Hydrolysis Of Bond Research Articles

Exploring the Structurally Conserved Regions and Functional Significance in Bacterial N-Terminal Nucleophile (Ntn) Amide-Hydrolases.

The initial adoption of penicillin as an antibiotic marked the start of exploring other compounds essential for pharmaceuticals, yet resistance to penicillins and their side effects has compromised their efficacy. The N-terminal nucleophile (Ntn) amide-hydrolases S45 family plays a key role in catalyzing amide bond hydrolysis in various compounds, including antibiotics like penicillin and cephalosporin. This study comprehensively analyzes the structural and functional traits of the bacterial N-terminal nucleophile (Ntn) amide-hydrolases S45 family, covering penicillin G acylases, cephalosporin acylases, and D-succinylase. Utilizing structural bioinformatics tools and sequence analysis, the investigation delineates structurally conserved regions (SCRs) and substrate binding site variations among these enzymes. Notably, sixteen SCRs crucial for substrate interaction are identified solely through sequence analysis, emphasizing the significance of sequence data in characterizing functionally relevant regions. These findings introduce a novel approach for identifying targets to enhance the biocatalytic properties of N-terminal nucleophile (Ntn) amide-hydrolases, while facilitating the development of more accurate three-dimensional models, particularly for enzymes lacking structural data. Overall, this research advances our understanding of structure-function relationships in bacterial N-terminal nucleophile (Ntn) amide-hydrolases, providing insights into strategies for optimizing their enzymatic capabilities.

Horizontally transferred glycoside hydrolase 26 may aid hemipteran insects in plant tissue digestion

Glycoside hydrolases are enzymes that break down complex carbohydrates into simple sugars by catalyzing the hydrolysis of glycosidic bonds. There have been multiple instances of adaptive horizontal gene transfer of genes belonging to various glycoside hydrolase families from microbes to insects, as glycoside hydrolases can metabolize constituents of the carbohydrate-rich plant cell wall. In this study, we characterize the horizontal transfer of a gene from the glycoside hydrolase family 26 (GH26) from bacteria to insects of the order Hemiptera. Our phylogenies trace the horizontal gene transfer to the common ancestor of the superfamilies Pentatomoidea and Lygaeoidea, which include stink bugs and seed bugs. After horizontal transfer, the gene was assimilated into the insect genome as indicated by the gain of an intron, and a eukaryotic signal peptide. Subsequently, the gene has undergone independent losses and expansions in copy number in multiple lineages, suggesting an adaptive role of GH26s in some insects. Finally, we measured tissue-level gene expression of multiple stink bugs and the large milkweed bug using publicly available RNA-seq datasets. We found that the GH26 genes are highly expressed in tissues associated with plant digestion, especially in the principal salivary glands of the stink bugs. Our results are consistent with the hypothesis that this horizontally transferred GH26 was co-opted by the insect to aid in plant tissue digestion and that this HGT event was likely adaptive.

Marine copepod culture as a potential source of bioplastic-degrading microbiome: The case of poly(butylene succinate-co-adipate)

The poly(butylene succinate-co-adipate) (PBSA) is emerging as environmentally sustainable polyester for applications in marine environment. In this work the capacity of microbiome associated with marine plankton culture to degrade PBSA, was tested. A taxonomic and functional characterization of the microbiome associated with the copepod Acartia tonsa, reared in controlled conditions, was analysed by 16S rDNA metabarcoding, in newly-formed adult stages and after 7 d of incubation. A predictive functional metagenomic profile was inferred for hydrolytic activities involved in bioplastic degradation with a particular focus on PBSA. The copepod-microbiome was also characterized in newly-formed carcasses of A. tonsa, and after 7 and 33 d of incubation in the plankton culture medium. Copepod-microbiome showed hydrolytic activities at all developmental stages of the alive copepods and their carcasses, however, the evenness of the hydrolytic bacterial community significantly increased with the time of incubation in carcasses. Microbial genera, never described in association with copepods: Devosia, Kordia, Lentibacter, Methylotenera, Rheinheimera, Marinagarivorans, Paraglaciecola, Pseudophaeobacter, Gaiella, Streptomyces and Kribbella sps., were retrieved. Kribbella sp. showed carboxylesterase activity and Streptomyces sp. showed carboxylesterase, triacylglycerol lipase and cutinase activities, that might be involved in PBSA degradation. A culturomic approach, adopted to isolate bacterial specimen from carcasses, led to the isolation of the bacterial strain, Vibrio sp. 01 tested for the capacity to promote the hydrolysis of the ester bonds. Granules of PBSA, incubated 82 d at 20 °C with Vibrio sp. 01, were characterized by scanning electron microscopy, infrared spectroscopy, thermogravimetric analysis, and differential scanning calorimetry, showing fractures compared to the control sample, and hydrolysis of ester bonds. These preliminary results are encouraging for further investigation on the ability of the microbiome associated with plankton to biodegrade polyesters, such as PBSA, and increasing knowledge on microorganisms involved in bioplastic degradation in marine environment.

A dual-site fluorescent probe for the detection of γ-glutamyl transpeptidase activity and its application in garlic

Developing convenient γ-glutamyl transpeptidase (GGT) activity detection methods is of great significance for soaking Laba garlic and human diseases detection. A dual-site fluorescent probe (probe 1) was developed for detection the activity of GGT. Probe 1 could recognize GGT by the enzymatic hydrolysis of peptide bond by GGT. There has a linear relationship between the fluorescence intensity of probe 1 at 416 nm and the activity of GGT. And the color of the probe solution gradually changed from colorless to blue with the increase of GGT activity under 365 nm ultraviolet light. Importantly, it has a linear relationship between the activity of GGT and the blue (B) value of probe solution photo. Therefore, probes can serve as a convenient tool for detecting GGT activity. More importantly, the probe has been successfully applied to detect of GGT activity in garlic.

Trypanosoma cruzi infection modulates secreted phospholipase A2 expression in the salivary glands of Rhodnius prolixus

Phospholipases A2 (PLA2) comprise a superfamily of enzymes that specifically catalyze hydrolysis of the ester bond at the sn-2 position of glycerophospholipids, generating lysophospholipids and fatty acids. In Rhodnius prolixus, one of the main vectors of the Chagas's disease etiologic agent Trypanosoma cruzi, it was previously shown that lysophosphatidylcholine, a bioactive lipid, found in the insect's saliva, contributes to the inhibition of platelet aggregation, and increases the production of nitric oxide, an important vasodilator. Due to its role in potentially generating LPC, here we studied the PLA2 present in the salivary glands of R. prolixus. PLA2 activity is approximately 100 times greater in the epithelium than in the contents of salivary glands. Our study reveals the role of the RpPLA2XIIA gene in the insect feeding performance and in the fatty acids composition of phospholipids extracted from the salivary glands. Knockdown of RpPLA2XIIA significantly altered the relative amounts of palmitic, palmitoleic, oleic and linoleic acids. A short-term decrease in the expression of RpPLA2III and RpPLA2XIIA in the salivary glands of R. prolixus was evident on the third day after infection by T. cruzi. Taken together, our results contribute to the understanding of the role of PLA2 in the salivary glands of hematophagous insects and show that the parasite is capable of modulating even tissues that are not colonized by it.

Effect of ph on migration patterns and degradation pathways of sulfamethazine in soil systems

Sulfonamide antibiotics (SAs) are widely used antimicrobial agents in livestock and aquaculture, and most of them entering the animal’s body will be released into the environment as prodrugs or metabolites, which ultimately affect human health through the food chain. Both acid deposition and salinization of soil may have an impact on the migration and degradation of antibiotics. Sulfamethazine (SM2), a frequently detected compound in agricultural soils, has a migration and transformation process in the environment that is closely dependent on environmental pH. Nevertheless, scarcely any studies have been conducted on the effect of soil pH changes on the environmental behavior of sulfamethazine. We analyzed the migration and degradation mechanisms of SM2 using simulation experiments and ultra-high performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UHPLC-Q-TOF-MS) techniques. The results showed that acidic conditions limited the vertical migration of sulfadimidine, and SM2 underwent different reaction processes under different pH conditions, including S-C bond breaking, S-N bond hydrolysis, demethylation, six-membered heterocyclic addition, methyl hydroxylation and ring opening. The study of the migration pattern and degradation mechanism of SM2 under different pH conditions can provide a solid theoretical basis for assessing the pollution risk of sulfamethazine degradation products under acid rain and saline conditions, and provide a guideline for remediation of antibiotic contamination, so as to better prevent, control and protect groundwater resources.

Mechanisms linking triclocarban biotransformation to functional response and antimicrobial resistome evolution in wastewater treatment systems

Evaluating the role of antimicrobials biotransformation in the regulation of metabolic functions and antimicrobial resistance evolution in wastewater biotreatment systems is crucial to ensuring water security. However, the associated mechanisms remain poorly understood. Here, we investigate triclocarban (TCC, one of the typical antimicrobials) biotransformation mechanisms and the dynamic evolution of systemic function disturbance and antimicrobial resistance risk in a complex anaerobic hydrolytic acidification (HA)-anoxic (ANO)/oxic (O) process. We mined key functional genes involved in the TCC upstream (reductive dechlorination and amide bonds hydrolysis) and downstream (chloroanilines catabolism) biotransformation pathways by metagenomic sequencing. Acute and chronic stress of TCC inhibit the production of volatile fatty acids (VFAs), NH4+ assimilation, and nitrification. The biotransformation of TCC via a single pathway cannot effectively relieve the inhibition of metabolic functions (e.g., carbon and nitrogen transformation and cycling) and enrichment of antimicrobial resistance genes (ARGs). Importantly, the coexistence of TCC reductive dechlorination and hydrolysis pathways and subsequent ring-opening catabolism play a critical role for stabilization of systemic metabolic functions and partial control of antimicrobial resistance risk. This study provides new insights into the mechanisms linking TCC biotransformation to the dynamic evolution of systemic functions and risks, and highlights critical regulatory information for enhanced control of TCC risks in complex biotreatment systems.

The Power of Molecular Dynamics Simulations and Their Applications to Discover Cysteine Protease Inhibitors.

A large family of enzymes with the function of hydrolyzing peptide bonds, called peptidases or cysteine proteases (CPs), are divided into three categories according to the peptide chain involved. CPs catalyze the hydrolysis of amide, ester, thiol ester, and thioester peptide bonds. They can be divided into several groups, such as papain-like (CA), viral chymotrypsin-like CPs (CB), papainlike endopeptidases of RNA viruses (CC), legumain-type caspases (CD), and showing active residues of His, Glu/Asp, Gln, Cys (CE). The catalytic mechanism of CPs is the essential cysteine residue present in the active site. These mechanisms are often studied through computational methods that provide new information about the catalytic mechanism and identify inhibitors. The role of computational methods during drug design and development stages is increasing. Methods in Computer-Aided Drug Design (CADD) accelerate the discovery process, increase the chances of selecting more promising molecules for experimental studies, and can identify critical mechanisms involved in the pathophysiology and molecular pathways of action. Molecular dynamics (MD) simulations are essential in any drug discovery program due to their high capacity for simulating a physiological environment capable of unveiling significant inhibition mechanisms of new compounds against target proteins, especially CPs. Here, a brief approach will be shown on MD simulations and how the studies were applied to identify inhibitors or critical information against cysteine protease from several microorganisms, such as Trypanosoma cruzi (cruzain), Trypanosoma brucei (rhodesain), Plasmodium spp. (falcipain), and SARS-CoV-2 (Mpro). We hope the readers will gain new insights and use our study as a guide for potential compound identifications using MD simulations.

Investigation of hydrothermal depolymerization of lignite under different conditions by 13C NMR spectroscopy

Efficient depolymerization of lignite under mild conditions is the key to realizing its low carbon conversion and high value utilization. This study focuses on three Chinese lignites: Xilinguole lignite (XL), Xiaolongtan lignite (XLT), and Zhaotong lignite (ZT), investigating the inherent structures effect on their depolymerization processes when subjected to alkali depolymerization (AD) and oxidation depolymerization (OD) under hydrothermal condition. The parent lignites and their depolymerized products were characterized by solid 13C NMR, FTIR, TGA, and elemental analysis. It was found that both AD and OD effectively broke down the macromolecular structure of lignite into humic acid (HA) and small molecular products including water-soluble components, with the highest depolymerization activity observed for ZT followed by XLT and XL, regardless of the method used. Notably, by AD at 80 oC, 91.4 % of ZT was depolymerized, producing 69.4 % of HA as the major product, while higher temperatures were required to efficiently depolymerize XLT and XL by either AD or OD. More than 80% of XLT and XL can be converted by AD at 200 oC, yielding 54.8 % and 52.9 % of HA, respectively. OD at 140 oC resulted in a 57.7 % conversion of XL and an HA yield of 50.2 %. Characterization of the products demonstrated that alkali addition significantly promotes lignite depolymerization by breaking oxygen-containing linkages such as ether and ester bonds, with ether bond hydrolysis occurring predominantly at high temperatures. High-temperature AD of lignite is dominated by the cleavage of oxygen-containing linkages, whereas OD at lower temperatures mainly depolymerizes lignite through oxy-cracking of C−C and C−O weak linkages, reducing carboxyl decomposition to achieve higher HA yields. These findings offer a new perspective on the low-carbon utilization of lignite.

A new method for amino acid geochronology of the shell of the bivalve mollusc Arctica islandica

Abstract. The bivalve mollusc Arctica islandica can live for hundreds of years, and its shell has provided a valuable resource for sclerochronological studies and geochemical analyses for understanding palaeoenvironmental change. Shell specimens recovered from the seabed need to be dated in order to aid sample selection, but existing methods using radiocarbon dating or cross-dating are both costly and time-consuming. We have investigated amino acid geochronology (AAG) as a potential alternative means of providing a less costly and more efficient range-finding method. In order to do this, we have investigated the complex microstructure of the shells, as this may influence the application of AAG. Each of the three microstructural layers of A. islandica have been isolated and their protein degradation examined (amino acid concentration, composition, racemization, and peptide bond hydrolysis). The intra-crystalline protein fraction was successfully extracted following oxidation treatment for 48 h, and high-temperature experiments at 140 °C established coherent breakdown patterns in all three layers, but the inner portion of the outer shell layer (iOSL) was the most appropriate component due to practicalities. Sampling of the iOSL layer in Holocene shells from early and late ontogeny (over 100–400 years) showed that the resolution of AAG is too low in A. islandica for within-shell age resolution. However, analysis of 52 subfossil samples confirmed that this approach could be used to establish a relative geochronology for this biomineral throughout the whole of the Quaternary. In the late Holocene the temporal resolution is ∼1500–2000 years. Relative dating of 160 dredged shells of unknown age was narrowed down using AAG as a range finder, showing that a collection of shells from Iceland and the North Sea covered the middle Holocene, late Holocene, later and post-medieval (1171–1713 CE), and modern day. This study confirms the value of A. islandica as a reliable material for range finding and for dating Quaternary deposits.

ASCC1 structures and bioinformatics reveal a novel helix-clasp-helix RNA-binding motif linked to a two-histidine phosphodiesterase

Activating signal co-integrator complex 1 (ASCC1) acts with ASCC-ALKBH3 complex in alkylation damage responses. ASCC1 uniquely combines two evolutionarily ancient domains: nucleotide-binding K-Homology (KH) (associated with regulating splicing, transcriptional, and translation) and two-histidine phosphodiesterase (PDE) (associated with hydrolysis of cyclic nucleotide phosphate bonds). Germline mutations link loss of ASCC1 function to spinal muscular atrophy with congenital bone fractures 2 (SMABF2). Herein analysis of The Cancer Genome Atlas (TCGA) suggests ASCC1 RNA overexpression in certain tumors correlates with poor survival, Signatures 29 and 3 mutations, and genetic instability markers. We determined crystal structures of Alvinella pompejana (Ap) ASCC1 and Human (Hs) PDE domain revealing high resolution details and features conserved over 500 million years of evolution. Extending understanding of the KH domain Gly-X-X-Gly sequence motif, we define a novel structural Helix-Clasp-Helix (HCH) nucleotide binding motif and show ASCC1 sequence–specific binding to CGCG-containing RNA. The V-shaped PDE nucleotide binding channel has two His-Φ-Ser/Thr-Φ (HXT) motifs (Φ being hydrophobic) positioned to initiate cyclic phosphate bond hydrolysis. A conserved atypical active-site histidine torsion angle implies a novel PDE substrate. Flexible active site loop and arginine-rich domain linker appear regulatory. Small angle X-ray scattering (SAXS) revealed aligned KH-PDE RNA binding sites with limited flexibility in solution. Quantitative evolutionary bioinformatic analyses of disease and cancer-associated mutations support implied functional roles for RNA binding, phosphodiesterase activity, and regulation. Collective results inform ASCC1 roles in transactivation and alkylation damage responses, its targeting by structure-based inhibitors, and how ASCC1 mutations may impact inherited disease and cancer.

Rapid and Definitive Identification of Cyclic Peptide Soft Spots by Isotope-Labeled Reductive Dimethylation and Mass Spectrometry Fragmentation.

Cyclic peptides are an emerging therapeutic modality over the past few decades. To identify drug candidates with sufficient proteolytic stability for oral administration, it is critical to pinpoint the amide bond hydrolysis sites, or soft spots, to better understand their metabolism and provide guidance on further structure optimization. However, the unambiguous characterization of cyclic peptide soft spots remains a significant challenge during early stage discovery studies, as amide bond hydrolysis forms a linearized isobaric sequence with the addition of a water molecule, regardless of the amide hydrolysis location. In this study, an innovative strategy was developed to enable the rapid and definitive identification of cyclic peptide soft spots by isotope-labeled reductive dimethylation and mass spectrometry fragmentation. The dimethylated immonium ion with enhanced MS signal at a distinctive m/z in MS/MS fragmentation spectra reveals the N-terminal amino acid on a linearized peptide sequence definitively and, thus, significantly simplifies the soft spot identification workflow. This approach has been evaluated to demonstrate the potential of isotope-labeled dimethylation to be a powerful analytical tool in cyclic peptide drug discovery and development.

Plant lipases – molecular structure, role in ontogeny and biotechnological potential

Lipases are enzymes commonly found in microorganisms, fungi, plants and animals. Their main function in cell metabolism is the hydrolysis (lipolysis) of ester bonds between fatty acids and glycerol in mono-, di- and triacylglycerols. In plants, lipases play an important role in ontogeny, participating in both vegetative development and generative stages. These enzymes may also be a component of plant responses to biotic and abiotic stresses. Based on the similarity of the amino acid sequence and vacuolar localization of some plant lipases to yeast Atg15, we present a hypothesis about the participation of lipases in autophagy (precisely, in the degradation of the autophagic body) in plants. Despite the narrow substrate specificity and the type of reactions catalysed in cells, lipases find numerous biotechnological applications. The physicochemical features of lipases, which determine, for example, wide substrate specificity in vitro or high stability in a wide range of pH and temperature, make these enzymes the subject of applied research, and plant lipases show an increasing potential in this area of science and industry.

A novel GH3-β-glucosidase from soda lake metagenomic libraries with desirable properties for biomass degradation.

Beta-glucosidases catalyze the hydrolysis of the glycosidic bonds of cellobiose, producing glucose, which is a rate-limiting step in cellulose biomass degradation. In industrial processes, β-glucosidases that are tolerant to glucose and stable under harsh industrial reaction conditions are required for efficient cellulose hydrolysis. In this study, we report the molecular cloning, Escherichia coli expression, and functional characterization of a β-glucosidase from the gene, CelGH3_f17, identified from metagenomics libraries of an Ethiopian soda lake. The CelGH3_f17 gene sequence contains a glycoside hydrolase family 3 catalytic domain (GH3). The heterologous expressed and purified enzyme exhibited optimal activity at 50°C and pH 8.5. In addition, supplementation of 1M salt and 300mM glucose enhanced the β-glucosidase activity. Most of the metal ions and organic solvents tested did not affect the β-glucosidase activity. However, Cu2+ and Mn2+ ions, Mercaptoethanol and Triton X-100 reduce the activity of the enzyme. The studied β-glucosidase enzyme has multiple industrially desirable properties including thermostability, andalkaline, salt, and glucose tolerance.

Enhancing Xylanase Production from Aspergillus tamarii Kita and Its Application in the Bioconversion of Agro-Industrial Residues into Fermentable Sugars Using Factorial Design

The endo-1,4-β-xylanases (EC 3.2.1.8) are the largest group of hydrolytic enzymes that degrade xylan, the major component of hemicelluloses, by catalyzing the hydrolysis of glycosidic bonds β-1,4 in this polymer, releasing xylooligosaccharides of different sizes. Xylanases have considerable potential in producing bread, animal feed, food, beverages, xylitol, and bioethanol. The fungus Aspergillus tamarii Kita produced xylanases in Adams’ media supplemented with barley bagasse (brewer’s spent grains), a by-product from brewery industries. The culture extract exhibited two xylanase activities in the zymogram, identified by mass spectrometry as glycosyl hydrolase (GH) families 10 and 11 (GH 10 and GH 11). The central composite design (CCD) showed excellent predictive capacity for xylanase production (23.083 U mL−1). Additionally, other enzyme activities took place during the submerged fermentation. Moreover, enzymatic saccharification based on a mixture design (MD) of three different lignocellulosic residues was helpful in the production of fermentable sugars by the A. tamarii Kita crude extract.

Study on the mechanism of lignin and lignin-carbohydrate complex hydrolysis under alkaline conditions by density functional theory

Lignin hydrolyzes during alkali-heat pretreatment of lignocellulose, due to the cleavage of covalent linkages between lignin and lignin-carbohydrate complex. Various structure of lignin monomers are responsible of the complicated hydrolysis mechanism of lignin and lignin-carbohydrate complex. This study used density functional theory to reveal the hydrolysis mechanism of lignin with various substituents and lignin-carbohydrates complex with different linkages. The results indicated that the SN2 reaction was observed to take place in the lignin. Methoxy groups and methyl group had an insignificant influence on hydrolysis reaction pathway of lignin, whereas the presence of a methyl group on the α-carbon atom had a hindering effect on the nucleophilic attack during alkaline pretreatment. The lignin-carbohydrate complex with different linkage showed a significant difference in hydrolysis reaction pathway. Additionally, the reaction energy barrier of ester bond hydrolysis was lowest among the hydrolysis of ester bond, phenyl glycosidic bond, benzyl ether bond, γ-ester bond, coumarin ester bond and acetal bond under alkaline condition. This study provides valuable insights into the process control, reactor design, and performance enhancement for lignocellulose pretreatment.

Structural and Dynamic Features of the Recognition of 8-oxoguanosine Paired with an 8-oxoG-clamp by Human 8-oxoguanine-DNA Glycosylase.

8-oxoguanine (oxoG) is formed in DNA by the action of reactive oxygen species. As a highly mutagenic and the most common oxidative DNA lesion, it is an important marker of oxidative stress. Human 8-oxoguanine-DNA glycosylase (OGG1) is responsible for its prompt removal in human cells. OGG1 is a bifunctional DNA glycosylase with N-glycosylase and AP lyase activities. Aspects of the detailed mechanism underlying the recognition of 8-oxoguanine among numerous intact bases and its subsequent interaction with the enzyme's active site amino acid residues are still debated. The main objective of our work was to determine the effect (structural and thermodynamic) of introducing an oxoG-clamp in model DNA substrates on the process of 8-oxoG excision by OGG1. Towards that end, we used DNA duplexes modeling OGG1-specific lesions: 8-oxoguanine or an apurinic/apyrimidinic site with either cytidine or the oxoG-clamp in the complementary strand opposite to the lesion. It was revealed that there was neither hydrolysis of the N-glycosidic bond at oxoG nor cleavage of the sugar-phosphate backbone during the reaction between OGG1 and oxoG-clamp-containing duplexes. Possible structural reasons for the absence of OGG1 enzymatic activity were studied via the stopped-flow kinetic approach and molecular dynamics simulations. The base opposite the damage was found to have a critical effect on the formation of the enzyme-substrate complex and the initiation of DNA cleavage. The oxoG-clamp residue prevented the eversion of the oxoG base into the OGG1 active site pocket and impeded the correct convergence of the apurinic/apyrimidinic site of DNA and the attacking nucleophilic group of the enzyme. An obtained three-dimensional model of the OGG1 complex with DNA containing the oxoG-clamp, together with kinetic data, allowed us to clarify the role of the contact of amino acid residues with DNA in the formation of (and rearrangements in) the enzyme-substrate complex.

Development of Improved Spectrophotometric Assays for Biocatalytic Silyl Ether Hydrolysis.

Reported herein is the development of assays for the spectrophotometric quantification of biocatalytic silicon-oxygen bond hydrolysis. Central to these assays are a series of chromogenic substrates that release highly absorbing phenoxy anions upon cleavage of the sessile bond. These substrates were tested with silicatein, an enzyme from a marine sponge that is known to catalyse the hydrolysis and condensation of silyl ethers. It was found that, of the substrates tested, tert-butyldimethyl(2-methyl-4-nitrophenoxy)silane provided the best assay performance, as evidenced by the highest ratio of enzyme catalysed reaction rate compared with the background (uncatalysed) reaction. These substrates were also found to be suitable for detailed enzyme kinetics measurements, as demonstrated by their use to determine the Michaelis-Menten kinetic parameters for silicatein.

Molecular Insights into Sequence-Specific Protein Hydrolysis by a Soluble Zirconium-Oxo Cluster Catalyst.

The development of catalysts for controlled fragmentation of proteins is a critical undertaking in modern proteomics and biotechnology. {Zr6O8}-based metal-organic frameworks (MOFs) have emerged as promising candidates for catalysis of peptide bond hydrolysis due to their high reactivity, stability, and recyclability. However, emerging evidence suggests that protein hydrolysis mainly occurs on the MOF surface, thereby questioning the need for their highly porous 3D nature. In this work, we show that the discrete and water-soluble [Zr6O4(OH)4(CH3CO2)8(H2O)2Cl3]+ (Zr6) metal-oxo cluster (MOC), which is based on the same hexamer motif found in various {Zr6O8}-based MOFs, shows excellent activity toward selective hydrolysis of equine skeletal muscle myoglobin. Compared to related Zr-MOFs, Zr6 exhibits superior reactivity, with near-complete protein hydrolysis after 24 h of incubation at 60 °C, producing seven selective fragments with a molecular weight in the range of 3-15 kDa, which are of ideal size for middle-down proteomics. The high solubility and molecular nature of Zr6 allow detailed solution-based mechanistic/interaction studies, which revealed that cluster-induced protein unfolding is a key step that facilitates hydrolysis. A combination of multinuclear nuclear magnetic resonance spectroscopy and pair distribution function analysis provided insight into the speciation of Zr6 and the ligand exchange processes occurring on the surface of the cluster, which results in the dimerization of two Zr6 clusters via bridging oxygen atoms. Considering the relevance of discrete Zr-oxo clusters as building blocks of MOFs, the molecular-level understanding reported in this work contributes to the further development of novel catalysts based on Zr-MOFs.

Activation of glycosyl methylpropiolates by TfOH

Activation of glycosyl methylpropiolates by TfOH was investigated. Armed and superarmed glycosyl donors can be activated by use of 0.2 equivalent TfOH whereas 1.0 equivalent of TfOH was required for the activation of the disarmed glycosyl donors. All the glycosidations gave very good yields. The method is suitable for synthesis of glycosides and disaccharides and it may result in the hydrolysis of the interglycosidic bond if the sugar at the non-reducing end is armed or superarmed. These problems are not seen when gold-catalyzed activation procedures are invoked for the activation of glycosyl alkynoates.