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Glycosylation is a predominant strategy plants use to fine-tune the properties of small molecule metabolites to affect their bioactivity, transport, and storage. It is also important in biotechnology and medicine as many glycosides are utilized in human health. Small molecule glycosylation is largely carried out by family 1 glycosyltransferases. Here, we report a structural and biochemical investigation of UGT95A1, a family 1 GT enzyme from Pilosella officinarum that exhibits a strong, unusual regiospecificity for the 3'-O position of flavonoid acceptor substrate luteolin. We obtained an apo crystal structure to help drive the analyses of a series of binding site mutants, revealing that while most residues are tolerant to mutations, key residues M145 and D464 are important for overall glycosylation activity. Interestingly, E347 is crucial for maintaining the strong preference for 3'-O glycosylation, while R462 can be mutated to increase regioselectivity. The structural determinants of regioselectivity were further confirmed in homologous enzymes. Our study also suggests that the enzyme contains large, highly dynamic, disordered regions. We showed that while most disordered regions of the protein have little to no implication in catalysis, the disordered regions conserved among investigated homologs are important to both the overall efficiency and regiospecificity of the enzyme. This report represents a comprehensive in-depth analysis of a family 1 GT enzyme with a unique substrate regiospecificity and may provide a basis for enzyme functional prediction and engineering.

Enzymes accelerate the rates of biomolecular reactions by many orders of magnitude compared to bulk solution, and it is widely understood that this catalytic effect arises from a combination of polar pre-organization and electrostatic transition state stabilization. A number of recent reports have also implicated ultrafast (femtosecond-picosecond) timescale motions in enzymatic activity. However, complications arising from spatially-distributed disorder, the occurrence of multiple substrate binding modes, and the influence of hydration dynamics on solvent-exposed active sites still confound many experimental studies. Here we use ultrafast two-dimensional infrared (2D IR) spectroscopy and covalently-tethered substrate analogs to examine dynamical properties of the promiscuous Pyrococcus horikoshii ene-reductase (PhENR) active site in two binding configurations mimicking proposed "inactive" and "reactive" Michaelis complexes. Spectral diffusion measurements of aryl-nitrile substrate analogs reveal an end-to-end tradeoff between fast (sub-ps) and slow (>5 ps) motions. Fermi resonant aryl-azide analogs that sense interactions of coupled oscillators are described. Lineshape and quantum beat analyses of these probes reveal characteristics that correlate with aryl-nitrile frequency fluctuation correlation functions parameters, demonstrating that this anisotropy is an intrinsic property of the water-exposed active site, where countervailing gradients of fast dynamics and disorder in the reactant ground state are maintained near the hydration interface. Our results suggest several plausible factors leading to state-selective rate enhancement and promiscuity in PhENR. This study also highlights a strategy to detect perturbations to vibrational modes outside the transparent window of the mid-IR spectrum, which may be extended to other macromolecular systems. [ABSTRACT FROM AUTHOR]

Classical theories of enzyme inhibition kinetics predict a monotonic decrease in the mean catalytic activity with the increase in inhibitor concentration. The steady-state result, derived from deterministic mass action kinetics, ignores molecular noise in enzyme-inhibition mechanisms. Here, we present a stochastic generalization of enzyme inhibition kinetics to mesoscopic enzyme concentrations by systematically accounting for molecular noise in competitive and uncompetitive mechanisms of enzyme inhibition. Our work reveals an activator-inhibitor duality as a non-classical effect in the transient regime in which inhibitors tend to enhance enzymatic activity. We introduce statistical measures that quantify this counterintuitive response through the stochastic analog of the Lineweaver–Burk plot that shows a merging of the inhibitor-dependent velocity with the Michaelis–Menten velocity. The statistical measures of mean and temporal fluctuations - fractional enzyme activity and waiting time correlations - show a non-monotonic rise with the increase in inhibitors before subsiding to their baseline value. The inhibitor and substrate dependence of the fractional enzyme activity yields kinetic phase diagrams for non-classical activator-inhibitor duality. Our work links this duality to a molecular memory effect in the transient regime, arising from positive correlations between consecutive product turnover times. The vanishing of memory in the steady state recovers all the classical results. [ABSTRACT FROM AUTHOR]

We present an analysis of high-resolution quasi-elastic neutron scattering spectra of phosphoglycerate kinase which elucidates the influence of the enzymatic activity on the dynamics of the protein. We show that in the active state the inter-domain motions are amplified and the intra-domain asymptotic power-law relaxation ∝t−α is accelerated, with a reduced coefficient α. Employing an energy landscape picture of protein dynamics, this observation can be translated into a widening of the distribution of energy barriers separating conformational substates of the protein. [ABSTRACT FROM AUTHOR]

A series of thiadiazole derivatives were designed and synthesized as dual inhibitors of acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE) for the treatment of Alzheimer's disease (AD). Furthermore, the compounds were assayed for their inhibitory activity to AChE and BuChE in vitro, and the results indicated that most of the compounds had moderate inhibitory activity to AChE and BuChE. Among them, compound 11 u showed the best inhibitory activity against AChE and BuChE (eeAChE, IC50=2.73 μM; eqBuChE, IC50=0.65 μM), which showed approximately 2‐fold more activity against AChE enzyme than galantamine and approximately 28‐fold more activity against BuChE enzyme than galantamine. In addition, molecular docking studies have shown that compound 11 u could bind to the catalytic active site (CAS) and peripheral anion site (PAS) of AChE and BuChE. Among them, compound 11 u combined with BuChE and exhibited a mixed inhibition pattern consistent with enzyme kinetics studies. The interaction's stability of 11 u‐AChE/BuChE were also assessed using a conventional atomistic 100 ns dynamics simulation study, which revealed the conformational stability of representative compound 11 u in the cavity of the AChE/BuChE. Moreover, the molecular properties of all compounds were predicted by online through the SwissADME, and the best active compound 11 u matched the properties of most orally administered drugs. All these suggested that 11 u could be considered as a lead compound for the development of drugs for AD. [ABSTRACT FROM AUTHOR]

To develop the drugs as a second line of preventing a serious form of illness, blocking the interaction between a receptor‐binding domain (RBD) in the SARS‐CoV‐2 S‐protein (spike protein) with human ACE2 (Angiotensin converting enzyme 2) can potentially prevent SARS‐CoV‐2 S‐protein from interacting with host cells. In this research, 20 drug compounds are examined using docking to identify potential drugs that can bind at the common level of the RBD‐ACE2 complex and compared the results with two standard drugs offered (Favipiravir, Arbidol). Among 20 drugs, Ozanimod and Prazosin are selected as the best drug compounds by reviewing the docking scores and drug interaction with the active position of RBD‐ACE2. The results of molecular dynamics simulation showed that Ozanimod with binding energy of −14.24 kcal mol−1 has a higher binding capability than Prazosin with binding energy of −9.55 kcal mol−1 to block the interaction between spike protein RBD and human ACE2 enzyme. Ozanimod effectively binds to the S‐protein RBD and inhibits residues critical to the spike and ACE2 protein interaction. This drug compound is expected to be a potentially effective inhibitor of the interaction between the S‐ RBD and the human ACE2 enzyme. [ABSTRACT FROM AUTHOR]

Purpose: This study explores the immobilisation of enzymes within porous catalysts of various geometries, including spheres, cylinders and flat pellets. The objective is to understand the irreversible Michaelis-Menten kinetic process within immobilised enzymes through advanced mathematical modelling. Design/methodology/approach: Mathematical models were developed based on reaction-diffusion equations incorporating nonlinear variables associated with Michaelis-Menten kinetics. This research introduces fractional derivatives to investigate enzyme reaction kinetics, addressing a significant gap in the existing literature. A novel approximation method, based on the independent polynomials of the complete bipartite graph, is employed to explore solutions for substrate concentration and effectiveness factor across a spectrum of parameter values. The analytical solutions generated through the bipartite polynomial approximation method (BPAM) are rigorously tested against established methods, including the Bernoulli wavelet method (BWM), Taylor series method (TSM), Adomian decomposition method (ADM) and fourth-order Runge-Kutta method (RKM). Findings: The study identifies two main findings. Firstly, the behaviour of dimensionless substrate concentration with distance is analysed for planar, cylindrical and spherical catalysts using both integer and fractional order Michaelis-Menten modelling. Secondly, the research investigates the variability of the dimensionless effectiveness factor with the Thiele modulus. Research limitations/implications: The study primarily focuses on mathematical modelling and theoretical analysis, with limited experimental validation. Future research should involve more extensive experimental verification to corroborate the findings. Additionally, the study assumes ideal conditions and uniform catalyst properties, which may not fully reflect real-world complexities. Incorporating factors such as mass transfer limitations, non-uniform catalyst structures and enzyme deactivation kinetics could enhance the model's accuracy and broaden its applicability. Furthermore, extending the analysis to include multi-enzyme systems and complex reaction networks would provide a more comprehensive understanding of biocatalytic processes. Practical implications: The validated bipartite polynomial approximation method presents a practical tool for optimizing enzyme reactor design and operation in industrial settings. By accurately predicting substrate concentration and effectiveness factor, this approach enables efficient utilization of immobilised enzymes within porous catalysts. Implementation of these findings can lead to enhanced process efficiency, reduced operating costs and improved product yields in various biocatalytic applications such as pharmaceuticals, food processing and biofuel production. Additionally, this research fosters innovation in enzyme immobilisation techniques, offering practical insights for engineers and researchers striving to develop sustainable and economically viable bioprocesses. Social implications: The advancement of enzyme immobilisation techniques holds promise for addressing societal challenges such as sustainable production, environmental protection and healthcare. By enabling more efficient biocatalytic processes, this research contributes to reducing industrial waste, minimizing energy consumption and enhancing access to pharmaceuticals and bio-based products. Moreover, the development of eco-friendly manufacturing practices through biocatalysis aligns with global efforts towards sustainability and mitigating climate change. The widespread adoption of these technologies can foster a more environmentally conscious society while stimulating economic growth and innovation in biotechnology and related industries. Originality/value: This study offers a pioneering approximation method using the independent polynomials of the complete bipartite graph to investigate enzyme reaction kinetics. The comprehensive validation of this method through comparison with established solution techniques ensures its reliability and accuracy. The findings hold promise for advancing the field of biocatalysts and provide valuable insights for designing efficient enzyme reactors. [ABSTRACT FROM AUTHOR]

Dihydrofolate reductase (DHFR) is ubiquitously present in all living organisms and plays a crucial role in the growth of the fungal pathogen R.solani. Sequence alignment confirmed the evolutionary conservation of the essential lid domain, with the amino acid 'P' within the PEKN lid domain appearing with a frequency of 89.5% in higher organisms and 11.8% in lower organisms. Consequently, a K65P variant was introduced into R.solani DHFR (rDHFR). Subsequent enzymatic kinetics assays were conducted for human DHFR (hDHFR), rDHFR, E. coli DHFR (eDHFR), and the K65P variant. hDHFR exhibited the highest kcat of 0.95 s−1, followed by rDHFR with 0.14 s−1, while eDHFR displayed the lowest kcat of 0.09 s−1. Remarkably, the K65P variant induced a significant reduction in Km, resulting in a 1.8-fold enhancement in catalytic efficiency (kcat/Km) relative to the wild type. Differential scanning fluorimetry and binding free energy calculations confirmed the enhanced substrate affinity for both folate and NADPH in the K65P variant. These results suggest that the K65P mutation enhances substrate affinity and catalytic efficiency in DHFR, highlighting the evolutionary and functional importance of the K65 residue. [ABSTRACT FROM AUTHOR]

Hormone receptor (HR)-positive breast cancer represents tumours that express estrogen and/or progesterone enzymes, which play a crucial role in the growth and proliferation of breast cancer cells. Aromatase inhibitors (AIs) are drugs that inhibit the enzyme aromatase, involved in the biosynthesis of estrogen and are used for the treatment of HR-positive breast cancer. The USFDA-approved nonsteroidal AIs contain 1,2,4-triazole heterocycle. So, in the present study, we screened seventy-eight 1,2,4-triazole analogues from different literature resources and generated a pharmacophore model. After several validation protocols, Hypo1 was selected as the best model and was used as a 3D query for screening 1,2,4-triazole analogues (15,583) obtained from the CHEMBL database. A dataset containing 320 ligands with estimated activity (IC50< 0.1 µM) was subjected to molecular docking against the aromatase enzyme (PDB ID: 3S79). Amongst the 320 ligands, 30 compounds exhibited better binding energy compared to the standard drug letrozole. These 30 hits were further considered for the design of two novel molecules which were initially assessed for their ADMET properties followed by pharmacophore mapping, docking and molecular dynamics simulation. The in silico findings suggest that both the designed molecules can be considered drug-like candidates for the treatment of breast cancer through aromatase inhibition. [ABSTRACT FROM AUTHOR]

Background and Purpose: Demand for new antidepressants has resulted in a re‐evaluation of the therapeutic potential of psychedelic drugs. Several tryptamines found in psilocybin‐containing "magic" mushrooms share chemical similarities with psilocybin. Early work suggests they may share biological targets. However, few studies have explored their pharmacological and behavioural effects. Experimental Approach: We compared baeocystin, norbaeocystin and aeruginascin with psilocybin to determine if they are metabolized by the same enzymes, similarly penetrate the blood–brain barrier, serve as ligands for similar receptors and modulate behaviour in rodents similarly. We also assessed the stability and optimal storage and handling conditions for each compound. Key Results: In vitro enzyme kinetics assays found that all compounds had nearly identical rates of dephosphorylation via alkaline phosphatase and metabolism by monoamine oxidase. Further, we found that only the dephosphorylated products of baeocystin and norbaeocystin crossed a blood–brain barrier mimetic to a similar degree as the dephosphorylated form of psilocybin, psilocin. The dephosphorylated form of norbaeocystin was found to activate the 5‐HT2A receptor with similar efficacy to psilocin and norpsilocin in in vitro cell imaging assays. Behaviourally, only psilocybin induced head twitch responses in rats, a marker of 5‐HT2A‐mediated psychedelic effects and hallucinogenic potential. However, like psilocybin, norbaeocystin improved outcomes in the forced swim test. All compounds caused minimal changes to metrics of renal and hepatic health, suggesting innocuous safety profiles. Conclusions and Implications: Collectively, this work suggests that other naturally occurring tryptamines, especially norbaeocystin, may share overlapping therapeutic potential with psilocybin, but without causing hallucinations. [ABSTRACT FROM AUTHOR]

• Total As, As fractions and phosphatase activity reached a significant level. • V max and V max / K m of phosphatase decreased with elevated As pollution. • V max and K m were significantly negatively correlated with soil pH. • Phosphatase is more sensitive to As contamination at the soil's pH. • V max / K m as an index of pollution degree in As field contaminated soil. The pollution and ecological risks posed by arsenic (As) entering the soil are the major environmental challenges faced by human beings. Soil phosphatase can serve as a useful indicator for assessing As contamination under specific soil pH conditions. However, the study of phosphatase kinetics in long-term field As-contaminated soil remains unclear, presenting a significant obstacle to the monitoring and evaluation of As pollution and toxicity. The purpose of this study was to determine phosphatase activity and explore enzyme kinetics in soils subjected to long-term field As contamination. Results revealed that the soil phosphatase activity varied among the tested soil samples, depending on the concentrations of As. The relationship between total As, As fractions and phosphatase activity was found to be significant through negative exponential function fitting. Kinetic parameters, including maximum reaction velocity (V max), Michaelis constant (K m) and catalytic efficiency (V max / K m), ranged from 3.14 × 10−2–53.88 × 10−2 mmol/(L·hr), 0.61–7.92 mmol/L, and 0.46 × 10−2–11.20 × 10−2 hr−1, respectively. V max and V max / K m of phosphatase decreased with increasing As pollution, while K m was less affected. Interestingly, V max / K m showed a significant negative correlation with all As fractions and total As. The ecological doses (ED 10) for the complete inhibition and partial inhibition models ranged from 0.22–70.33 mg/kg and 0.001–55.27 mg/kg, respectively, indicating that V max / K m can be used as an index for assessing As pollution in field-contaminated soil. This study demonstrated that the phosphatase kinetics parameters in the soil's pH system were better indicators than the optimal pH for evaluating the field ecotoxicity of As. [Display omitted] [ABSTRACT FROM AUTHOR]

Kinetic chemical reactions find applications across various fields. In industrial processes, they drive the production of essential materials like fertilizers and pharmaceuticals. In environmental science, they are crucial to understanding pollution dynamics. Additionally, in biochemistry, they underpin vital cellular processes, offering insights into disease mechanisms and drug development. In this work, we present a new advancement of a dynamical system for kinetically controlled chemical reactions and the dependency of its solution on the initial conditions using mathematical techniques for fractional orders. By utilizing this fixed-point approach, we can derive the existence and uniqueness theorem of the proposed model. We further show that the chemical kinetics of the fractional model are stable through the Hyers-Ulam stability condition. We finally run a numerical simulation to verify our conclusions. The manuscript concludes with demonstrative examples. [ABSTRACT FROM AUTHOR]

An analytic solution is presented for the simultaneous substrate elimination problem that combines Michaelis-Menten (MM) consumption with an irreversible homo-dimerization process. The implicit solution involves logarithm and inverse tangent functions and perfectly agrees with the numerical solution of the differential equation. A solution is also presented for the generalized dynamical problem that simultaneously combines MM kinetics with first and second-order processes. The exact expressions for the half-life and the area under the curve are also presented for these problems. [ABSTRACT FROM AUTHOR]

Adaptation of the response to stimuli is a fundamental process for all organisms. Here, we show that the adaptation enzyme CheB methylesterase of Escherichia coli assembles to the ON state receptor array after exposure to the repellent l-isoleucine and dissociates from the array after adaptation is complete. The duration of increased CheB localization and the time of highly clockwise-biased flagellar rotation were similar and depended on the strength of the stimulus. The increase in CheB at the receptor array and the decrease in cytoplasmic CheB were both ~100 molecules, which represents 15 to 20% of the total cellular content of CheB. We confirmed that the main binding site for CheB in the ON state array is the P2 domain of phosphorylated CheA, with a second minor site being the carboxyl-terminal pentapeptide of the serine chemoreceptor. Thus, we have been able to quantify the regulation of the signal output of the receptor array by the intracellular dynamics of an adaptation enzyme. [ABSTRACT FROM AUTHOR]

Age-related macular degeneration (AMD) is a major cause of blindness that affects people over 60. While aging is the prominent factor in AMD, studies have reported a higher prevalence of AMD in women compared to age-matched men. Higher levels of the innate immune response's effector proteins complement factor B and factor I were also found in females compared to males in intermediate AMD. However, the mechanisms underlying these differences remain elusive. Peroxisome proliferator-activated receptor gamma coactivator-1 alpha (PGC-1α) is a key regulator of mitochondrial biogenesis and metabolic pathways. Previously, we showed that Pgc-1α repression and high-fat diet induce drastic AMD-like phenotypes in mice. Our recent data revealed that Pgc-1α repression alone can also induce retinal pigment epithelium (RPE) and retinal dysfunction in mice, and its inhibition in vitro results in lipid droplet accumulation in human RPE. Whether sex is a contributing factor in these phenotypes remains to be elucidated. Using electroretinography, we demonstrate that sex could influence RPE function during aging independent of Pgc-1α in wild-type (WT) mice. We further show that Pgc-1α repression exacerbates RPE and retinal dysfunction in females compared to aged-match male mice. Gene expression analyses revealed that Pgc-1α differentially regulates genes related to antioxidant enzymes and mitochondrial dynamics in males and females. RPE flat mounts immunolabeled with TOMM20 and DRP1 indicated a sex-dependent role for Pgc-1α in regulating mitochondrial fission. Analyses of mitochondrial network morphology suggested sex-dependent effects of Pgc-1α repression on mitochondrial dynamics. Together, our study demonstrates that inhibition of Pgc-1α induces a sex-dependent decline in RPE and retinal function in mice. These observations on the sex-dependent regulation of RPE and retinal function could offer novel insights into targeted therapeutic approaches for age-related RPE and retinal degeneration. [ABSTRACT FROM AUTHOR]

Transcriptional silencing in Saccharomyces cerevisiae is a persistent and highly stable form of gene repression. It involves DNA silencers and repressor proteins that bind nucleosomes. The silenced state is influenced by numerous factors including the concentration of repressors, nature of activators, architecture of regulatory elements, modifying enzymes and the dynamics of chromatin.Silencers function to increase the residence time of repressor Sir proteins at silenced domains while clustering of silenced domains enables increased concentrations of repressors and helps facilitate long-range interactions. The presence of an accessible NDR at the regulatory regions of silenced genes, the cycling of chromatin configurations at regulatory sites, the mobility of Sir proteins, and the non-uniform distribution of the Sir proteins across the silenced domain, all result in silenced chromatin that only stably silences weak promoters and enhancers via changes in transcription burst duration and frequency.These data collectively suggest that silencing is probabilistic and the robustness of silencing is achieved through sub-optimization of many different nodes of action such that a stable expression state is generated and maintained even though individual constituents are in constant flux. [ABSTRACT FROM AUTHOR]

Biomolecular condensates are membraneless organelles that orchestrate various metabolic pathways in living cells. Understanding how these crowded structures regulate enzyme reactions remains yet challenging due to their dynamic and intricate nature. Coacervate microdroplets formed by associative liquid‐liquid phase separation of oppositely charged polyions have emerged as relevant condensate models to study enzyme catalysis. Enzyme reactions within these droplets show altered kinetics, influenced by factors such as enzyme and substrate partitioning, crowding, and interactions with coacervate components; it is often challenging to disentangle the contributions of each. Here, we investigate the peroxidase activity of a de novo enzyme within polysaccharide‐based coacervates. By comparing the reaction kinetics in buffer, in a suspension of coacervates and in the bulk coacervate phase collected after centrifugation of the droplets, we show that the coacervate phase significantly increases the enzyme catalytic efficiency. We demonstrate that the main origin of this enhanced activity lies in macromolecular crowding coupled to changes in the conformational dynamics of the enzyme within the coacervate environment. Altogether, these findings underline the crucial role of the coacervate matrix in enzyme catalysis, beyond simple partitioning effects. The observed boost in enzyme activity within the coacervate phase provides insights for designing biocatalytically active synthetic organelles. [ABSTRACT FROM AUTHOR]

A few computational studies indicated that some inhibitors of viral RNA–polymerase such as favipiravir could also inhibit cysteine proteases. The potential dual action of favipiravir as an inhibitor for both RNA–polymerase and proteases promises enhanced therapeutic efficacy of the drug against coronaviruses. To shed more light on this phenomenon, in view of the chemical structure of favipiravir and the recent advances in this field, six novel derivatives of 3-methyl quinoxaline were synthesized. In silico methods confirmed the abilities of these compounds to occupy the active-site clefts of both 3CLpro and PLpro with favorable interactions, while the ADMET evaluations predicted low toxicity and high bioavailability for them. Then, due to the high similarities between PLpro and papain, the inhibitory impacts of favipiravir and the synthesized quinoxalines on the kinetics of papain were thoroughly investigated. The outcome revealed that the potential dual-action of favipiravir-like compounds is a possibility that should be taken into account in designing more effective and safe drugs against coronavirus. [ABSTRACT FROM AUTHOR]

Loss-of-function Parkin mutations lead to early-onset of Parkinson’s disease. Parkin is an auto-inhibited ubiquitin E3 ligase activated by dual phosphorylation of its ubiquitin-like (Ubl) domain and ubiquitin by the PINK1 kinase. Herein, we demonstrate a competitive binding of the phospho-Ubl and RING2 domains towards the RING0 domain, which regulates Parkin activity. We show that phosphorylated Parkin can complex with native Parkin, leading to the activation of autoinhibited native Parkin in trans. Furthermore, we show that the activator element (ACT) of Parkin is required to maintain the enzyme kinetics, and the removal of ACT slows the enzyme catalysis. We also demonstrate that ACT can activate Parkin in trans but less efficiently than when present in the cis molecule. Furthermore, the crystal structure reveals a donor ubiquitin binding pocket in the linker connecting REP and RING2, which plays a crucial role in Parkin activity [ABSTRACT FROM AUTHOR]

The heterogeneous distribution of lipids and lipid-bound proteins in a plasma membrane has functional advantages. Herein, in a synthetic system, we demonstrate the assembly of three enzymes involved in cascade reactions, in response to the substrate of the first enzyme at the oil–water interface being stabilized by a Zn(II)-metallosurfactant. Then we show substrate-mediated catalytically-active cluster formation of the metallosurfactant in a binary mixture with another non-catalytic surfactant at the interface. The catalytic ability can be tuned by controlling clustering through the addition of phosphate ions. Overall this work demonstrates functionally diverse supramolecular nanoarchitectonics at the oil–water interface. [ABSTRACT FROM AUTHOR]

Organic carbon fixed in chloroplasts through the Calvin–Benson–Bassham Cycle can be diverted toward different metabolic fates, including cytoplasmic and mitochondrial respiration, gluconeogenesis, and synthesis of diverse plastid metabolites via the pyruvate hub. In plants, pyruvate is principally produced via cytoplasmic glycolysis, although a plastid-targeted lower glycolytic pathway is known to exist in non-photosynthetic tissue. Here, we characterized a lower plastid glycolysis–gluconeogenesis pathway enabling the direct interconversion of glyceraldehyde-3-phosphate and phospho-enol-pyruvate in diatoms, ecologically important marine algae distantly related to plants. We show that two reversible enzymes required to complete diatom plastid glycolysis–gluconeogenesis, Enolase and bis-phosphoglycerate mutase (PGAM), originated through duplications of mitochondria-targeted respiratory isoforms. Through CRISPR-Cas9 mutagenesis, integrative 'omic analyses, and measured kinetics of expressed enzymes in the diatom Phaeodactylum tricornutum, we present evidence that this pathway diverts plastid glyceraldehyde-3-phosphate into the pyruvate hub, and may also function in the gluconeogenic direction. Considering experimental data, we show that this pathway has different roles dependent in particular on day length and environmental temperature, and show that the cpEnolase and cpPGAM genes are expressed at elevated levels in high-latitude oceans where diatoms are abundant. Our data provide evolutionary, meta-genomic, and functional insights into a poorly understood yet evolutionarily recurrent plastid metabolic pathway. Environmental and experimental methods reveal the importance of plastid-targeted Enolase and bis-phosphoglycerate mutase enzymes to diatoms, marine algae that contribute to global primary production. [ABSTRACT FROM AUTHOR]

Alginate is a polysaccharide consumed by humans in edible seaweed and different foods where it is applied as a texturizing hydrocolloid or in encapsulations of drugs and probiotics. While gut bacteria are found to utilize and ferment alginate to health-beneficial short-chain fatty acids, knowledge on the details of the molecular reactions is sparse. Alginates are composed of mannuronic acid (M) and its C-5 epimer guluronic acid (G). An alginate-related polysaccharide utilization locus (PUL) has been identified in the gut bacterium Bacteroides eggerthii DSM 20697. The PUL encodes two polysaccharide lyases (PLs) from the PL6 (BePL6) and PL17 (BePL17) families as well as a KdgF-like metalloprotein (BeKdgF) known to catalyze ring-opening of 4,5-unsaturated monouronates yielding 4-deoxy-L-erythro-5-hexoseulose uronate (DEH). B. eggerthii DSM 20697 does not grow on alginate, but readily proliferates with a lag phase of a few hours in the presence of an endo-acting alginate lyase A1-I from the marine bacterium Sphingomonas sp. A1. The B. eggerthii lyases are both exo-acting and while BePL6 is strictly G-block specific, BePL17 prefers M-blocks. BeKdgF retained 10−27% activity in the presence of 0.1−1 mM EDTA. X-ray crystallography was used to investigate the three-dimensional structure of BeKdgF, based on which a catalytic mechanism was proposed to involve Asp102, acting as acid/base having pKa of 5.9 as determined by NMR pH titration. BePL6 and BePL17 cooperate in alginate degradation with BeKdgF linearizing producing 4,5-unsaturated monouronates. Their efficiency of alginate degradation was much enhanced by the addition of the A1-I alginate lyase. [ABSTRACT FROM AUTHOR]

In the pentose phosphate pathway, dehydroepiandrosterone (DHEA) uncompetitively inhibits glucose‐6‐phosphate dehydrogenase (G6PD), reducing NADPH production and increasing oxidative stress, which can influence the onset and/or progression of several diseases, including cancer. 2‐Deoxy‐D‐glucose (2‐DG), a glucose mimetic, competes with glucose for cellular uptake, inhibiting glycolysis and competing with glucose‐6‐phosphate (G‐6‐P) for G6PD activity. In this study, we report that DHEA‐α‐2‐DG (5), an α‐covalent conjugate of DHEA and 2‐DG, exhibits better anticancer activity than DHEA, 2‐DG, DHEA +2‐DG, and polydatin in MCF‐7 cells, and reduces NADPH/NADP+ ratio in cellular assays. In vitro enzyme kinetics and molecular docking studies showed that 5 uncompetitively inhibits human G6PD activity and binds to the structural NADP+ site but not to the catalytic NADP+ site. Further combining 5 with the FDA‐approved drug tamoxifen enhanced its cytotoxicity against MCF‐7 cells, suggesting that it could serve as a candidate for combination of drug strategies. [ABSTRACT FROM AUTHOR]

This study aims to investigate the potential impact of inhibitors targeting the papain-like protease (PLpro) of SARS-CoV-2 on viral replication and the host immune response. A mathematical model was developed to simulate the interaction among susceptible cells, infected cells, PLpro, and immune cells, incorporating data on PLpro inhibition. Through numerical simulations using MATLAB, the model parameters were estimated based on available statistical data. The results indicate that strategically positioned inhibitors could impede the virus’s access to host cellular machinery, thereby enhancing the immune response and gradually reducing susceptible and infected cells over time. The dynamics of the viral enzyme PLpro showed reduced activity with the introduction of the inhibitor, leading to a decline in viral replication. Moreover, the immune cell population exhibited functional recovery as the inhibitor suppressed PLpro activity. These findings suggest that inhibitors targeting PLpro may serve as therapeutic interventions against SARS-CoV-2 by inhibiting viral replication and bolstering the immune response. [ABSTRACT FROM AUTHOR]

Biological soil crusts (biocrusts) are crucial elements of desert ecosystems, exhibiting patchy distribution patterns across the soil surface and significantly impacting surface soil nutrient dynamics. However, the influence of biocrust patch units, serving as fundamental functional entities, on microbial nutrient restriction remains underexplored. This study conducted measurements on moss crust patches of varying sizes and subcrust soils. Stoichiometric analysis of extracellular enzyme activities (EEAs) related to carbon, nitrogen, and phosphorus was performed, along with vector and redundancy analyses to evaluate microbial nutrient limitation and key influencing factors. The findings reveal that both patch size and soil layer of biocrusts collectively influence soil nutrients and enzyme dynamics, with heightened enzyme activity observed in the crust layer. Vector analysis based on EEA stoichiometry indicates that moss crust patch size insignificantly impacts microbial nutrient restriction within the crust layer. However, microbial nitrogen restriction in the subcrust layer demonstrates a “single-peak” trend, initially increasing before gradually declining. This suggests that microorganisms in medium-sized crust patches exhibit peak activity, intensifying nutrient competition. This research underscores the pivotal role of biocrust patch units as fundamental functional entities, offering comprehensive insights into microbial metabolic constraints under crust cover. The findings underscore the significant implications of enzyme stoichiometric characteristics for desert land management and conservation. [ABSTRACT FROM AUTHOR]

In early stages of drug development, the absence of authentic metabolite standards often results in semi-quantitative measurements of metabolite formation in reaction phenotyping studies using mass spectrometry (MS), leading to inaccuracies in the determination of enzyme kinetic parameters, such as the Michaelis constant (K m). Moreover, it is impossible to ascertain the maximum rate of enzyme-catalyzed reactions (k cat or V max). The use of radiolabeled parent compounds can circumvent this problem. However, radiometric detection exhibits significantly lower sensitivity compared to MS. To address these challenges, we have developed a stepwise approach that leverages biosynthesized radiolabeled and non-radiolabeled metabolites as standards, enabling accurate determination of K m , k cat or V max without the need for authentic metabolite standards. This approach, using the carbon-14 [14C] labeled metabolite to calibrate the unlabeled metabolite (14C calibration method), combines radiometric with LC-MS/MS detection to generate both [14C]-labeled and unlabeled metabolite standard curves to ensure that the sample concentrations measured are accurately quantitated. Two case studies were presented to demonstrate the utility of this method. We first compared the accuracy of the 14C calibration method to the use of authentic standards for quantitating imipramine metabolites. Next, we biosynthesized and quantitated the metabolites of BI 894416 using 14C calibration method and evaluated the enzyme kinetics of metabolite formation. The K m values of the metabolite formation demonstrated substantially improved accuracy compared to MS semi-quantitation. Moreover, the 14C calibration method offers a streamlined approach to prepare multiple metabolite standards from a single biosynthesis, reducing the time required for structure elucidation and metabolite synthesis. [ABSTRACT FROM AUTHOR]

Ciliates are a well‐defined, species‐rich, versatile group of heterotrophic and mixotrophic protists. Their response to increased temperature during global warming is critical for the structure and functioning of freshwater food webs.I conducted a meta‐analysis of the literature from field studies and experimental evidence to assess the parameters characterising the thermal response of freshwater ciliates. The shape of the thermal performance curve predicts the ciliates' survival at supraoptimal temperatures (i.e., the width of the thermal safety margin).The ciliates' typical thermal safety margin is c. 5°C. More than two‐thirds of the freshwater ciliates dwelling permanently or occasionally in the pelagial cannot survive at temperatures exceeding 30°C. Likewise, cold‐stenothermic species, which represent a significant fraction of euplanktonic ciliates, cannot survive by evolutionary adaptation to rapidly warming environments.The statistical analysis revealed that the ciliates' thermal performance is affected by their planktonic lifestyle (euplanktonic vs. tychoplanktonic), ability to form cysts and nutritional ecology. Bactivorous ciliates have the widest temperature niche, and algivorous ciliates have the narrowest temperature niche.Phenotypic plasticity and genetic variation, favouring the selection of pre‐adapted species in a new environment, are widespread among freshwater ciliates. However, the lack of evidence for the temperature optima and imprecisely defined tolerance limits of most species hampers the present analysis. The extent of acclimation and adaptation requires further research with more ciliate species than the few chosen thus far.Recent eco‐evolutionary experimental work and modelling approaches have demonstrated that the ciliates' thermal responses follow general trends predicted by the metabolic theory of ecology and mechanistic functions inherent in enzyme kinetics. The present analysis identified current knowledge gaps and avenues for future research that may serve as a model study for other biota. Thermal adaptation may conflict with adaptation to other stressors (predators, food availability, pH), making general predictions on the future role of freshwater ciliates in a warmer environment difficult, if not impossible, at present. [ABSTRACT FROM AUTHOR]

Diabetes mellitus (DM) has become a growing concern to global public health, being at the forefront of acute disorders and causes of mortality across the globe. Clinically approved drugs that are currently being used are faced with severe side effects, consequently necessitating the development of new drugs with no/fewer side effects and improved pharmacological potency. Herein, we report a rapid and efficient synthesis of thiazolidinone Schiff bases (2a-2t) from benzylidenehydrazines and thioglycolic acid under neat conditions through ultra-sonication. All the synthesized compounds were obtained in exceptional yields (89–95%) and confirmed by 1D and 2D nuclear magnetic resonance (NMR) spectroscopy, as well as High-resolution mass spectrometry (HRMS). The synthesized compounds were then evaluated for their antidiabetic activity through α-glucosidase and α-amylase inhibitory potentials and their antioxidant activity through Nitric Oxide (NO), 2,2′-diphenyl-1-picrylhydrazyl (DPPH), and Ferric reducing antioxidant power (FRAP) assays. Among them, 2q (IC50 = 96.63 μM) and 2h (IC50 = 125.27 μM) emerged as the most potent derivatives against α-amylase relative to reference drug acarbose (IC50 = 131.63 µM), respectively. Antioxidant evaluation further revealed that the synthesized derivatives were excellent NO scavengers disclosing 2n (IC50 = 44.95 µM) as the most potent derivative. Moreover, in silico ADME calculations predicted these compounds to have excellent drug-like properties. Kinetic studies disclosed the mode of α-amylase inhibition as competitive while molecular docking studies of the most active derivatives performed into the binding active site of human pancreatic α-amylase enzyme deciphered their ligand-protein interactions that explicated their observed experimental potencies. [ABSTRACT FROM AUTHOR]

The intracellular environment displays complex dynamics influenced by factors such as molecular crowding and the low Reynolds number of the cytoplasm. Enzymes exhibiting active matter properties further heighten this complexity which can lead to memory effects. Molecular simulations often neglect these factors, treating the environment as a "thermal bath" using the Langevin equation (LE) with white noise. One way to consider these factors is by using colored noise instead within the generalized Langevin equation (GLE) framework, which allows for the incorporation of memory effects that have been observed in experimental data. We investigated the structural and dynamic differences in Shikimate kinase (SK) using LE and GLE simulations. Our results suggest that GLE simulations, which reveal significant changes, could be utilized for assessing conformational motions' impact on catalytic reactions. [ABSTRACT FROM AUTHOR]

BACKGROUND: The industrial‐scale application of enzymes faces obstacles due to elevated costs and difficulties in stability and reuse. In this study, magnetic spent coffee grounds, an ecotoxic waste, have been utilized successfully for the first time to immobilize β‐glucosidase to overcome these challenges. RESULTS: The spent coffee grounds were magnetized and amine‐functionalized, followed by characterization using various techniques. Under optimized conditions, forming an imine bond between the functionalized support and β‐glucosidase resulted in a 62% immobilization yield (92.81 mg g−1 enzyme loading) and 12.5 U mg−1 activity after immobilization. A relatively small kinetic change was observed in the Km value (902 to 946 μmol L−1) after immobilization, suggesting minimal hindrance by AMSCG3 on substrate access or product release. Moreover, Glu@AMSCG3 showed exceptional stability (>90% residual activity) within a pH range of 3 to 6 after 2 h of incubation at 25 °C. A residual activity of 87.94% was maintained even at 80 °C and pH 5 after 2 h of incubation compared to the free β‐glucosidase, which showed only 6.5% residual activity at the same temperature. When cellobiose was hydrolyzed using Glu@AMSCG3 under optimum conditions, 91.33% cellobiose conversion was achieved initially, and over 79% conversion was maintained for 10 reusability cycles. CONCLUSION: The improved stability of β‐glucosidase after covalent immobilization on amine‐modified magnetically separable spent coffee grounds indicates their potential as a support matrix for application in enzyme immobilization. © 2024 Society of Chemical Industry (SCI). [ABSTRACT FROM AUTHOR]

Serine proteases have been receiving special attention from the industrial point of view, due to their thermo-stable properties and activity over wide ranges of pH. In the present investigation, a serine protease (49.3 kDa) from jackfruit latex has been purified using chromatographic techniques. Fold purification of the serine protease in the final purification step was 92.41 with 24% yield. The protease is completely inhibited by PMSF, a serine protease-specific inhibitor at a minimal concentration (100 µM). The purified serine protease was immobilized with sodium alginate (2.5%) and calcium chloride (0.3 M) solution. The kinetic studies of immobilized enzyme showed stable activity up to pH 7, and can withstand temperatures up to 45 °C. The immobilization process improves the catalytic efficiency of the enzyme over purified soluble enzyme (for Kcat 1.4 times and for Kcat/Km 1.21 times). Our results depicted that alginate mediated immobilization of serine protease greatly improves the pH and temperature optima which broadens the scope of usage of the enzyme further. [ABSTRACT FROM AUTHOR]

Peroxyacid synthesis is the first step in Prilezhaev epoxidation, which is an industrial method to form epoxides. Motivated by the development of a kinetic model as a tool for solvent selection, the effect of solvent type and acid chain length on the lipase‐catalyzed peroxyacid synthesis was studied. A thermodynamic activity‐based ping‐pong kinetic expression was successfully applied to predict the effect of the reagent loadings in hexane. The activity‐based reaction quotients provided a prediction of solvent‐independent equilibrium constants. However, this strategy did not achieve satisfactory estimations of initial rates in solvents of higher polarity. The lack of compliance with some assumptions of this methodology could be confirmed through molecular dynamics calculations i.e. independent solvation energies and lack of solvent interaction with the active site. A novel approach is proposed combining the activity‐based kinetic expression and the free binding energy of the solvent with the active site to predict kinetics upon solvent change. Di‐isopropyl ether generated a strong interaction with the enzyme's active site, which was detrimental to kinetics. On the other hand, toluene or limonene gave moderate interaction with the active site rendering improved catalytic yield compared with less polar solvents, a finding sharpened when peroctanoic acid was produced. [ABSTRACT FROM AUTHOR]

Neuraminic acid synthases are an important yet underexplored group of enzymes. Thus, in this research, we performed a detailed kinetic and stability analysis and a comparison of previously known neuraminic acid synthase from Neisseria meningitidis, and a novel enzyme, PNH5, obtained from a metagenomic library. A systematic analysis revealed a high level of similarity of PNH5 to other known neuraminic acid synthases, except for its pH optimum, which was found to be at 5.5 for the novel enzyme. This is the first reported enzyme from this family that prefers an acidic pH value. The effect of different metal cofactors on enzyme activity, i.e. Co2+, Mn2+ and Mg2+, was studied systematically. The kinetics of neuraminic acid synthesis was completely elucidated, and an appropriate kinetic model was proposed. Enzyme stability study revealed that the purified enzyme exhibits changes in its structure during time as observed by differential light scattering, which cause a drop in its activity and protein concentration. The operational enzyme stability for the neuraminic acid synthase from N. meningitidis is excellent, where no activity drop was observed during the batch reactor experiments. In the case of PNH5, some activity drop was observed at higher concentration of substrates. The obtained results present a solid platform for the future application of these enzymes in the synthesis of sialic acids. Key points: • A novel neuraminic acid synthase was characterized. • The effect of cofactors on NeuS activity was elucidated. • Kinetic and stability characterization of two neuraminic acid synthases was performed. [ABSTRACT FROM AUTHOR]

Here we investigate the evolutionary dynamics of five enzyme superfamilies (CYPs, GSTs, UGTs, CCEs and ABCs) involved in detoxification in Helicoverpa armigera. The reference assembly for an African isolate of the major lineages, H. a. armigera, has 373 genes in the five superfamilies. Most of its CYPs, GSTs, UGTs and CCEs and a few of its ABCs occur in blocks and most of the clustered genes are in subfamilies specifically implicated in detoxification. Most of the genes have orthologues in the reference genome for the Oceania lineage, H. a. conferta. However, clustered orthologues and subfamilies specifically implicated in detoxification show greater sequence divergence and less constraint on non‐synonymous differences between the two assemblies than do other members of the five superfamilies. Two duplicated CYPs, which were found in the H. a. armigera but not H. a. conferta reference genome, were also missing in 16 Chinese populations spanning two different lineages of H. a. armigera. The enzyme produced by one of these duplicates has higher activity against esfenvalerate than a previously described chimeric CYP mutant conferring pyrethroid resistance. Various transposable elements were found in the introns of most detoxification genes, generating diverse gene structures. Extensive resequencing data for the Chinese H. a. armigera and H. a. conferta lineages also revealed complex copy number polymorphisms in 17 CCE001s in a cluster also implicated in pyrethroid metabolism, with substantial haplotype differences between all three lineages. Our results suggest that cotton bollworm has a versatile complement of detoxification genes which are evolving in diverse ways across its range. [ABSTRACT FROM AUTHOR]

Hyperthermophilic archaea such as Pyrococcus furiosus survive under very aggressive environmental conditions by occupying niches inaccessible to representatives of other domains of life. The ability to survive such severe living conditions must be ensured by extraordinarily efficient mechanisms of DNA processing, including repair. Therefore, in this study, we compared kinetics of conformational changes of DNA Endonuclease Q from P. furiosus during its interaction with various DNA substrates containing an analog of an apurinic/apyrimidinic site (F-site), hypoxanthine, uracil, 5,6-dihydrouracil, the α-anomer of adenosine, or 1,N6-ethenoadenosine. Our examination of DNA cleavage activity and fluorescence time courses characterizing conformational changes of the dye-labeled DNA substrates during the interaction with EndoQ revealed that the enzyme induces multiple conformational changes of DNA in the course of binding. Moreover, the obtained data suggested that the formation of the enzyme–substrate complex can proceed through dissimilar kinetic pathways, resulting in different types of DNA conformational changes, which probably allow the enzyme to perform its biological function at an extreme temperature. [ABSTRACT FROM AUTHOR]

The presence of the odorant 2-methylisoborneol (2-MIB) in drinking water sources is undesirable. Although 2-MIB production is known to be influenced by temperature, its regulation at the gene level and its relationship with Chlorophyll-a (Chl-a) at different temperatures remain unclear. This study investigates the impact of temperature on 2-MIB production and related gene expression in Pseudanabaena strains PD34 and PD35 isolated from Lake Paldang, South Korea. The strains were cultured at three temperatures (15, 25, and 30 °C) to examine cell growth, 2-MIB production, and mic gene expression levels. 2-MIB production per cell increased with higher temperatures, whereas mic gene expression levels were higher at lower temperatures, indicating a complex regulatory mechanism involving post-transcriptional and enzyme kinetics factors. Additionally, the relationship between Chl-a and 2-MIB involved in metabolic competition was analyzed, suggesting that high temperatures appear to favor 2-MIB synthesis more than Chl-a synthesis. The distinct difference in the total amount of the two products and the proportion of 2-MIB between the two strains partially explains the variations in 2-MIB production. These findings highlight the significant effect of temperature on 2-MIB biosynthesis in Pseudanabaena and provide a valuable background for gene data-based approaches to manage issues regarding 2-MIB in aquatic environments. [ABSTRACT FROM AUTHOR]

Background: Aminoglycoside-modifying enzymes (AMEs) play an essential role in bacterial resistance to aminoglycoside antimicrobials. With the development of sequencing techniques, more bacterial genomes have been sequenced, which has aided in the discovery of an increasing number of novel resistance mechanisms. Methods: The bacterial species was identified by 16S rRNA gene homology and average nucleotide identity (ANI) analyses. The minimum inhibitory concentration (MIC) of each antimicrobial was determined by the agar dilution method. The protein was expressed with the pCold I vector in E. coli BL21, and enzyme kinetic parameters were examined. The whole-genome sequence of the bacterium was obtained via the Illumina and PacBio sequencing platforms. Reconstruction of the phylogenetic tree, identification of conserved functional residues, and gene context analysis were performed using the corresponding bioinformatic techniques. Results: A novel aminoglycoside resistance gene, designated aph(3')-Ie, which confers resistance to ribostamycin, kanamycin, sisomicin and paromomycin, was identified in the chromosome of the animal bacterium Citrobacter gillenii DW61, which exhibited a multidrug resistance phenotype. APH(3')-Ie showed the highest amino acid identity of 74.90% with the functionally characterized enzyme APH(3')-Ia. Enzyme kinetics analysis demonstrated that it had phosphorylation activity toward four aminoglycoside substrates, exhibiting the highest affinity (Km, 4.22 ± 0.88 µM) and the highest catalytic efficiency [kcat/Km, (32.27 ± 8.14) × 104] for ribomycin. Similar to the other APH(3') proteins, APH(3')- Ie contained all the conserved functional sites of the APH family. The aph(3')-Ie homologous genes were present in C. gillenii isolates from different sources, including some of clinical significance. Conclusion: In this work, a novel chromosomal aminoglycoside resistance gene, designated aph(3')-Ie, conferring resistance to aminoglycoside antimicrobials, was identified in a rabbit isolate C. gillenii DW61. The elucidation of the novel resistance mechanism will aid in the effective treatment of infections caused by pathogens carrying such resistance genes. [ABSTRACT FROM AUTHOR]

Lactate dehydrogenase A (LDHA) is highly expressed in many tumor cells and promotes the conversion of pyruvate to lactic acid in the glucose pathway, providing energy and synthetic precursors for rapid proliferation of tumor cells. Therefore, inhibition of LDHA has become a widely concerned tumor treatment strategy. However, the research and development of highly efficient and low toxic LDHA small molecule inhibitors still faces challenges. To discover potential inhibitors against LDHA, virtual screening based on molecular docking techniques was performed from Specs database of more than 260,000 compounds and Chemdiv-smart database of more than 1,000 compounds. Through molecular dynamics (MD) simulation studies, we identified 12 potential LDHA inhibitors, all of which can stably bind to human LDHA protein and form multiple interactions with its active central residues. In order to verify the inhibitory activities of these compounds, we established an enzyme activity assay system and measured their inhibitory effects on recombinant human LDHA. The results showed that Compound 6 could inhibit the catalytic effect of LDHA on pyruvate in a dose-dependent manner with an EC50 value of 14.54 ± 0.83 µM. Further in vitro experiments showed that Compound 6 could significantly inhibit the proliferation of various tumor cell lines such as pancreatic cancer cells and lung cancer cells, reduce intracellular lactic acid content and increase intracellular reactive oxygen species (ROS) level. In summary, through virtual screening and in vitro validation, we found that Compound 6 is a small molecule inhibitor for LDHA, providing a good lead compound for the research and development of LDHA related targeted anti-tumor drugs. [ABSTRACT FROM AUTHOR]

Phosphoryl transfer is a fundamental reaction in cellular signaling and metabolism that requires Mg2+ as an essential cofactor. While the primary function of Mg2+ is electrostatic activation of substrates, such as ATP, the full spectrum of catalytic mechanisms exerted by Mg2+ is not known. In this study, we integrate structural biology methods, molecular dynamic (MD) simulations, phylogeny, and enzymology assays to provide molecular insights into Mg2+-dependent structural reorganization in the active site of the metabolic enzyme adenylate kinase. Our results demonstrate that Mg2+ induces a conformational rearrangement of the substrates (ATP and ADP), resulting in a 30° adjustment of the angle essential for reversible phosphoryl transfer, thereby optimizing it for catalysis. MD simulations revealed transitions between conformational substates that link the fluctuation of the angle to large-scale enzyme dynamics. The findings contribute detailed insight into Mg2+ activation of enzymes and may be relevant for reversible and irreversible phosphoryl transfer reactions. [ABSTRACT FROM AUTHOR]

This article explores the synthesis of β-N-oxalyl-l-α,β-diaminopropionic acid (β-ODAP) in grass pea, a legume commonly grown in Asia and Africa. The authors present conflicting findings regarding the enzymes responsible for β-ODAP synthesis. They challenge a previous study's claim that the enzyme LsAAE3 is involved, instead proposing that LsBOS is responsible. The authors provide evidence supporting their own two-step mechanism for β-ODAP synthesis and refute the claim that LsAAE3 has evolved to repurpose its activity. Understanding the production of β-ODAP is crucial for developing grass pea cultivars without the neurotoxic compound. [Extracted from the article]

Human terminal deoxynucleotidyl transferase (TdT) can catalyze template-independent DNA synthesis during the V(D)J recombination and DNA repair through nonhomologous end joining. The capacity for template-independent random addition of nucleotides to single-stranded DNA makes this polymerase useful in various molecular biological applications involving sequential stepwise synthesis of oligonucleotides using modified dNTP. Nonetheless, a serious limitation to the applications of this enzyme is strong selectivity of human TdT toward dNTPs in the order dGTP > dTTP ≈ dATP > dCTP. This study involved molecular dynamics to simulate a potential impact of amino acid substitutions on the enzyme's selectivity toward dNTPs. It was found that the formation of stable hydrogen bonds between a nitrogenous base and amino acid residues at positions 395 and 456 is crucial for the preferences for dNTPs. A set of single-substitution and double-substitution mutants at these positions was analyzed by molecular dynamics simulations. The data revealed two TdT mutants—containing either substitution D395N or substitutions D395N+E456N—that possess substantially equalized selectivity toward various dNTPs as compared to the wild-type enzyme. These results will enable rational design of TdT-like enzymes with equalized dNTP selectivity for biotechnological applications. [ABSTRACT FROM AUTHOR]

Melanin naturally exists in organisms and is synthetized by tyrosinase (TYR); however, its over-production may lead to aberrant pigmentation and skin conditions. Loquat (Eriobotrya japonica (Thunb.) Lindl.) flowers contain a variety of bioactive compounds, while studies on their suppressive capabilities against melanin synthesis are limited. Loquat flower isolate product (LFP) was obtained by ethanol extraction and resin purification, and its inhibitory efficiency against TYR activity was investigated by enzyme kinetics and multiple spectroscopy analyses. In addition, the impact of LFP on melanin synthesis-related proteins' expression in mouse melanoma B16 cells was analyzed using Western blotting. HPLC-MS/MS analysis indicated that LFP was composed of 137 compounds, of which 12 compounds, including flavonoids (quercetin, isorhamnoin, p-coumaric acid, etc.) and cinnamic acid and its derivatives, as well as benzene and its derivatives, might have TYR inhibitory activities. LFP inhibited TYR activity in a concentration-dependent manner with its IC50 value being 2.8 mg/mL. The inhibition was an anti-competitive one through altering the enzyme's conformation rather than chelating copper ions at the active center. LFP reduced the expression of TYR, tyrosinase-related protein (TRP) 1, and TRP2 in melanoma B16 cells, hence inhibiting the synthesis of melanin. The research suggested that LFP had the potential to reduce the risks of hyperpigmentation caused by tyrosinase and provided a foundation for the utilization of loquat flower as a natural resource in the development of beauty and aging-related functional products. [ABSTRACT FROM AUTHOR]

Polyphenol oxidase (PPO) is an industrially important enzyme associated with browning reactions. In the present study, a set of ten new dihydropyridine [2,3-d] pyrimidines (TD-Hid-1-10) were synthesized and was found to be proven characteristically by 1H NMR, 13C NMR, IR, elemental analysis, and assessed as possible PPO inhibitors. PPO was purified from banana using three-phase partitioning, achieving an 18.65-fold purification and 136.47% activity recovery. Enzyme kinetics revealed that the compounds TD-Hid-6 and TD-Hid-7 are to be the most potent inhibitors, exhibiting mixed-type inhibition profile with IC50 values of 1.14 µM, 5.29 µM respectively against purified PPO enzyme. Electronic structure calculations at the B3LYP/PBE0 level of theories using def-2 SVP, def2-TZVP basis sets with various molecular descriptors characterized the electronic behavior of studied derivatives TD-Hid-1-10. Molecular electrostatic potential (MEP) and reduced density gradient analyses of RDG-NCI provided insights into charge distributions and weak intermolecular interactions. Docking study simulations predicted binding poses within crucial amino acid sequence in the 2y9x enzyme's active site, which is typically similar in sequence to the PPO form is not allowed. Ligands were analysed in terms of binding energies, inhibitor concentrations (mM) and various molecular interactions such as H-bonds, H-carbon, π-carbon, π-sigma, π-sigma, π-π T-shaped, π-π stacked, π-alkyl, Van der Waals and Cu interactions. The lowest binding energy (-7.83 kcal/mol) and the highest inhibitory effect (1.83 mM) were shown by the ligand Td-Hid-6, which forms H-bonds with Met280 and Asn260, exhibits π-sigma interactions with His61 and π-alkyl interactions with Val283. Other ligands also showed different interactions with various amino acids; for example, the Td-Hid-1 ligand formed H-bonds with His244 and showed π-sigma interactions with His244 and Val283. [ABSTRACT FROM AUTHOR]

Fructose bisphosphate aldolases (FBAs) catalyze the reversible cleavage of fructose 1,6‐bisphosphate into dihydroxyacetone phosphate and glyceraldehyde 3‐phosphate. We analyzed two previously uncharacterized cytosolic Arabidopsis FBAs, AtFBA4 and AtFBA5. Based on a recent report, we examined the interaction of AtFBA4 with calmodulin (CaM)‐like protein 11 (AtCML11). AtFBA4 did not bind AtCML11; however, we found that CaM bound AtFBA5 in a Ca2+‐dependent manner with high specificity and affinity (KD ~ 190 nm) and enhanced its stability. AtFBA4 and AtFBA5 exhibited Michaelis–Menten kinetics with Km and Vmax values of 180 μm and 4.9 U·mg−1 for AtFBA4, and 6.0 μm and 0.30 U·mg−1 for AtFBA5, respectively. The flavonoid morin inhibited both isozymes. Our study suggests that Ca2+ signaling and flavanols may influence plant glycolysis/gluconeogenesis. [ABSTRACT FROM AUTHOR]

Cover crops between rows in orchards can improve the development of soil resources and increase agricultural productivity. However, there have been few reports of cover crops that can act as a "green manure" in apple orchards across arid and semiarid zones. This study investigated the effects of planting interrow vegetation on soil properties and apple tree performance during a 32-month experiment. There were six treatments: clean cultivation as a control; natural grass planting; planting with ryegrass; planting with alfalfa; planting with tall fescue; and planting with villous wild pea cover crops. The treatments primarily affected the 0- to 20-cm surface soil layer. Soil carbon, nitrogen, and enzyme levels initially decreased (during the first 12-24 months); then, they increased (24-32 months). The cover crops significantly increased nutrient contents (soluble organic carbon, microbial carbon and nitrogen, alkaline dissolved nitrogen, nitrate nitrogen, and ammonium nitrogen) in the 0- to 20-cm soil layer by more than 19.6% and increased the related enzyme activities by more than 25.2%. The alfalfa and wild pea alleys had a stronger effect on the soil environment than the control, natural grass, ryegrass, and tall fescue alley treatments; however, after 32 months, the alfalfa treatment inhibited fruit tree growth and development. This was unexpected because alfalfa seemed to have a positive effect on soil fertility characteristics. Under local ecological conditions, villous wild pea had the greatest effect on apple orchard productivity and significantly increased short branching by 15.9%, fruit weight per fruit by 12.6%, yield per plant by 8.6%, and soluble sugar content by 10.5% compared with clean cultivation. The correlation analysis showed that there were significant or highly significant positive correlations between fruit tree performance and soil carbon, nitrogen, and enzyme activity levels as the soil layer depth increased. Therefore, under local ecological conditions, cover crops have a greater effect on orchard surface soil fertility than on deeper soils, and intercropping with villous wild pea potentially produces the greatest improvement in apple orchard productivity. [ABSTRACT FROM AUTHOR]

Polygonatum sibiricum polysaccharide (PSP) was extracted and purified from raw material obtained from P. sibiricum. The structural features of PSP were investigated by Congo red, circular dichroism spectrum, high‐performance gel permeation chromatography, scanning electron microscope, atomic force microscope, ultraviolet spectroscopy, and Fourier transform infrared spectroscopy analysis. In vitro simulations were conducted to investigate the kinetics of PSP enzyme inhibition. Moreover, a type II diabetes mouse model (T2DM) with streptozotocin‐induced insulin resistance was established, and the indexes of lipid quadruple, insulin resistance index, oral glucose tolerance (OGTT), organ index, and pancreatic morphology of model mice were measured. The results showed that PSP mainly consists of monosaccharides, such as mannose, glucose, galactose, xylose, and arabinose. It also has a β‐glycosidic bond of a pyranose ring and an irregular reticulated aggregated structure with a triple helix. In vitro enzyme inhibition assays revealed that PSP acts as a reversible competitive inhibitor of α‐glucosidase and α‐amylase. Furthermore, PSP was found to reduce insulin resistance index, increase OGTT and serum insulin levels, decrease free fatty acid content to improve lipid metabolism, and lower glycated serum protein content to enhance glucose metabolism in T2DM mice, thereby leading to a reduction in blood glucose concentration. Additionally, PSP exhibited reparative effects on the damaged liver tissue cells and pancreatic tissue in T2DM mice. The experiment results provide a preliminary basis for the therapeutic mechanism of PSP about type II diabetes and a theoretical reference for application in food and pharmaceutical development. [ABSTRACT FROM AUTHOR]

Daucosterol (DAU) was isolated from the methanol-chloroform crude extract of six Nepeta species (N. aristata , N. baytopii, N. italica, N. nuda albiflora, N. stenantha and N. trachonitica) using sephadex and silica-gel columns via bioactivity-guided isolation. Spectroscopic methods and comparisons with similar data in the literature determined its structure. DAU was evaluated for enzyme inhibitions, kinetics, DNA protection, and molecular interactions. The inhibition activities of AChE, tyrosinase, BChE, and urease were found to be 21.32±1.24, 3.17±0.45, 16.73±0.10 and 12.95±0.21 μM, respectively. The K i values of the inhibition kinetics of the same enzymes were observed as 0.11, 0.05, 0.12, and 0.12 mM, respectively. DAU exhibited effective protection activity against DNA damage induced by H 2 O 2 and ultraviolet radiation in DNA protection tests. DFT analysis showed low hardness and high softness values. The best binding affinity of DAU was achieved by the enzymes AChE and BChE (for both: −9.90 kcal/mol). As a result of the interaction of standards and DAU with enzymes, it was observed that DAU bound with a higher potential than the standards. Molecular dynamics simulations of these enzymes were examined for 100 ns, and the energy results of the simulation were determined by MM/PBSA calculation in the last 10 ns. Additionally, its pharmacokinetic properties were investigated with SwissADMET, and it was noted that it had low toxic effects and gastrointestinal absorption. Thus, in vitro and in silico analysis determined that the DAU molecule could protect against DNA oxidative damage and an active metabolic enzyme inhibitor. [Display omitted] • Daucosterol was isolated from six different Nepeta species by activity-guided isolation • Daucosterol had potent enzyme inhibition and DNA protection activities • Urease inhibition kinetics and molecular interactions of daucosterol were studied for the first time • Daucosterol exhibited favorable binding constants and affinities with BChE and tyrosinase. [ABSTRACT FROM AUTHOR]

Thrombosis is a dangerous condition that can result in major damage. Fibrinolytic enzymes are significant therapeutic agents for thrombosis. This study focused on MsFE, a fibrinolytic protease from M. subtilissimus UCP1262, exploring its physicochemical traits and the impact of gamma radiation on its activity. Investigations included: fibrinogenolytic activity, effects of solvents and ions, gamma rays, enzyme shelf life, FTIR, CD, clotted times determination, and enzymatic kinetics. Notably, the major results obtained show the protease retained 90 % activity in organic solvents, FTIR indicated carbonyl functional groups and Circular dichroism spectroscopic studies indicated that the secondary structure (β-sheet) of enzyme remains mostly unaffected over pH 2.0–9.0, whereas considerable changes were observed in the tertiary structure. Kinetic analysis revealed altered parameters post-irradiation. Gamma radiation initially enhanced enzyme activity (10 kGy) but progressively decreased beyond 20 kGy. Metallic ions, especially magnesium, augmented irradiated enzyme activity. This study highlights gamma radiation's potential as a modulator for enhanced fibrinolytic activity, suggesting future biomedical applications. [Display omitted] • Mucor subtilissimus proves its significance as a producer of fibrinolytic proteases. • The protease degrades the α, β and γ chains of fibrinogen. • The 10 kGy radiation increased the activity of the enzyme by approximately 10 %. • Fe2+, Cu2+ and Mg2+ were able to increase the activity of the irradiated enzyme. • Produced enzymes can be a highly productive fibrinolytic for medical applications. [ABSTRACT FROM AUTHOR]

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Anaerobic fungi found in the guts of large herbivores are prolific biomass degraders whose genomes harbor a wealth of carbohydrate-active enzymes (CAZymes), of which only a handful are structurally or biochemically characterized. Here, we report the structure and kinetic rate parameters for a glycoside hydrolase (GH) family 5 subfamily 4 enzyme (CelD) from Piromyces finnis, a modular, cellulosome-incorporated endoglucanase that possesses three GH5 domains followed by two C-terminal fungal dockerin domains (double dockerin). We present the crystal structures of an apo wild-type CelD GH5 catalytic domain and its inactive E154A mutant in complex with cellotriose at 2.5 and 1.8 Å resolution, respectively, finding the CelD GH5 catalytic domain adopts the (β/α)8-barrel fold common to many GH5 enzymes. Structural superimposition of the apo wild-type structure with the E154A mutant-cellotriose complex supports a catalytic mechanism in which the E154 carboxylate side chain acts as an acid/base and E278 acts as a complementary nucleophile. Further analysis of the cellotriose binding pocket highlights a binding groove lined with conserved aromatic amino acids that when docked with larger cellulose oligomers is capable of binding seven glucose units and accommodating branched glucan substrates. Activity analyses confirm P. finnis CelD can hydrolyze mixed linkage glucan and xyloglucan, as well as carboxymethylcellulose (CMC). Measured kinetic parameters show the P. finnis CelD GH5 catalytic domain has CMC endoglucanase activity comparable to other fungal endoglucanases with kcat = 6.0 ± 0.6 s-1 and Km = 7.6 ± 2.1 g/L CMC. Enzyme kinetics were unperturbed by the addition or removal of the native C-terminal dockerin domains as well as the addition of a non-native N-terminal dockerin, suggesting strict modularity among the domains of CelD. KEY POINTS: • Anaerobic fungi host a wealth of industrially useful enzymes but are understudied. • P. finnis CelD has endoglucanase activity and structure common to GH5_4 enzymes. • CelDs kinetics do not change with domain fusion, exhibiting high modularity.