Hydrolysis Of Bond Research Articles

Relationship between Composition and Environmental Degradation of Poly(isosorbide-co-diol oxalate) (PISOX) Copolyesters.

To reduce the global CO2 footprint of plastics, bio- and CO2-based feedstock are considered the most important design features for plastics. Oxalic acid from CO2 and isosorbide from biomass are interesting rigid building blocks for high Tg polyesters. The biodegradability of a family of novel fully renewable (bio- and CO2-based) poly(isosorbide-co-diol) oxalate (PISOX-diol) copolyesters was studied. We systematically investigated the effects of the composition on biodegradation at ambient temperature in soil for PISOX (co)polyesters. Results show that the lag phase of PISOX (co)polyester biodegradation varies from 0 to 7 weeks. All (co)polyesters undergo over 80% mineralization within 180 days (faster than the cellulose reference) except one composition with the cyclic codiol 1,4-cyclohexanedimethanol (CHDM). Their relatively fast degradability is independent of the type of noncyclic codiol and results from facile nonenzymatic hydrolysis of oxalate ester bonds (especially oxalate isosorbide bonds), which mostly hydrolyzed completely within 180 days. On the other hand, partially replacing oxalate with terephthalate units enhances the polymer's resistance to hydrolysis and its biodegradability in soil. Our study demonstrates the potential for tuning PISOX copolyester structures to design biodegradable plastics with improved thermal, mechanical, and barrier properties.

Complete degradation of PET waste using a thermophilic microbe-enzyme system

Enzymatic degradation has been proposed as a suitable solution for addressing PET pollution, but approximately 10 % of PET is left as nonbiodegradable. Microbes can completely degrade PET at the gram level per year. Based on the complementary benefits of microbes and enzymes, a microbe-enzyme system was created to completely degrade PET. Here, a thermophilic microbe-enzyme (TME) system composed of Bacillus thermoamylovorans JQ3 and leaf-branch compost cutinase variant (ICCG) was used to demonstrate the synergistic degradation of PET, enabling 100 % degradation of PET waste at a high PET loading level (360 g/L). Six endogenous PET hydrolases of strain JQ3 were discovered by employing an ester bond hydrolysis function-first genome mining (EGM) strategy and first successfully expressed in E. coli. These hydrolases could release TPA as the final product from PET and preferentially degraded BHET instead of MHET. Of these, carboxylesterase 39_5 and ICCG could degrade PET in a synergistic manner to generate 50 μM of TPA, which was greater than the sum of the individual treatments. Finally, the degradation pathway of the TME system was speculated to include biofilm formation, PET degradation and utilization. The successful implementation of this study rendered a scale-up degradation feasible of PET at a lower cost.

Fucanases Related to the GH107 Family from Members of the PVC Superphylum

The glycoside hydrolase 107 (GH107) family includes fucanase enzymes from only two bacterial phyla, Bacteroidota and Pseudomonadota. The goal of this work was to explore the diversity of putative fucanase enzymes related to this family in organisms of the PVC superphylum (Planctomycetota, Verrucomicrobiota, Chlamydiota), in order to expand our knowledge of the fucoidan-degrading potential in this ecologically and biotechnologically relevant group. Using hidden Markov model- and peptide-based annotation tools, 26 GH107 homolog sequences were identified in metagenome and genome datasets. The sequences formed two distinct clusters in a phylogenetic analysis, only one including members of the GH107 family. The endo-acting fucoidan degrading activity was confirmed in an enzyme included in the most divergent cluster. The fucanase, which probably originated in an uncultured planctomycete from the sampled subantarctic sediments, was cloned and expressed in Escherichia coli. The enzyme catalyzed the rapid hydrolysis of internal glycosidic bonds of fucoidan from Macrocystis pyrifera, a macroalgae species abundant at the site. It was active in a wide range of temperatures (5–45 °C), salinities (9.5–861 mM NaCl), and pH values (4.5–9), mainly producing sulfated α-(1,3)-linked fuco-oligosaccharides of various lengths. The PVC superphylum represents a promising source of fucanase enzymes with various biotechnological applications.

Supramolecular Hydrolase Mimics in Equilibrium and Kinetically Trapped States

AbstractThe folding of proteins into intricate three‐dimensional structures to achieve biological functions, such as catalysis, is governed by both kinetic and thermodynamic controls. The quest to design artificial enzymes using minimalist peptides seeks to emulate supramolecular structures existing in a catalytically active state. Drawing inspiration from the nuanced process of protein folding, our study explores the enzyme‐like activity of amphiphilic peptide nanosystems in both equilibrium and non‐equilibrium states, featuring the formation of supramolecular nanofibrils and nanosheets. In contrast to thermodynamically stable nanosheets, the kinetically trapped nanofibrils exhibit dynamic characteristics (e.g., rapid molecular exchange and relatively weak intermolecular packing), resulting in a higher hydrolase‐mimicking activity. We emphasize that a supramolecular microenvironment characterized by an optimal local polarity, microviscosity, and β‐sheet hydrogen bonding is conducive to both substrate binding and ester bond hydrolysis. Our work underscores the pivotal role of both thermodynamic and kinetic control in impacting biomimetic catalysis and sheds a light on the development of artificial enzymes.

Supramolecular Hydrolase Mimics in Equilibrium and Kinetically Trapped States.

The folding of proteins into intricate three-dimensional structures to achieve biological functions, such as catalysis, is governed by both kinetic and thermodynamic controls. The quest to design artificial enzymes using minimalist peptides seeks to emulate supramolecular structures existing in a catalytically active state. Drawing inspiration from the nuanced process of protein folding, our study explores the enzyme-like activity of amphiphilic peptide nanosystems in both equilibrium and non-equilibrium states, featuring the formation of supramolecular nanofibrils and nanosheets. In contrast to thermodynamically stable nanosheets, the kinetically trapped nanofibrils exhibit dynamic characteristics (e.g., rapid molecular exchange and relatively weak intermolecular packing), resulting in a higher hydrolase-mimicking activity. We emphasize that a supramolecular microenvironment characterized by an optimal local polarity, microviscosity, and β-sheet hydrogen bonding is conducive to both substrate binding and ester bond hydrolysis. Our work underscores the pivotal role of both thermodynamic and kinetic control in impacting biomimetic catalysis and sheds a light on the development of artificial enzymes.

Impact of Point Defects, External Surfaces Sites, and Si/Al Ratio on Al–O Bonds Hydrolysis Kinetics at the Initiation of Faujasite Dealumination

Impact of Point Defects, External Surfaces Sites, and Si/Al Ratio on Al–O Bonds Hydrolysis Kinetics at the Initiation of Faujasite Dealumination

Lubricating Microneedles System with Multistage Sustained Drug Delivery for the Treatment of Osteoarthritis.

Osteoarthritis (OA) is a typical joint degenerative disease that is prevalent worldwide and significantly affects the normal activities of patients. Traditional treatments using diclofenac (DCF) as an anti-inflammatory drug by oral administration and transdermal delivery have many inherent deficiencies. In this study, a lubricating microneedles (MNs) system for the treatment of osteoarthritis with multistage sustained drug delivery and great reduction in skin damage during MNs penetration is developed. The bilayer dissolvable MNs system, namely HA-DCF@PDMPC, is prepared by designating the composite material of hyaluronic acid (HA) and covalently conjugated drug compound (HA-DCF) as the MNs tips and then modifying the surface of MNs tips with a self-adhesive lubricating copolymer (PDMPC). The MNs system is designed to achieve sustained drug release of DCF via ester bond hydrolysis, physical diffusion from MNs tips, and breakthrough of lubrication coating. Additionally, skin damage is reduced due to the presence of the lubrication coating on the superficial surface. Therefore, the lubricating MNs with multistage sustained drug delivery show good compliance as a transdermal patch for OA treatment, which is validated from anti-inflammatory cell tests and therapeutic animal experiments, down-regulating the expression levels of pro-inflammatory factors and alleviating articular cartilage destruction.

Effects of Activation Barriers on Quenching to Stabilize Prebiotic Chemical Systems.

We have previously shown in model studies that rapid quenches of systems of monomers interacting to form polymer chains can fix nonequilibrium chemistries with some lifelike properties. We suggested that such quenching processes might have occurred at very high rates on early Earth, giving an efficient mechanism for natural sorting through enormous numbers of nonequilibrium chemistries from which the most lifelike ones could be naturally selected. However, the model used for these studies did not take account of activation barriers to polymer scission (peptide bond hydrolysis in the case of proteins). Such barriers are known to exist and are expected to enhance the quenching effect. Here, we introduce a modified model which takes activation barriers into account and we compare the results to data from experiments on quenched systems of amino acids. We find that the model results turn out to be sensitive to the width of the distribution of barrier heights but quite insensitive to its average value. The results of the new model are in significantly better agreement with the experiments than those found using our previous model. The new parametrization of the model only requires one new parameter and the parametrization is more physical than the previous one, providing a chemical interpretation of the parameter p in our previous models. Within the model, a characteristic temperature Tc emerges such that if the temperature of the hot stage is above Tc and the temperature of the cold stage is below it, then the 'freezing out', in a quench, of a disequilibrium ensemble of long polymers is expected. We discuss the possible relevance of this to models of the origin of life in emissions from deep ocean rifts.

A Broad-Spectrum α-Glucosidase of Glycoside Hydrolase Family 13 from Marinovum sp., a Member of the Roseobacter Clade.

Glycoside hydrolases (GHs) are a diverse group of enzymes that catalyze the hydrolysis of glycosidic bonds. The Carbohydrate-Active enZymes (CAZy) classification organizes GHs into families based on sequence data and function, with fewer than 1% of the predicted proteins characterized biochemically. Consideration of genomic context can provide clues to infer possible enzyme activities for proteins of unknown function. We used the MultiGeneBLAST tool to discover a gene cluster in Marinovum sp., a member of the marine Roseobacter clade, that encodes homologues of enzymes belonging to the sulfoquinovose monooxygenase pathway for sulfosugar catabolism. This cluster lacks a gene encoding a classical family GH31 sulfoquinovosidase candidate, but which instead includes an uncharacterized family GH13 protein (MsGH13) that we hypothesized could be a non-classical sulfoquinovosidase. Surprisingly, recombinant MsGH13 lacks sulfoquinovosidase activity and is a broad-spectrum α-glucosidase that is active on a diverse array of α-linked disaccharides, including maltose, sucrose, nigerose, trehalose, isomaltose, and kojibiose. Using AlphaFold, a 3D model for the MsGH13 enzyme was constructed that predicted its active site shared close similarity with an α-glucosidase from Halomonas sp. H11 of the same GH13 subfamily that shows narrower substrate specificity.

Brazilin-Ce nanoparticles attenuate inflammation by de/anti-phosphorylation of IKKβ

Inflammation is associated with a series of diseases like cancer, cardiovascular disease and infection, and phosphorylation/dephosphorylation modification of proteins are important in inflammation regulation. Here we designed and synthesized a novel Brazilin-Ce nanoparticle (BX-Ce NPs) using Brazilin, which has been used for anti-inflammation in cardiovascular diseases but with narrow therapeutic window, and Cerium (IV), a lanthanide which has the general activity in catalyzing the hydrolysis of phosphoester bonds, to conferring de/anti-phosphorylation of IKKβ. We found that BX-Ce NPs specifically bound to Asn225 and Lys428 of IKKβ and inhibited its phosphorylation at Ser181, contributing to appreciably anti-inflammatory effect in cellulo (IC50 = 2.5 μM). In vivo mouse models of myocardial infarction and sepsis also showed that the BX-Ce NPs significantly ameliorated myocardial injury and improved survival in mice with experimental sepsis through downregulating phosphorylation of IKKβ. These findings provided insights for developing metal nanoparticles for guided ion interfere therapy, particularly synergistically target de/anti-phosphorylation as promising therapeutic agents for inflammation and related diseases.

Smart zwitterionic coatings with precise pH-responsive antibacterial functions for bone implants to combat bacterial infections.

Hydrophilic antifouling coatings based on zwitterionic polymers have been widely applied for the surface modification of bone implants to combat biofilm formation and reduce the likelihood of implant-related infections. However, their long-term effectiveness is significantly limited by the lack of effective and precise antibacterial activity. Here, a pH-responsive smart zwitterionic antibacterial coating (PSB/GS coating) was designed and robustly fabricated onto titanium-base bone implants by using a facile two-step method. First, dopamine (DA) and a poly(sulfobetaine methacrylate-co-dopamine methacrylamide) (PSBDA) copolymer were deposited on implants via mussel-inspired surface chemistry, resulting in a hydrophilic base coating with abundant catechol residues. Next, an amino-rich antibiotic, gentamicin sulfate (GS), was covalently linked to the coating through the formation of acid-sensitive Schiff base bonds between the amine groups of GS and the catechol residues present in both the zwitterionic polymer and the DA component. During the initial implantation period, the hydrophilic zwitterionic polymers demonstrated the desired anti-fouling properties that could effectively reduce protein and bacterial adhesion by over 90%. With time, the bacterial proliferation led to a decrease in the microenvironment pH value, resulting in the hydrolysis of the acid-sensitive Schiff base bonds, thereby releasing GS on demand and effectively enhancing the anti-biofilm properties of coatings. Benefiting from this synergistic antifouling and smart antibacterial activities, the PSB/GS coating exerted an excellent anti-infective activity in both in vivo preoperative and postoperative infection rat models. This proposed facile yet effective coating strategy is expected to provide a promising solution to combat bone implant-related infections.

Effect of multi arm-PEG-NHS (polyethylene glycol n-hydroxysuccinimide) branching on cell adhesion to modified decellularized bovine and porcine pericardium.

Implanting physical barrier materials to separate wounds from their surroundings is a promising strategy for preventing postoperative adhesions. Herein, we develop a material that switches from an anti-adhesive surface to an adhesive surface, preventing adhesion in the early stage of transplantation and then promoting recellularization. In this study, 2-arm, 4-arm, and 8-arm poly(ethylene glycol) succinimidyl glutarate (2-, 4-, 8-arm PEG-NHS) were used to modify the surface of decellularized porcine and bovine pericardium. The number of free amines on the surface of each material significantly decreased following modification regardless of the reaction molar ratio of NH2 and NHS, the number of PEG molecule branches, and the animal species of the decellularized tissue. The structure and mechanical properties of the pericardium were maintained after modification with PEG molecules. The time taken for the PEG molecules to detach through hydrolysis of the ester bonds differed between the samples, which resulted in different cell repulsion periods. By adjusting the reaction molar ratio, the number of PEG molecule branches, and the animal species of the decellularized pericardium, the duration of cell repulsion can be controlled and is expected to provide an anti-adhesion material for a variety of surgical procedures.

Optimization of Protease Activity byBacillus haynesiiBK1H Using Response Surface Methodology

Proteases are enzymes that catalyze the hydrolysis of peptide bonds into oligopeptides and amino acids. Previous bacterial studies reported that eight proteolytic isolates had been isolated from Bledug Kuwu mud, Central Java. One of these isolates is BK1H which has a proteolytic index of 2.960 making it possible to be studied further. In this study, optimization of the protease activity of BK1H was carried out using 3 factors namely temperature, pH, and divalent metal cations. This research was conducted through several stages, (1) Bacterial culture regeneration, (2) Protease fermentation using the SmF method, (3) Determination of the type of protease, (4) One Factor at a Time (OFAT), (5) Plackett-Burman Design (PBD), (6) Response Surface Methodology-Central Composite Design (RSM-CCD), and (7) Confirmation of RSM-CCD optimization results on experimental results. OFAT experiment results showed the lowest activity and the highest activity was obtained at 37°C and 57°C; pH 6 and 8; and CaCl2 0.5 and 1.0 mM. The significance test of the 2 factors namely temperature and pH has a p value <0.05, which indicates that these factors have a significant effect on protease activity. The optimum factor value in the RSM-CCD has a temperature of 63.10°C and pH 10.82, with the predicted activity of 149.910 U/mL, while the experimental results have activity of 157.630 ± 16.240 U/mL.

A chalcone-based ESIPT and AIE fluorophore for β-gal imaging in living cells.

β-Galactosidase (β-gal), which is responsible for the hydrolysis of the glycosidic bond of lactose to galactose, has been recognized as an important biomarker of cell or organism status, especially cell senescence and primary ovarian cancer. Extensive efforts have been devoted to develop probes for detecting and visualizing β-gal in cells. Herein, a fluorescent probe gal-HCA which possesses both excited-state intramolecular proton transfer (ESIPT) and aggregation-induced emission (AIE) properties was prepared to monitor β-gal in living cells. The probe consists of 2-hydroxy-4'-dimethylamino-chalcone (HCA) capped with a D-galactose group. The cleavage of the glycosidic bond in gal-HCA triggered by β-gal releases HCA, which results in a significant bathochromic shift in fluorescence from 532 to 615 nm. The probe exhibited high selectivity and sensitivity toward β-gal with a detection limit as low as 0.0122 U mL-1. The confocal imaging investigation demonstrated the potential of gal-HCA in monitoring the endocellular overexpressed β-gal in senescent cells and ovarian cancer cells. This study provides a straightforward approach for the development of fluorescent probes to monitor β-gal and detection of β-gal-associated diseases.

On the biocatalytic synthesis of silicone polymers.

Polysiloxanes, with poly(dimethyl)siloxane (PDMS) being the most common example, are widely used in various industrial and consumer applications due to the physicochemical properties imparted by their Si-O-Si backbone structure. The conventional synthesis of PDMS involves the hydrolysis of dichlorodimethylsilane, which raises environmental concerns due to the usage of chlorinated compounds. Herein, a biocatalytic approach for PDMS synthesis is demonstrated using silicatein-α (Silα), an enzyme from marine sponges that is known to catalyse the hydrolysis and condensation of Si-O bonds. Using dialkoxysilane precursors, it was found that Silα catalyses the formation of PDMS in non-aqueous media, yielding polymers with higher molecular weights (approximately 1000-2000 Da). However, on prolonged exposure, the gradual degradation of the polymers was also observed. Overall these observations indicate that Silα catalyses the formation polysiloxanes, demonstrating the potential of biocatalysis for more sustainable polysiloxane production.

The identification and expression analysis of walnut Acyl-ACP thioesterases.

Walnuts (Juglans regia L.), renowned for their nutritional potency, are a rich source of unsaturated fatty acids. Their regular intake plays a pivotal role in health maintenance and recuperation from a myriad of ailments. Fatty acyl-acyl carrier protein thioesterases, which orchestrate the hydrolysis of acyl-ACP thioester bonds, thereby yielding fatty acids of varying chain lengths, are instrumental in augmenting plant fatty acid content and modulating the balance between saturated and unsaturated fatty acids. Despite some investigative efforts into the synthesis and metabolic pathways of fatty acids in walnuts, our comprehension of Fat in walnuts remains rudimentary. This research undertook a comprehensive characterization of the JrFat family, predicated on the complete genome sequence of walnuts, leading to the identification of 8 JrFat genes and an exploration of their protein physicochemical properties. Utilizing Arabidopsis and soybean Fat genes as outgroups, JrFat genes can be categorized into 5 distinct subgroups, three of which encompass a pair of homologous gene pairs. These genes have demonstrated remarkable conservation throughout the evolutionary process, with highly analogous conserved base sequences. The promoter region of JrFats genes predominantly harbors light response and plant hormone response regulatory elements, with no discernible disparity in promoter elements among different JrFats. Predictive analyses indicate that JrFats proteins engage extensively with walnut fatty acid synthesis and metabolism-associated proteins. qRT-PCR analysis reveals an initial surge in the expression of JrFats during the development of walnut kernels, which either stabilizes or diminishes following the hard core period. Homologous gene pairs exhibit analogous expression patterns, and the expression trajectory of JrFats aligns with the dynamic accumulation of fatty acids in kernels. The expression of JrFatA2 exhibits a strong correlation with the content of Alpha-linolenic acid, while the expression of JrFatB2 is inversely correlated with the content of two saturated fatty acids. Collectively, these findings enrich our understanding of fatty acid synthesis and metabolism in walnuts and furnish gene resources for enhancing the content and ratio of fatty acids in walnuts.

Hydrolysis of amide bonds in dipeptides and nylon 6 over a ZrO2 catalyst

The amphoteric ZrO2 surface catalyzed the hydrolysis of various amide compounds: dipeptides into amino acids; small organic amides into the equimolar amount of carboxylic acids and amines; and nylon 6 into ε-caprolactam and ε-aminocaproic acid.

Structural basis of the activation of MARTX cysteine protease domain from Vibrio vulnificus.

The multifunctional autoprocessing repeat-in-toxin (MARTX) toxin is the primary virulence factor of Vibrio vulnificus displaying cytotoxic and hemolytic properties. The cysteine protease domain (CPD) is responsible for activating the MARTX toxin by cleaving the toxin precursor and releasing the mature toxin fragments. To investigate the structural determinants for inositol hexakisphosphate (InsP6)-mediated activation of the CPD, we determined the crystal structures of unprocessed and β-flap truncated MARTX CPDs of Vibrio vulnificus strain MO6-24/O in complex with InsP6 at 1.3 and 2.2Å resolution, respectively. The CPD displays a conserved domain with a central seven-stranded β-sheet flanked by three α-helices. The scissile bond Leu3587-Ala3588 is bound in the catalytic site of the InsP6-loaded form of the Cys3727Ala mutant. InsP6 interacts with the conserved basic cleft and the β-flap inducing the active conformation of catalytic residues. The β-flap of the post-CPD is flexible in the InsP6-unbound state. The structure of the CPD Δβ-flap showed an inactive conformation of the catalytic residues due to the absence of interaction between the active site and the β-flap. This study confirms the InsP6-mediated activation of the MARTX CPDs in which InsP6-binding induces conformational changes of the catalytic residues and the β-flap that holds the N terminus of the CPD in the active site, facilitating hydrolysis of the scissile bond.

Design strategies and biological applications of β-galactosidase fluorescent sensor in ovarian cancer research and beyond.

Beta-galactosidase (β-galactosidase), a lysosomal hydrolytic enzyme, plays a critical role in the catalytic hydrolysis of glycosidic bonds, leading to the conversion of lactose into galactose. This hydrolytic enzyme is used as a biomarker in various applications, including enzyme-linked immunosorbent assays (ELISAs), gene expression studies, tuberculosis classification, and in situ hybridization. β-Galactosidase abnormalities are linked to various diseases, such as ganglioside deposition, primary ovarian cancer, and cell senescence. Thus, effective detection of β-galactosidase activity may aid disease diagnoses and treatment. Activatable optical probes with high sensitivity, specificity, and spatiotemporal resolution imaging capabilities have become powerful tools for visualization and real time tracking in vivo in the past decade. This manuscript reviews the sensing mechanism, molecular design strategies, and advances of fluorescence probes in the biological application of β-galactosidase, particularly in the field of ovarian cancer research. Current challenges in tracking β-galactosidase and future directions are also discussed.

Phosphoester bond hydrolysis by a discrete zirconium-oxo cluster: mechanistic insights into the central role of the binuclear ZrIV-ZrIV active site.

Effective degradation of non-natural phosphate triesters (PTs) widely used in pesticides and warfare agents is of paramount relevance for human and environmental safety, particularly under acidic conditions where they are highly stable. Here, we present a detailed reactivity and mechanistic study pioneering discrete {Zr6O8} clusters, which are commonly employed as building blocks for Zr-MOFs and as non-classical soluble coordination compounds for the degradation of PTs using the pesticide ethyl paraoxon as a model. Combined computational studies, mechanistic experiments, and EXAFS analysis show that the reactivity of these clusters arises from their ZrIV-ZrIV bimetallic sites, which hydrolyze ethyl paraoxon under acidic conditions through an intramolecular pathway. Remarkably, the energetics of the reaction is dependent on the protonation state of the active sites, and a weakly acidic medium favors the reaction. Moreover, catalyst stability allowed for its recovery and reuse. Such a mechanism is in close analogy to enzymatic reactions and different from that previously reported for Zr-MOFs. These findings outline the potential of MIV-MIV active sites for PT degradation under challenging aqueous acidic conditions and contribute to the development of bioinspired catalysts and materials.