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Offers a series of experiments which introduce students to the general principles of enzymology. The experiment demonstrates several basic enzyme properties and the chromatographic exercises provide an analysis of each enzymatic activity. Questions are also presented for extending discussion on the activities. (ML)

Discusses the importance of teaching about enzymes in chemistry. Mentions several applications of enzyme technology to other fields. Describes an experiment involving the immobilization of yeast cells as a biocatalyst for the ethanol production from glucose. Argues for more biotechnology to be integrated into basic chemistry courses. (TW)

Illustrates the 29 steps involved in the development of a model of a coordination polyhedron that represents the hexagonal closest packed structure. Points out it is useful in teaching stereochemistry. (TW)

Describes the kinetic mechanisms of reversible activators of enzymes that normally follow Michaelis-Menten kinetics. Examines reversible activators of the enzyme carboxypeptidase A (CPA). (TW)

Modeled after the program "Mastermind," this program teaches students the art of protein sequencing. The program (written in Turbo Pascal for the IBM PC, requiring 128K, a graphics adapter, and an 8070 mathematics coprocessor) generates a polypeptide whose sequence and length can be user-defined (for practice) or computer-generated (for grading). (JN)

Describes a simple high-performance liquid chromatography experiment for undergraduate biochemistry laboratories. The experiment illustrates the separation of polypeptides by a step gradient elution using a single pump instrument with no gradient attachments. Discusses instrumentation, analysis, a sample preparation, and results. (CW)

Describes an activity to simulate enzyme activity. Discusses the processes demonstrated and variations in the assembly line method. (CW)

Describes a three-week sequence to take undergraduate students through the study of enzyme kinetics in an integrated manner that reinforces the basic concepts of initial velocity and the effects of varying operational parameters. Discusses laboratory sessions and the use of a microcomputer in instruction. (CW)

Describes an experiment that provides a fundamental understanding of the kinetics of the enzyme papain. Discusses background, materials, procedures and results. Mentions analogous experiments that can be conducted with enzymatic contact-lens cleaning solutions. (CW)

Discusses a laboratory technique of enzyme purification by affinity chromatography as part of an undergraduate biochemical methodology course. Provides preparation details of the rat muscle homogenate and reagents. Proposes column requirements and assaying information. (MVL)

Describes a program which allows students to identify and characterize several kinetic inhibitory mechanisms. Uses the generic model of reversible inhibition of a monosubstrate enzyme but can be easily modified to run other models such as bisubstrate enzymes. Uses MS-DOS BASIC. (MVL)

Examines the influence of enzyme and substrate concentrations, pH, temperature, and inhibitors on catalytic activity. Follows the influence of different phosphate concentrations in the growth medium on enzyme activity. Studies regulation of enzyme synthesis by repression. Includes methodology for six experiments. (MVL)

Develops an experiment that could be done in two- to three-hour blocks and does not rely on cold room procedures for most of the purification. Describes the materials, methods, and results of the purification of bovine heart lactate dehydrogenase using ammonium sulfate fractionation, dialysis, and separation using affinity chromatography and elution. (YP)

A laboratory experiment designed as a model for studying enzyme activity with a basic spectrometer is presented. Included are background information, experimental procedures, and a discussion of probable results. Stressed is the value of the use of Nuclear Magnetic Resonance in biochemistry. (CW)

Describes a three-hour experiment designed to introduce students to chemistry of the angiotensis-converting enzyme, illustrate design of a quenched fluorescence substrate, and examine considerations necessary in designing a clinical assay. Includes background information on the biochemistry of hypertension, reagents/materials needed, procedures used, and typical results. (JM)

The continuous measurement of oxygen consumption in an enzymatic reaction is a frequent experimental fact and extremely important in the enzymatic activity of oxygenase. An electrochemical system, based on a polarographic method, has been developed to monitor the oxygen uptake. The system developed and electrode used are described. (JN)

Presented are procedures used to assay the activity of lipase during storage at three different temperatures. Since lipase solutions can decay even when refrigerated, it is recommended that the enzyme be freshly prepared prior to laboratory sessions in which they are used. (JN)

Describes an undergraduate biochemistry laboratory experiment on enzyme kinetics using the D-amino acid oxidase system and an ammonia electrode. Preparation of an ammonia standard curve, a sample preparation, and inhibition studies are discussed. (YP)

Diabetic foot ulcers (DFU) are chronic, refractory wounds caused by diabetic neuropathy, vascular disease, and bacterial infection, and have become one of the most serious and persistent complications of diabetes mellitus because of their high incidence and difficulty in healing. Its malignancy results from a complex microenvironment that includes a series of unfriendly physiological states secondary to hyperglycemia, such as recurrent infections, excessive oxidative stress, persistent inflammation, and ischemia and hypoxia. However, current common clinical treatments, such as antibiotic therapy, insulin therapy, surgical debridement, and conventional wound dressings all have drawbacks, and suboptimal outcomes exacerbate the financial and physical burdens of diabetic patients. Therefore, development of new, effective and affordable treatments for DFU represents a top priority to improve the quality of life of diabetic patients. In recent years, nanozymes-based diabetic wound therapy systems have been attracting extensive interest by integrating the unique advantages of nanomaterials and natural enzymes. Compared with natural enzymes, nanozymes possess more stable catalytic activity, lower production cost and greater maneuverability. Remarkably, many nanozymes possess multienzyme activities that can cascade multiple enzyme-catalyzed reactions simultaneously throughout the recovery process of DFU. Additionally, their favorable photothermal-acoustic properties can be exploited for further enhancement of the therapeutic effects. In this review we first describe the characteristic pathological microenvironment of DFU, then discuss the therapeutic mechanisms and applications of nanozymes in DFU healing, and finally, highlight the challenges and perspectives of nanozyme development for DFU treatment.

QS-21 is a potent vaccine adjuvant and remains the only saponin-based adjuvant that has been clinically approved for use in humans1,2. However, owing to the complex structure of QS-21, its availability is limited. Today, the supply depends on laborious extraction from the Chilean soapbark tree or on low-yielding total chemical synthesis3,4. Here we demonstrate the complete biosynthesis of QS-21 and its precursors, as well as structural derivatives, in engineered yeast strains. The successful biosynthesis in yeast requires fine-tuning of the host's native pathway fluxes, as well as the functional and balanced expression of 38 heterologous enzymes. The required biosynthetic pathway spans seven enzyme families-a terpene synthase, P450s, nucleotide sugar synthases, glycosyltransferases, a coenzyme A ligase, acyl transferases and polyketide synthases-from six organisms, and mimics in yeast the subcellular compartmentalization of plants from the endoplasmic reticulum membrane to the cytosol. Finally, by taking advantage of the promiscuity of certain pathway enzymes, we produced structural analogues of QS-21 using this biosynthetic platform. This microbial production scheme will allow for the future establishment of a structure-activity relationship, and will thus enable the rational design of potent vaccine adjuvants.

Introduction: Africa faces immense food and health insecurity challenges, a problem partly attributed to food loss and waste during postharvest handling and distribution. In the context of research to meet the sustainable development goals, this project specifically addressed the postharvest loss of the ripe indigenous eggplant (Solanum anguivi lam) fruit called Igba Yinrin by Yoruba in South-West Nigeria, which is usually discarded in farms. The study was carried out on ripe and unripe fruits to better understand their value by comparing their effects in diabetes treatment. Methods: The study sought to assess the effects of a diet including ripe or unripe mature eggplant fruits in the sucrose-induced diabetic-like fruit fly. Bioactive compounds were identified and quantified with HPLC-UV, while the antioxidant vitamin (A, C, E), carotenoid, and mineral (Na, K, Ca, Mg, Fe, P, and Zn) content was analyzed in the fruits. Extracts were used to investigate their in vitro anti-inflammatory properties on cyclooxygenases (COX 1 and 2), 5-lipoxygenase (5-LOX), and anti-diabetes enzymes [α-amylase and α-glucosidase], while extract-supplemented diets (0.25-1% concentration) were fed to the fruit flies for 14 days. Results: Interestingly, the results showed that the ripe fruits had a significantly (p < 0.05) higher total phenol and flavonoid content, as well as a higher content of vitamins, carotenoids, and minerals, than the unripe fruits. The in vivo activities of antioxidant enzymes [superoxide dismutase (SOD), catalase (CAT), and glutathione transferase (GST)] and the total thiol level increased, while the blood glucose, reactive oxygen species (ROS), and malondialdehyde (MDA) levels decreased in Drosophila melanogaster (fruit fly). An in silico docking analysis showed strong binding affinity of the above-mentioned enzymes under investigation with the ligands hesperidin, naringin, and myricetin, which are bioactive compounds contained in the examined extracts. Conclusions: There was no significant difference in the biological effects of the ripe and unripe fruit extracts on inflammatory and anti-diabetes enzyme activities, which means that the ripe fruit, usually discarded, could serve as a sustainable alternative source of food nutrients.

The effective design of combinatorial libraries to balance fitness and diversity facilitates the engineering of useful enzyme functions, particularly those that are poorly characterized or unknown in biology. We introduce MODIFY, a machine learning (ML) algorithm that learns from natural protein sequences to infer evolutionarily plausible mutations and predict enzyme fitness. MODIFY co-optimizes predicted fitness and sequence diversity of starting libraries, prioritizing high-fitness variants while ensuring broad sequence coverage. In silico evaluation shows that MODIFY outperforms state-of-the-art unsupervised methods in zero-shot fitness prediction and enables ML-guided directed evolution with enhanced efficiency. Using MODIFY, we engineer generalist biocatalysts derived from a thermostable cytochrome c to achieve enantioselective C-B and C-Si bond formation via a new-to-nature carbene transfer mechanism, leading to biocatalysts six mutations away from previously developed enzymes while exhibiting superior or comparable activities. These results demonstrate MODIFY's potential in solving challenging enzyme engineering problems beyond the reach of classic directed evolution.

Cellulose derivatives and composites garnered significant attention as a fluorescent sensor for bioimaging applications. Their inherent properties such as biocompatibility and ease of functionalization make it an ideal candidate for developing sensitive and selective fluorescence sensors capable of detecting various biomolecules and ions within biological systems. Additionally, cellulose derivatives and composites have emerged as promising agents in anticancer therapy. These materials have excellent potential to inhibit the growth of various cancer cell lines. This review aims to elucidate the recent advancements from 2020 to 2024 in the application of cellulose derivatives and composites in bioimaging and anticancer therapies. This includes an exploration of their potential as anticancer agents, highlighting the mechanisms by which cellulose derivatives can inhibit cancer cell growth and proliferation. Additionally, this review examines the role of cellulose composites as carriers in drug delivery systems, focusing on how these materials can enhance the delivery and efficacy of anticancer drugs while minimizing systemic toxicity. Finally, the review delves into the emerging field of bioimaging applications of cellulose composites, particularly in the context of cancer diagnosis and monitoring. It highlights the innovative approaches being developed to functionalize cellulose-based composite materials with imaging agents, enhancing their ability to provide detailed and accurate imaging of cancerous tissues. [ABSTRACT FROM AUTHOR]

Non-specific amplification (NSA, amplification in the absence of a target analyte) in bioanalytical rolling circle amplification (RCA) assays, especially those involving pre-synthesized circular DNA (cDNA), affects its analytical sensitivity. Despite extensive development of RCA-based bioanalytical methods, the NSA in RCA remains uncharacterized in terms of its magnitude or origin. NSA may originate from inefficient ligation or succeeding cDNA purification steps. This study comprehensively quantifies NSA across several ligation and digestion techniques for the first time since the innovation of RCA. To quantify the NSA in RCA, cDNAs were prepared using self-annealing, splint-padlock, or cohesive end ligations. The cDNAs were then subjected to nine different exonuclease digestion steps and quantified for NSA under linear as well as hyperbranched RCA conditions. We investigated buffer compositions, divalent ion concentrations, single or dual enzyme digestion, cohesive end lengths, and splint lengths. The optimized conditions successfully mitigated absolute NSA by 30–100-fold and relative NSA (normalized against primer-assisted RCA) to ∼5%. Besides understanding the mechanistic origin of NSA, novel aspects of enzyme–substrate selectivity, buffer composition, and the role of divalent ions were discovered. With increasing bioanalytical RCA applications, this study will help standardize NSA-free assays. [ABSTRACT FROM AUTHOR]

Levulinic acid, which can be obtained from biomass, has sparked great interest as a biologically-based chemical building block with wide versatility and potential. Its esterification with alcohols of different chain lengths is a promising valorization process for obtaining esters with various applications in the areas of biofuels/biolubricants, food and cosmetics, among others. In this work, the enzymatic esterification of levulinic acid and 1-octanol using a biocatalyst derived from Araujia sericifera latex was studied in systems with and without solvent. The influence of the molar ratio between alcohol and acid (ranging from 2:1–1:9), the biocatalyst loading (between 7.5 % and 17.5 % relative to the acid), the volume of n -heptane used as reaction solvent (from 0 to 4 ml), and the reaction time (6 hours) were investigated. The activity and stability of the biocatalyst in successive uses were also analyzed. A conversion of 49 % was achieved when the reaction was carried out in a solvent-free system, using an alcohol/acid molar ratio of 1:7 and after 5 h of reaction. On the other hand, the conversion was 65.1 % when the reaction was conducted in a system containing 1 ml of n -heptane as solvent, an alcohol/acid molar ratio of 1:8, and 5 h of reaction. In both cases, a temperature as low as 30 °C and an agitation speed of 300 RPM were used. • Enzymatic route for levulinic acid esterification using biocatalyst. • Araujia sericifera latex-derived biocatalyst demonstrates high activity. • Achieved 65.1 % conversion of levulinic acid in the synthesis of octyl levulinate. • Solvent-free and n-heptane solvent systems investigated. • Studied reaction parameters for optimal conversion. [ABSTRACT FROM AUTHOR]

The development of strategies that can permit to adjust the size specificity of immobilized proteases by the generation of steric hindrances may enlarge its applicability. Using as a model ficin immobilized on glyoxyl agarose, two strategies were assayed to generate tailor made steric hindrances. First, ficin has been coimmobilized on supports coated with large proteins (hemoglobin or bovine serum albumin (BSA)). While coimmobilization of ficin with BSA presented no effect on the activity versus any of the assayed substrates, coimmobilization with hemoglobin permitted to improve the immobilized ficin specificity for casein versus hemoglobin, but still significant activity versus hemoglobin remained. Second, aldehyde-dextran has been employed to modify the immobilized ficin, trying to generate steric hindrances to avoid the entry of large proteins (hemoglobin) while enabling the entry of small ones (casein). This also increased the size specificity of ficin, but still did not suppress the activity versus hemoglobin. The combination of both strategies and the use of 37ºC during the proteolysis enabled to almost fully nullify the hydrolytic activity versus hemoglobin while preserving a high percentage of the activity versus casein. The modifications improved enzyme stability and the biocatalyst could be reused for 5 cycles without alteration of its properties. • Ficin extract immobilized on glyoxyl was able to hydrolyze casein and hemoglobin. • Ficin coimmobilization with large hemoglobin increases its specificity by casein. • Ficin modification with aldehyde dextran increases its specificity by casein. • Both strategies together almost fully nullify the activity versus hemoglobin. [ABSTRACT FROM AUTHOR]

Carboxylesterases comprise a major class of α/β‐fold hydrolases responsible for the cleavage and formation of ester bonds. Found ubiquitously in nature, these enzymes are crucial for the metabolism of both endogenous and exogenous carboxyl esters in animals, plants and microorganisms. Beyond their essential physiological roles, carboxylesterases stand out as one of the important classes of biocatalysts for biotechnology. BlEst2, an enzyme previously classified as Bacillus licheniformis esterase, remains largely uncharacterized. In the present study, we elucidate the structural biology, molecular dynamics and biochemical features of BlEst2. Our findings reveal a canonical α/β‐hydrolase fold similar to the ESTHER block L of lipases, further augmented by two additional accessory C‐terminal domains. Notably, the catalytic domain demonstrates two insertions, which occupy conserved locations in α/β‐hydrolase proteins and commonly form the lid domain in lipase structures. Intriguingly, our in vitro cleavage of C‐terminal domains revealed the structure of the active form of BlEst2. Upon activation, BlEst2 showed a markedly elevated hydrolytic activity. This observation implies that the intramolecular C‐terminal domain serves as a regulatory intramolecular inhibitor. Interestingly, despite exhibiting esterase‐like activity, BlEst2 structural characteristics align more closely with lipases. This suggests that BlEst2 could potentially represent a previously unrecognized subgroup within the realm of carboxyl ester hydrolases. [ABSTRACT FROM AUTHOR]

Field experiments during rabi seasons of 2017-18 and 2018-19 were conducted to asses the groundnut production, soil biological characteristics, micronutrient content in soil and plant parts, and their uptake influenced by graded levels of phosphorus (15, 30, 45 and 60 kg ha−1), Arbuscular Mycorrhizal Fungi (AMF) and Phosphorus Solubilizing Bacteria (PSB) application in Alfisols at Botany farm, Dr. BSKKV, Dapoli in a factorial randomized block design with twenty treatment combinations which were replicated thrice. Results indicated that higher dose of phosphours (60 kg ha−1), biofertilizers (AMF + PSB @ 10 kg ha−1 each) and their interaction was found prominent in augmenting the highest bacterial, actinomycetes, fungal populations. Further, the combined application of phosphate and the AMF and PSB strain at higher level significantly improved the enzyme activities viz., dehydrogenase, urease, alkaline and acid phosphatase, CO2 evolution and SMBC compared to lower dose of phosphorus and non-inoculated treatment was on par with application of phosphorus @ 45 kg ha−1 with dual inoculation of AMF + PSB @ 10 kg ha−1 each. However, DTPA-extractable micronutrients (Fe, Mn, Zn and Cu) status showed significant improvement because of various treatment combinations. Similarly, the application of phosphorus @ 60 kg ha−1 exhibited the highest uptake in edible portion of crops which was resulted in significantly highest pod yield (35.86 q ha−1) of groundnut which was at par with application of phosphorus @ 45 kg ha−1 (31.96 q ha−1) indicating beneficial effect for improving as well sustaining soil health in long term aspects. [ABSTRACT FROM AUTHOR]

The C−C or C−N bond formation is critical in the synthesis of pharmaceuticals and other value‐added products; however, traditional metal‐catalysed synthesis has brought about environmental and resource issues. A plethora of engineered heme‐dependent enzymes, such as cytochrome P450, have exhibited enormous potential in biocatalysis for C−C or C−N bond formation. With the development of computational and spectroscopic methods, the mechanisms underlying heme‐catalysed C−C or C−N bond formation have been extensively investigated. In the presence of carbene or nitrene precursor, an active iron porphyrin carbene (IPC) or iron porphyrin nitrene (IPN) is formed, which subsequently reacts with a second substrate to form new C−C or C−N bonds. Apart from the widely studied IPC/IPN‐facilitated catalytic pathway, halide‐initiated radical cyclization pathway and Cpd‐I‐catalysed diradical pathway have also been proposed. These mechanistic insights have enabled rational engineering and de novo design of heme enzymes. This review summarises recent mechanistic advances in heme enzymatic C−C or C−N bond formation and presents successful applications of mechanism‐based enzyme design. It would shed light on the development of tailored biocatalysts for the synthesis of complex but valuable industrial products. [ABSTRACT FROM AUTHOR]

In this Perspective, the use of DNA nanotechnology is explored as a powerful tool for studying a family of enzymes known as topoisomerases. These enzymes regulate DNA topology within a living cell and play a major role in the pharmaceutical field, serving as anti‐cancer and anti‐bacterial targets. This Perspective will provide a short historical overview of the methods employed in studying these enzymes and emphasizing recent advancements in assays using DNA nanotechnology. These innovations have substantially improved accuracy and expanded the understanding of enzyme activity. This perspective will showcase the versatile utility of DNA nanotechnology in advancing scientific knowledge and its application in exploring new drug candidates, particularly in the study of topoisomerase enzymes. [ABSTRACT FROM AUTHOR]

MICAL proteins play a crucial role in cellular dynamics by binding and disassembling actin filaments, impacting processes like axon guidance, cytokinesis, and cell morphology. Their cellular activity is tightly controlled, as dysregulation can lead to detrimental effects on cellular morphology. Although previous studies have suggested that MICALs are autoinhibited, and require Rab proteins to become active, the detailed molecular mechanisms remained unclear. Here, we report the cryo-EM structure of human MICAL1 at a nominal resolution of 3.1 Å. Structural analyses, alongside biochemical and functional studies, show that MICAL1 autoinhibition is mediated by an intramolecular interaction between its N-terminal catalytic and C-terminal coiled-coil domains, blocking F-actin interaction. Moreover, we demonstrate that allosteric changes in the coiled-coil domain and the binding of the tripartite assembly of CH-L2α1-LIM domains to the coiled-coil domain are crucial for MICAL activation and autoinhibition. These mechanisms appear to be evolutionarily conserved, suggesting a potential universality across the MICAL family. The study reveals the cryo-EM structure of human MICAL1, an enzyme that depolymerizes F-actin. Structural analyses show a conserved autoinhibition mechanism through intramolecular interactions between the N-terminal and C-terminal domains. [ABSTRACT FROM AUTHOR]

Enzymes encapsulated in extracellular vesicles (EVs) hold promise as biomarkers for early cancer diagnosis. However, precise measurement of their catalytic activities within EVs remains a notable challenge. Here, we report an enzymatically triggered spherical DNA nanomotor (EDM) that enables one‐pot, cascaded, and highly sensitive analysis of the activity of EV‐associated or free apurinic/apyrimidinic endonuclease 1 (APE1, a key enzyme in base excision repair) across various biological samples. The EDM capitalizes on APE1‐triggered activation of DNAzyme (Dz) and its autonomous cleavage of substrates to achieve nonlinear signal amplification. Using EDM, we demonstrate a strong correlation between APE1 activity in EVs and that of their parental cancer cells. Additionally, EV APE1 mirrors the fluctuation of cellular APE1 activity in response to chemotherapy‐induced DNA damage. In a pilot clinical study (n=63), the EDM‐based assay reveals that more than 80 % of active APE1 in serum samples is EV‐encapsulated. Notably, EV APE1 can differentiate early prostate cancer (PCa) patients from healthy donors (HDs) with an overall accuracy of 92 %, outperforming free APE1 in sera. We anticipate that EDM will become a versatile tool for quantifying EV‐associated enzymes. [ABSTRACT FROM AUTHOR]

Biocatalytic membranes have great potential in various industrial sectors, with the immobilization of enzymes being a crucial stage. Immobilizing enzymes through covalent bonds is a complex and time-consuming process for large-scale applications. Polydopamine (PDA) offers a more sustainable and eco-friendly alternative for enzyme immobilization. Therefore, surface modification with polydopamine as mussel-inspired antifouling coatings has increased resistance to fouling. In this study, α-amylase enzyme was covalently bound to a bioactive PDA-coated polyethersulfone (PES) membrane surface using cyanuric chloride as a linker. The optimal activity of α-amylase enzyme immobilized on PES/PDA membrane was obtained at temperature and pH of 55°C and 6.5, respectively. The immobilized enzyme can be reused up to five reaction cycles with 55 % retention of initial activity. Besides, it maintained 60 % of its activity after being stored for five weeks at 4°C. Additionally, the immobilized enzyme demonstrated increased Michaelis constant and maximum velocity values during starch hydrolysis. The results of the biofouling experiment of various membranes in a dead-end cell demonstrated that the PES membrane's water flux increased from 6722.7 Lmh to 7560.2 Lmh after PDA modification. Although α-amylase immobilization reduced the flux to 7458.5 Lmh due to enhanced hydrophilicity, compared to unmodified membrane. The findings of this study demonstrated that the membrane produced through co-deposition exhibited superior hydrophilicity, enhanced coating stability, and strong antifouling properties, positioning it as a promising candidate for industrial applications. [Display omitted] • α-Amylase was covalently immobilized onto polydopamine-functionalized polyethersulfone membrane. • Surface modification with polydopamine generated a mussel-inspired coating to inhibit fouling. • The immobilization technique effectively preserved the activity of α-amylase enzyme. • The biocatalyst membrane exhibited superior stability and strong antifouling properties. [ABSTRACT FROM AUTHOR]

Multi‐enzymatic cascade reaction provides a new avenue for C─C coupling directly from CO2 under mild conditions. In this study, a new pathway with four enzymes including formate dehydrogenase (PaFDH), formaldehyde dehydrogenase (BmFADH), glycolaldehyde synthase (PpGALS), and alcohol dehydrogenase (GoADH) is developed for directly converting CO2 gas molecules to ethylene glycol (EG) in vitro. A rhodium‐based NADH regeneration electrode is constructed to continuously provide the proton and electron of this multi‐enzymatic cascade reaction. The prepared electrode can reach the Faradaic Efficiency (FE) of 82.9% at −0.6 V (vs. Ag/AgCl) and the NADH productivity of 0.737 mM h−1. Shortening the reaction path is crucial for multi‐enzymatic cascade reactions. Here, a hydrogen‐bonded organic framework (HOF) nano‐reactor is successfully developed to immobilize four enzymes in one pot with a striking enzyme loading capacity (990 mg enzyme g−1 material). Through integrating and optimization of NADH electro‐regeneration and enzymatic catalysis in one pot, 0.15 mM EG is achieved with an average conversion rate of 7.15 × 10−7 mmol CO2 min−1 mg−1 enzymes in 6 h. These results shed light on electro‐driven multi‐enzymatic cascade conversion of C─C coupling from CO2 in the nano‐reactor. [ABSTRACT FROM AUTHOR]

For multi‐enzymatic cases, the determination of the batch reactor (BR) optimal operating policy often translates into a difficult multi‐objective problem. Exemplification is made here for the enzymatic reduction of D‐fructose to mannitol by using the mannitol dehydrogenase (MDH) enzyme and nicotinamide adenine dinucleotide (NADH) cofactor, with in situ regeneration of NADH at the expense of formate degradation by using the FDH enzyme. This paper presents an original rule to in silico generate the problem solution, by using the Pareto optimal‐front approach with accounting for pairs of competing economic goals and constraints. The optimal BR is then compared to an optimal fed‐BR (FBR), or a series of equal BRs (SeqBR). As proved, the Pareto‐optimal front alternative is an advantageous option, compared to the classical nonlinear programming technique, being simple to apply, by considering pairs of opposite objective functions. In the present case study, the Pareto‐optimal BR operating mode predicts an M‐productivity 1.5x better than those of an optimized FBR, with comparable enzymes consumption. The MDH consumption of this Pareto‐optimal BR is 10x smaller than an optimal SeqBR, and 130x smaller vs. heuristic (sub)optimal BR. [ABSTRACT FROM AUTHOR]

Light-responsive Pickering interfacial biocatalysis (LPIB) is desirable because of its convenient catalyst recovery, product separation and clean external stimuli trigger. However, the recyclability of LPIB is still limited due to its enzyme inactivation. Herein, lipase-entrapped colloidosomes as particulate emulsifiers and biocatalysts were fabricated using the one-step co-assembly of lipases and TiO2 nanoparticles (with light-responsive wettability). The obtained LPIB exhibited a 4.31-fold enhancement of enzyme activity compared with the traditional biphasic system. Impressively, the LPIB maintained nearly 90% of its initial enzyme activity even after 20 cycles, which is the highest among the currently reported LPIBs. It is attributed that the TiO2 nanoparticle layer on the colloidosome surface reflects UV light, thus protecting the enzyme from photodegradation. This green platform can be widely applied to construct recyclable and efficient biphasic biocatalytic systems. [ABSTRACT FROM AUTHOR]

The use of the laccase enzyme from the fungus Trametes versicolor, coupled with the mediator 1-hydroxybenzotriazole (1-HBT) has been shown to be effective for the biocatalytic conversion of a hexameric lignin model compound containing three of the most common linkages found in native lignin. Cleavage of the model takes place over a 24 hours period predominantly at the β-O-4 ether linkage to give a previously known β-5 dimer intermediate which in turn was rapidly consumed to further degradation products. There is also mass spectrometric evidence of repolymerisation of the β-5 dimer and other degradation intermediates to form higher oligomers. Mechanistic pathways to account for the major catalytic processes are proposed. [ABSTRACT FROM AUTHOR]

Obesity stands out as one of the most significant health problems in the modern world. The prevalence of high‐calorie diets (HCDs) globally exacerbates this condition. Throughout history, plants and plant‐derived food products have been utilized for medicinal purposes, demonstrating their efficacy in the treatment and prevention of various diseases. Gundelia tournefortii (GT), a plant of interest, is known to possess beneficial properties. Hence, this study aimed to investigate the immunotoxic and neurotoxic effects of two different doses of GT plant extract on the liver, brain, and heart tissues of obese rats. For this purpose, Wistar male rats were divided into four groups: “CG,” “HCDG,” “HCDGUN1,” and “HCDGUN2” At the conclusion of the study, adenosine deaminase (ADA) and myeloperoxidase (MPO) activities, as well as acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) biomarkers, were evaluated in the liver, heart, and brain tissues. The study results revealed a statistically significant increase in ADA and MPO activities in the HCDG group compared to the CG group, alongside a significant decrease in the HCDGUN groups compared to the HCDG group. Regarding AChE and BChE activities, a statistically significant decrease was observed in the HCDG group compared to the CG group, whereas an increase was noted in the HCDGUN groups relative to the HCDG group, with the latter approaching values similar to those of the control group. In conclusion, the intake of GT plant extract exhibited positive effects on the immunotoxic and neurotoxic effects induced by HCD in rats with an experimental obesity model, as evidenced by tissue biomarker evaluations. [ABSTRACT FROM AUTHOR]

Fermented foods and beverages have been produced around the world for millennia, providing humans with a range of gastronomic, cultural, health, and scientific benefits. Building on these traditional forms, a convergence of factors, including culinary innovation, globalization, shifts in consumer preferences, and advances in microbiome sciences, has led to the emergence of so-called 'novel fermentations'. In this review, we define novel fermentation as the confluence of traditional food practices and rational microbiome design. Using principles of microbial ecology and evolution, we develop a microbiological framework that outlines several strategies for producing and characterizing novel fermentations, including switching substrates, engrafting target species, assembling whole-community chimeras, and generating novel phenotypes. A subsequent analysis of existing traditional ferments points to gaps in 'fermentation space' where novel ferments could potentially be produced using new combinations of microbes and food substrates. We highlight some important safety and sociocultural issues presented by the repurposing and modification of microbes from traditional ferments that fermented-food producers and microbiologists need to address. Fermented foods have been produced for millennia. In modern times, culinary innovation, globalization, and advances in microbiome science have led to the emergence of novel fermentations. Arrigan et al. review the ecological and evolutionary processes shaping microbial ferments and develop a framework for the generation of novel fermented products. [ABSTRACT FROM AUTHOR]

The cytochrome P450s enzyme family metabolizes ∼80% of small molecule drugs. Variants in cytochrome P450s can substantially alter drug metabolism, leading to improper dosing and severe adverse drug reactions. Due to low sequence conservation, predicting variant effects across cytochrome P450s is challenging. Even closely related cytochrome P450s like CYP2C9 and CYP2C19, which share 92% amino acid sequence identity, display distinct phenotypic properties. Using variant abundance by massively parallel sequencing, we measured the steady-state protein abundance of 7,660 single amino acid variants in CYP2C19 expressed in cultured human cells. Our findings confirmed critical positions and structural features essential for cytochrome P450 function, and revealed how variants at conserved positions influence abundance. We jointly analyzed 4,670 variants whose abundance was measured in both CYP2C19 and CYP2C9, finding that the homologs have different variant abundances in substrate recognition sites within the hydrophobic core. We also measured the abundance of all single and some multiple wild type amino acid exchanges between CYP2C19 and CYP2C9. While most exchanges had no effect, substitutions in substrate recognition site 4 reduced abundance in CYP2C19. Double and triple mutants showed distinct interactions, highlighting a region that points to differing thermodynamic properties between the 2 homologs. These positions are known contributors to substrate specificity, suggesting an evolutionary tradeoff between stability and enzymatic function. Finally, we analyzed 368 previously unannotated human variants, finding that 43% had decreased abundance. By comparing variant effects between these homologs, we uncovered regions underlying their functional differences, advancing our understanding of this versatile family of enzymes. [ABSTRACT FROM AUTHOR]

In yeast, control of sulfur amino acid metabolism relies upon Met4 , a transcription factor that activates the expression of a network of enzymes responsible for the biosynthesis of cysteine and methionine. In times of sulfur abundance, the activity of Met4 is repressed via ubiquitination by the SCF Met30 E3 ubiquitin ligase, but the mechanism by which the F-box protein Met30 senses sulfur status to tune its E3 ligase activity remains unresolved. Herein, we show that Met30 responds to flux through the trans-sulfuration pathway to regulate the MET gene transcriptional program. In particular, Met30 is responsive to the biological gas hydrogen sulfide, which is sufficient to induce ubiquitination of Met4 in vivo. Additionally, we identify important cysteine residues in Met30 's WD-40 repeat region that sense the availability of sulfur in the cell. Our findings reveal how SCF Met30 dynamically senses the flow of sulfur metabolites through the trans-sulfuration pathway to regulate the synthesis of these special amino acids. [ABSTRACT FROM AUTHOR]

Edible and medicinal mushrooms possess excellent nutritional properties due to their incredible versatility in growing on different substrates and producing extracellular enzymes with a wide range of specificity. These features make them excellent candidates for various biotechnological applications. In this context, biotechnological applications using edible and medicinal mushrooms can focus on the bioprocessing of agro‐industrial wastes, an economical and environmentally friendly strategy. This review, based on recent original research and scientific reviews, highlights the versatility and potential of mushrooms in terms of sustainability and efficiency. We emphasized the biotechnological applications of edible and medicinal mushrooms and their enzymes including food production with high nutraceutical value by enhancing the quality and flavor of food industry products. Other biotechnological applications addressed in this review were cosmeceutical and biomedical development using mushroom extracts with bioactive compounds; wood pulp pretreatment processes in the pulp and paper industry; bioethanol production; and bioremediation for decontaminating soils and polluted effluents. These applications explain how edible and medicinal mushrooms have gained significance in biotechnology over the years, opening new avenues for innovation. The current tendency to study edible and medicinal mushrooms has gained the attention of researchers because these are still less known organisms becoming an attractive and natural source of novel bioactive compounds that could be integrated into a circular model production. [ABSTRACT FROM AUTHOR]

The thermo-solvent-tolerant lipase-producing actinomycete, Streptomyces sp. A3301, was utilized as a biocatalyst for poly (lactic acid) or PLA polymerization. The study aimed to optimize lipase immobilization conditions, characterize the immobilized lipase and apply it for PLA polymerization. The results showed using a sponge as the immobilizing matrix was the most effective method, achieving a maximum activity of 277 U/g of sponge. The optimal sponge size was determined to be 0.125 cm³ and pre-soaking the sponge in 0.1 M phosphate buffer at pH 7.0 for 24 h before use proved advantageous. Immobilization significantly enhanced the thermo-stability of the enzyme, with a relative activity ranging from 140 to 190% within the temperature range of 30 to 60 °C. In contrast, the crude lipase exhibited thermo-stability only within the 30 - 50 °C range. The immobilized lipase demonstrated stability under PLA polymerization conditions, which involved a reaction mixture containing toluene and lactic acid and performed at 60 °C for 8 h. The immobilized lipase maintained its activity under this condition for 5 h, retaining a relative activity of 230%, which was 1.2 times higher than the activity of the crude lipase. When the immobilized lipase was used in PLA polymerization, the resulting PLA product exhibited a molecular weight of 5,333 ± 0.02 Da, and the degree of polymerization was approximately 72. These findings underscore the potential of the immobilization technique to enhance lipase activity for PLA polymerization. [ABSTRACT FROM AUTHOR]

Chitin, an extracellular polysaccharide, is synthesized by membrane-embedded chitin synthase (CHS) utilizing intracellular substrates. The mechanism of the translocation of synthesized chitin across the membrane to extracellular locations remains unresolved. We prove that the chitin synthase from Phytophthora sojae (PsCHS) is a processive glycosyltransferase, which can rapidly produce and tightly bind with the highly polymerized chitin. We further demonstrate that PsCHS is a bifunctional enzyme, which is necessary and sufficient to translocate the synthesized chitin. PsCHS was purified and then reconstituted into proteoliposomes (PLs). The nascent chitin is generated and protected from chitinase degradation unless detergent solubilizes the PLs, showing that PsCHS translocates the newly produced chitin into the lumen of the PLs. We also attempted to resolve the PsCHS structure of the synthesized chitin-bound state, although it was not successful; the obtained high-resolution structure of the UDP/Mn2+-bound state could still assist in describing the characterization of the PsCHS's transmembrane channel. Consistently, we demonstrate that PsCHS is indispensable and capable of translocating chitin in a process that is tightly coupled to chitin synthesis. [ABSTRACT FROM AUTHOR]

Crotonylation is a recently discovered protein acyl modification that shares many enzymes with acetylation. However, it possesses a distinct regulatory mechanism and biological function due to its unique crotonyl structure. Since the discovery of crotonylation in 2011, numerous crotonylation sites have been identified in both histones and other proteins. In recent studies, crotonylation was found to play a role in various diseases and biological processes. This paper reviews the initial discovery and regulatory mechanisms of crotonylation, including various writer, reader, and eraser proteins. Finally, we emphasize the relationship of dysregulated protein crotonylation with eight common malignancies, including cervical, prostate, liver, and lung cancer, providing new potential therapeutic targets. [ABSTRACT FROM AUTHOR]

Soil contaminated with petroleum-derived products should be used to cultivate energy crops. One such crop is Zea mays. Therefore, a study was performed to determine the suitability of Zea mays biomass obtained from gasoline-contaminated soil for energy purposes. The analysis included determining the heat of combustion and calorific value of the biomass, as well as the content of nitrogen, carbon, hydrogen, oxygen, sulfur, and ash in the biomass. Additionally, the suitability of vermiculite, dolomite, perlite, and agrobasalt for the phytostabilization of gasoline-contaminated soil was evaluated. It was found that the application of sorbents to gasoline-contaminated soil significantly reduced the severe negative effects of this petroleum product on the growth and development of Zea mays. Gasoline contamination of the soil caused a significant increase in ash, nitrogen, and sulfur, along with a decrease in carbon and oxygen content. However, it had no negative effect on the heat of combustion or calorific value of the biomass, although it did reduce the energy production from Zea mays biomass due to a reduction in yield. An important achievement of the study is the demonstration that all the applied sorbents have a positive effect on soil stabilization, which in turn enhances the amount of Zea mays biomass harvested and the energy produced from it. The best results were observed after the application of agrobasalt, dolomite, and vermiculite on gasoline-contaminated soil. Therefore, these sorbents can be recommended for the phytostabilization of gasoline-contaminated soil intended for the cultivation of energy crops. [ABSTRACT FROM AUTHOR]

Herein, a dissipative system tailored for the controlled loading and release of CpG oligodeoxynucleotides (CpG ODNs), known for their pharmacological immunostimulatory properties, is reported. The approach involves multiple cycles of deactivation and activation of the CpG ODNs via its hybridization with a complementary fuel strand, followed by its selective release mediated by the enzymatic activity of T7 exonuclease. The autonomous and temporal behavior of this dissipative system can be tuned by three factors: the design of the fuel strand and its concentration that governs the kinetics of the forward hybridization reaction, as well as the concentration of T7 exonuclease, which regulates the backward energy dissipation reaction. Furthermore, the enzyme's tolerance toward waste accumulation is demonstrated, and the system's robust performance when utilizing various fuel strands in alternating fashion is showcased. The findings underscore the potential of this approach for precise and programmable delivery of therapeutic nucleic acids in multiple cycles, with implications for enhancing immunotherapeutic strategies in which controlled kinetics of the nucleic acid is highly desired. [ABSTRACT FROM AUTHOR]

When studying the carbon cycle in the biosphere, special attention is paid in Russia to the transformation of organic matter in the surface layer of supergene zone. The group composition of the organic matter (OM) in peats of different genesis in the taiga zone of Western Siberia is studied. Our data show that it is important to take into account the botanical composition of peat that make up natural and reclaimed forest swamps, well as their spatial heterogeneity, which is a necessary component when estimating the carbon stocks in peat soils of forest ecosystems within the national monitoring system for carbon pools and greenhouse gas fluxes. The experiments on peat OM transformation demonstrate that its efficiency is determined by its botanical composition. According to the rate of OM decomposition, the oligotrophic peats form a sequence: sphagnum–hollow > complex > fuscum > scheuchzeria–sphagnum > cotton grass–sphagnum > scheuchzeria > cotton grass peats and eutrophic peats: hypnum > sedge > sedge–hypnum > menyanthes > woody > wood–sedge peats. According to two-year field experiments on the transformation rate and direction of the OM of peat-forming plants, the component and chemical compositions of their OM significantly changes but in an individual manner for each plant. The content of aromatic polyconjugated systems and carboxyl groups increases, while the amount of carbohydrate fragments decreases. A 60 years long forest amelioration influences the transformation of peat OM. The degree of grass and sedge peat species in the process of amelioration increases by 5% in the 75-cm layer; the content of bitumens decreases, whereas the contents of easily hydrolyzable substances, humic acids, and lignin, increases. The microbiomes and enzymes of the peats in forest swamps of Western Siberian taiga are characterized. Our results confirm the hypothesis by V.E. Rakovsky that the differences in the species composition of peat-forming plants manifest themselves in the chemical and biological characteristics of peat. [ABSTRACT FROM AUTHOR]

There has been a growing interest in ecofriendly enzymatic processes. However, enzyme solubility limits the application of many biocatalysts in continuous systems, requiring the development of cost‐effective strategies for enzyme immobilization. Based on this premise, this study investigated the application of lipase immobilized in starch–alginate beads for oil transesterification in a tubular reactor. An economical derivative was produced by immobilizing Eversa Transform 2.0 in 50:50 (w/w) starch–alginate beads using the jet‐cutting technique. The biocatalyst had a particle size of about 500 μm and activity of 138.67 ± 18.53 U g−1. X‐ray photoelectron spectroscopy showed nitrogen content ranging from 6.38% to 7.29%, with uniform distribution of lipase throughout the beads. Nitrogen isotherms were characteristic of mesoporous materials, with an average pore diameter of 48.09 Å and low surface area (0.69 m2 g−1). A face‐centered central composite design was used to study soybean oil transesterification. In the best four runs, the process achieved a mean triglyceride conversion of 45%. High ester productivity levels (2.05 × 10−2% ester g−1 biocatalyst min−1 or 1.5 × 10−4% ester U−1 min−1) were obtained. Biocatalyst reuse led to a twofold increase in ester concentration (14.57% vs 7.7%). These findings confirm the successful development of a low‐cost biocatalyst suitable for use in continuous reactions. [ABSTRACT FROM AUTHOR]

Objectives We aimed to analyse the interplay between impaired iron uptake and β-lactamases on cefiderocol resistance in Pseudomonas aeruginosa. Methods Thirty-one transferable β-lactamases and 16 intrinsic P. aeruginosa AmpC (PDC) variants were cloned and expressed in wild-type (PAO1) and iron uptake-deficient (PAO Δ piuC) P. aeruginosa backgrounds. MICs of cefiderocol and antipseudomonal β-lactams were determined by reference broth microdilution. Results Relative to PAO1, deletion of piuC caused a specific 16-fold decrease in cefiderocol activity but negligible effects on the activity of other β-lactams. Among transferable β-lactamases, SHV-12, KPC Ω-loop mutants, NDMs and OXA-15 showed cefiderocol MIC values above the clinical breakpoint (2 mg/L) when expressed in PAO1. When expressed in PAO Δ piuC , these and the transformants harbouring PER-1, VEB-1, KPC-2, KPC-3, VIM-1, CMY-2, OXA-2 and OXA-14 showed increased MIC values from 16 to >256 mg/L. The PDC variants carrying the Ω-loop changes ΔP215-G222 (PDC-577), E219K (PDC-221 and PDC-558) and the H10 helix change L293P (PDC-219) had the greatest impact on cefiderocol resistance, with MICs of 2–4 mg/L in PAO1 and of up to 32–64 mg/L in PAO Δ piuC. Widespread enzymes such as GES, CTX-M-9, CTX-M-15, VIM-2-like enzymes, IMPs, DHA-1, FOX-4, OXA-10, OXA-48 and the other PDC variants tested had weaker effects on cefiderocol resistance. Conclusion We add evidence about the effect of the interplay between iron uptake and β-lactamases on the acquisition of cefiderocol resistance in P. aeruginosa. These findings may help to anticipate the emergence of resistance and optimize the use of cefiderocol against P. aeruginosa infections. [ABSTRACT FROM AUTHOR]