTS: To lay a solid technological foundation for large-scale commercialized bioproduction of 5-ALA, an industrial workhorse Corynebacterium glutamicum was metabolically engineered for high-level 5-ALA biosynthesis from cheap renewable bioresources. After evaluation of 5-ALA synthetases from different sources, the 5-ALA biosynthetic pathway and anaplerotic pathway were rebalanced by regulating intracellular activities of 5-ALA synthetase and phosphoenolpyruvate carboxylase. The engineered biocatalyst produced 5.5 g/L 5-ALA in shake flasks and 16.3 g/L in 5-L bioreactors with a one-step fermentation process from glucose. To lower the cost of feedstock, cheap raw materials were used to replace glucose. Enzymatically hydrolyzed cassava bagasse was proven to be a perfect alternative to refined sugars since the final 5-ALA titer further increased to 18.5 g/L. Use of corn starch hydrolysate resulted in a similar 5-ALA production level (16.0 g/L) with glucose, whereas use of beet molasses caused seriously inhibition. The results obtained here represent a new record of 5-ALA bioproduction. It is estimated that replacing glucose with cassava bagasse will reduce the carbon source cost by 90.1%. CONCLUSIONS: The high-level biosynthesis of 5-ALA from cheap bioresources will brighten the prospects for industrialization of this sustainable and environment-friendly process. The strategy for balancing metabolic flux developed in this study can also be used for improving the bioproduction of other value-added chemicals.

The reaction mechanism and selectivity of acetylene hydrogenation over Ni-Ga intermetallic compound catalysts: a density functional theory study.

Intermetallic compounds (IMCs) have shown excellent catalytic performance toward the selective hydrogenation of acetylene, but the theoretical understanding on this reaction over Ni-based IMCs is rather limited. In this work, the adsorptions of the C2 species, Bader charge, projected density of states (PDOS) and the reaction pathways were calculated by the density functional theory (DFT) method to investigate the mechanism and selectivity for the acetylene hydrogenation on the (111) surface of NinGa (n = 1, 3) IMCs, with a comparative study on the pristine Ni(111) surface. The results indicate that the adsorption energy of acetylene increased along with the Ni/Ga ratio, therefore a feasible acetylene adsorption on the Ga-rich surface guaranteed a low effective barrier, leading to the best activity for the NiGa(111) surface among three surfaces. Bader charge analysis shows that electrons transferred from Ga atoms to Ni atoms and further delivered to C2 species, decreasing the adsorption capacity of C2 species on NiGa(111) in comparison with those on Ni(111) and Ni3Ga(111). The reaction pathway of acetylene hydrogenation to ethylene via vinyl or even over-hydrogenation to ethane via ethyl is more favorable than the pathway involving the ethylidene intermediate on all surfaces. Moreover, the ethylene selectivity has a positive correlation with the gallium content by comparing the desorption barrier with the hydrogenation barrier of ethylene, thus the NiGa(111) surface also exhibits the best selectivity. Therefore, the NiGa(111) surface demonstrates to be an excellent reaction facet for the semihydrogenation of acetylene, which agreed with the experimental findings, and would provide helpful instructions for designing and preparing highly-selective and noble-substitute catalysts of alkyne semihydrogenation.

Hierarchical CoNi-Sulfide Nanosheet Arrays Derived from Layered Double Hydroxides toward Efficient Hydrazine Electrooxidation.

A hierarchical CoNi-sulfide nanosheet array is fabricated via an in situ reduction of CoNi-layered double hydroxide (LDH) nanosheets, then a vulcanization process. The material inherits the morphology of the LDH precursor, consisting of well-distributed CoNi-alloy@CoNi-sulfide nanoparticles with a core-shell structure, and demonstrates promising performance toward hydrazine electrooxidation.