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Initial velocity and product inhibition studies of Toxoplasma gondii adenosine kinase (TgAK, EC 2.7.1.20) demonstrated that the basic mechanism of this enzyme is a hybrid random bi-uni ping-pong uni-bi. Initial velocity studies showed an intersecting pattern, consistent with substrate-enzyme-co-substrate complex formation and a binding pattern indicating that binding of the substrate interferes with the binding of the co-substrate and vice versa. Estimated kinetic parameters were KAdo=0.002±0.0002 mM, KATP=0.05±0.008 mM, and Vmax=920±35 μmol/min/mg protein. Ado exhibited substrate inhibition suggesting the presence of more than one binding site for Ado on the enzyme. ATP relieved substrate inhibition by Ado. Thus, Ado also binds to the ATP binding site. AMP was competitive with ATP, inferring that AMP binds to the same site as ATP. AMP, ADP and ATP were non-competitive with Ado, therefore, none of these nucleotides binds to the Ado binding site. Combining ATP with ADP was additive. Therefore, the binding of either ATP or ADP does not interfere with the binding of the other. It is concluded that for every ATP consumed, TgAK generates three new AMPs. These findings along with the fact that a wide range of nucleoside 5'-mono, di, and triphosphates could substitute for ATP as phosphate donors in this reaction may explain the efficient and central role played by TgAK in the utilization of Ado as the major source from which all other purines can be synthesized in T. gondii., (Copyright © 2015 Elsevier Inc. All rights reserved.)

An increased understanding of how the acceptor site in Gcn5-related N-acetyltransferase (GNAT) enzymes recognizes various substrates provides important clues for GNAT functional annotation and their use as chemical tools. In this study, we explored how the PA3944 enzyme from Pseudomonas aeruginosa recognizes three different acceptor substrates, including aspartame, NANMO, and polymyxin B, and identified acceptor residues that are critical for substrate specificity. To achieve this, we performed a series of molecular docking simulations and tested methods to identify acceptor substrate binding modes that are catalytically relevant. We found that traditional selection of best docking poses by lowest S scores did not reveal acceptor substrate binding modes that were generally close enough to the donor for productive acetylation. Instead, sorting poses based on distance between the acceptor amine nitrogen atom and donor carbonyl carbon atom placed these acceptor substrates near residues that contribute to substrate specificity and catalysis. To assess whether these residues are indeed contributors to substrate specificity, we mutated seven amino acid residues to alanine and determined their kinetic parameters. We identified several residues that improved the apparent affinity and catalytic efficiency of PA3944, especially for NANMO and/or polymyxin B. Additionally, one mutant (R106A) exhibited substrate inhibition toward NANMO, and we propose scenarios for the cause of this inhibition based on additional substrate docking studies with R106A. Ultimately, we propose that this residue is a key gatekeeper between the acceptor and donor sites by restricting and orienting the acceptor substrate within the acceptor site.

Objectives An Escherichia coli isolate, WGS1363, showed resistance to piperacillin/tazobactam but susceptibility to cephalosporins and contained a previously unrecognized β-lactamase, CTX-M-255, as the only acquired β-lactamase. CTX-M-255 was identical to CTX-M-27 except for a G239S substitution. Here, we characterize the hydrolytic spectrum of CTX-M-255 and a previously reported β-lactamase, CTX-M-178, also containing a G239S substitution and compare it to their respective parental enzymes, CTX-M-27 and CTX-M-15. Methods All β-lactamase genes were expressed in E. coli TOP10 and MICs to representative β-lactam-antibiotics were determined. Furthermore, bla CTX-M-15,   bla CTX-M-27, bla CTX-M-178 and bla CTX-M-255 with C-terminal His-tag fusions were affinity purified for enzyme kinetic assays determining Michaelis–Menten kinetic parameters against representative β-lactam-antibiotics and IC50s of clavulanate, sulbactam, tazobactam and avibactam. Results TOP10-transformants expressing bla CTX-M-178 and bla CTX-M-255 showed resistance to penicillin/β-lactamase combinations and susceptibility to cephalothin and cefotaxime in contrast to transformants expressing bla CTX-M-15 and bla CTX-M-27. Determination of enzyme kinetic parameters showed that CTX-M-178 and CTX-M-255 both lacked hydrolytic activity against cephalosporins and showed impaired hydrolytic efficiency against penicillin antibiotics compared to their parental enzymes. Both enzymes appeared more active against piperacillin compared to benzylpenicillin and ampicillin. Compared to their parental enzymes, IC50s of β-lactamase-inhibitors were increased more than 1000-fold for CTX-M-178 and CTX-M-255. Conclusions CTX-M-178 and CTX-M-255, both containing a G239S substitution, conferred resistance to piperacillin/tazobactam and may be characterized as inhibitor-resistant CTX-M β-lactamases. Inhibitor resistance was accompanied by loss of activity against cephalosporins and monobactams. These findings add to the necessary knowledge base for predicting antibiotic susceptibility from genotypic data. [ABSTRACT FROM AUTHOR]

Background: The enzyme phenylalanine ammonia lyase (PAL) controls the transition from primary to secondary metabolism by converting L-phenylalanine (L-Phe) to cinnamic acid. However, the function of PAL in pear plants (Pyrus bretschneideri) has not yet been fully elucidated. Results: We identified three PAL genes (PbPAL1, PbPAL2 and PbPAL3) from the pear genome by exploring pear genome databases. The evolutionary tree revealed that three PbPALs were classified into one group. We expressed PbPAL1 and PbPAL2 recombinant proteins, and the purified PbPAL1 and PbPAL2 proteins showed strict substrate specificity for L-Phe, no activity toward L-Tyr in vitro, and modest changes in kinetics and enzyme characteristics. Furthermore, overexpression of PbAL1 and PbPAL1-RNAi, respectively, and resulted in significant changes in stone cell and lignin contents in pear fruits. The results of yeast one-hybrid (Y1H) assays that PbWLIM1 could bind to the conserved PAL box in the PbPAL promoter and regulate the transcription level of PbPAL2. Conclusions: Our findings not only showed PbPAL's potential role in lignin biosynthesis but also laid the foundation for future studies on the regulation of lignin synthesis and stone cell development in pear fruit utilizing molecular biology approaches. [ABSTRACT FROM AUTHOR]

Sarcoplasmic reticulum Ca2+-ATPases (SERCAs) regulate cellular calcium homeostasis and are targeted for age-related diseases. Among 14 SERCA mRNA splice variants, SERCA1a is specific to adult fast-twitch skeletal muscle. Quercetin derivatives (monochloropivaloylquercetin (CPQ), IC50 = 195.7 µM; 2-chloro-1,4-naphthoquinonequercetin (CHNQ), IC50 = 60.3 µM) were studied for their impact on SERCA1a using molecular modeling and enzyme kinetics. While there were some similarities in kinetic parameters and molecular modeling, the compounds exhibited diverse actions on SERCA1a. Quercetin reduced activity by 48% at 250 μM by binding to the cytosolic ATP-binding pocket with increased ATP affinity. CPQ bound near the Ca2+-binding site, possibly altering the transmembrane domain. CHNQ significantly reduced activity by 94% at 250 μM without binding to substrate sites. It was proposed that CHNQ induced global protein structure changes, inhibiting Ca2+-ATPase activity [ABSTRACT FROM AUTHOR]

Monoamine oxidase (MAO, EC 1.4.3.4) is responsible for the oxidative breakdown of both endogenous and exogenous amines and exists in MAO-A and MAO-B isomers. Eighteen indole-based phenylallylidene derivatives were synthesized via nucleophilic addition reactions comprising three sub-series, IHC, IHMC, and IHNC, and were developed and examined for their ability to inhibit MAO. Among them, compound IHC3 showed a strong MAO-B inhibitory effect with an IC50 (half-maximal inhibitory concentration) value of 1.672 μM, followed by IHC2 (IC50 = 16.934 μM). Additionally, IHC3 showed the highest selectivity index (SI) value of >23.92. The effectiveness of IHC3 was lower than the reference pargyline (0.14 μM); however, the SI value was higher than pargyline (17.16). Structurally, the IHC (-H in the B-ring) sub-series exhibited relatively stronger MAO-B inhibition than the others. In the IHC series, IHC3 (-F in the A-ring) exhibited stronger MAO-B suppression than the other substituted derivatives in the order -F > -Br > -Cl > -OCH3, -CH3, and -H at the 2-position in the A-ring. In the reversibility and enzyme kinetics experiments, IHC3 was a reversible inhibitor with a Ki value of 0.51 ± 0.15 μM for MAO-B. Further, it was observed that IHC3 greatly decreased the cell death caused by rotenone in SH-SY5Y neuroblastoma cells. A molecular docking study of the lead molecule was also performed to determine hypothetical interactions in the enzyme-binding cavity. These findings suggest that IHC3 is a strong, specific, and reversible MAO-B inhibitor that can be used to treat neurological diseases. [ABSTRACT FROM AUTHOR]

Featured Application: This manuscript describes the microwave inactivation kinetics of α-amylase enzyme for application as a time-temperature integrator in conventional or microwave heating. The demonstrated pH-dependent inactivation kinetics of α-amylase are valuable because they show that the thermal resistance of α-amylase varies with pH, and, therefore, a suitable pH can be used to employ α-amylase as a model for testing the efficiency of different thermal processes. The inactivation kinetics of an α-amylase enzymatic time-temperature integrator (TTI) from Bacillus subtilis (BAA) under continuous-flow microwave (MW) and conventional heating conditions were evaluated and compared in this study. The TTI dispersed in a buffer solution (pH 5.0 to 6.9) at 20 °C initially, and it was continuously circulated through two helical coils connected in a series for heating. The two coils were positioned in two domestic microwave ovens (2450 MHz and 1000 W nominal capacity each) and connected by a short tube. The sample flow rates were adjusted to result in a specific exit temperature in the range of 65 to 80 °C. A short fully insulated helical coil at the exit of the second oven was used as a holding tube. Test samples were drawn either at the exit of the second MW oven or immediately after the holding tube. The decimal reduction times obtained under conventional batch heating conditions decreased from 66 to 24 s as the temperature changed from 70 to 75 °C at pH 5.0 while they decreased from 8 to 5 s under MW in the same temperature range, but at pH 6.0, they increased both under conventional and microwave heating conditions (138 to 120 s and 89 to 61 s, respectively). The D-values under conventional thermal holding were four–eight times higher than under a continuous-flow MW heating condition. By varying the pH, the D-values could be modified to suit the validation of appropriate processing conditions. [ABSTRACT FROM AUTHOR]

Copyright of Journal of East China University of Science & Technology is the property of Journal of East China University of Science & Technology Editorial Office and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Currently, there are three major assaying methods used to validate in vitro whitening activity from natural products: methods using mushroom tyrosinase, human tyrosinase, and dopachrome tautomerase (or tyrosinase-related protein-2, TRP-2). Whitening agent development consists of two ways, melanin synthesis inhibition in melanocytes and downregulation of melanocyte stimulation. For melanin levels, the melanocyte cell line has been used to examine melanin synthesis with the expression levels of TRP-1 and TRP-2. The proliferation of epidermal surfaced cells and melanocytes is stimulated by cellular signaling receptors, factors, or mediators including endothelin-1, α-melanocyte-stimulating hormone, nitric oxide, histamine, paired box 3, microphthalmia-associated transcription factor, pyrimidine dimer, ceramide, stem cell factors, melanocortin-1 receptor, and cAMP. In addition, the promoter region of melanin synthetic genes including tyrosinase is upregulated by melanocyte-specific transcription factors. Thus, the inhibition of growth and melanin synthesis in gene expression levels represents a whitening research method that serves as an alternative to tyrosinase inhibition. Many researchers have recently presented the bioactivity-guided fractionation, discovery, purification, and identification of whitening agents. Melanogenesis inhibition can be obtained using three different methods: tyrosinase inhibition, copper chelation, and melanin-related protein downregulation. There are currently four different types of inhibitors characterized based on their enzyme inhibition mechanisms: competitive, uncompetitive, competitive/uncompetitive mixed-type, and noncompetitive inhibitors. Reversible inhibitor types act as suicide substrates, where traditional inhibitors are classified as inactivators and reversible inhibitors based on the molecule-recognizing properties of the enzyme. In a minor role, transcription factors can also be downregulated by inhibitors. Currently, the active site copper iron-binding inhibitors such as kojic acid and chalcone exhibit tyrosinase inhibitory activity. Because the tyrosinase catalysis site structure is important for the mechanism determination of tyrosinase inhibitors, understanding the enzyme recognition and inhibitory mechanism of inhibitors is essential for the new development of tyrosinase inhibitors. The present review intends to classify current natural products identified by means of enzyme kinetics and copper chelation to exhibit tyrosinase enzyme inhibition. [ABSTRACT FROM AUTHOR]

Isocitrate dehydrogenase 1 (IDH1) catalyzes the reversible NADP+-dependent conversion of isocitrate to α-ketoglutarate (αKG) to provide critical cytosolic substrates and drive NADPH-dependent reactions like lipid biosynthesis and glutathione regeneration. In biochemical studies, the forward reaction is studied at neutral pH, while the reverse reaction is typically characterized in more acidic buffers. This led us to question whether IDH1 catalysis is pH-regulated, which would have functional implications under conditions that alter cellular pH, like apoptosis, hypoxia, cancer, and neurodegenerative diseases. Here, we show evidence of catalytic regulation of IDH1 by pH, identifying a trend of increasing kcat values for αKG production upon increasing pH in the buffers we tested. To understand the molecular determinants of IDH1 pH sensitivity, we used the pHinder algorithm to identify buried ionizable residues predicted to have shifted pKa values. Such residues can serve as pH sensors, with changes in protonation states leading to conformational changes that regulate catalysis. We identified an acidic residue buried at the IDH1 dimer interface, D273, with a predicted pKa value upshifted into the physiological range. D273 point mutations had decreased catalytic efficiency and, importantly, loss of pH-regulated catalysis. Based on these findings, we conclude that IDH1 activity is regulated, at least in part, by pH. We show this regulation is mediated by at least one buried acidic residue ∼12 Å from the IDH1 active site. By establishing mechanisms of regulation of this well-conserved enzyme, we highlight catalytic features that may be susceptible to pH changes caused by cell stress and disease.

Formate oxidation to carbon dioxide is a key reaction in one-carbon compound metabolism, and its reverse reaction represents the first step in carbon assimilation in the acetogenic and methanogenic branches of many anaerobic organisms. The molybdenum-containing dehydrogenase FdsABG is a soluble NAD+-dependent formate dehydrogenase and a member of the NADH dehydrogenase superfamily. Here, we present the first structure of the FdsBG subcomplex of the cytosolic FdsABG formate dehydrogenase from the hydrogen-oxidizing bacterium Cupriavidus necator H16 both with and without bound NADH. The structures revealed that the two iron-sulfur clusters, Fe4S4 in FdsB and Fe2S2 in FdsG, are closer to the FMN than they are in other NADH dehydrogenases. Rapid kinetic studies and EPR measurements of rapid freeze-quenched samples of the NADH reduction of FdsBG identified a neutral flavin semiquinone, FMNH•, not previously observed to participate in NADH-mediated reduction of the FdsABG holoenzyme. We found that this semiquinone forms through the transfer of one electron from the fully reduced FMNH-, initially formed via NADH-mediated reduction, to the Fe2S2 cluster. This Fe2S2 cluster is not part of the on-path chain of iron-sulfur clusters connecting the FMN of FdsB with the active-site molybdenum center of FdsA. According to the NADH-bound structure, the nicotinamide ring stacks onto the re-face of the FMN. However, NADH binding significantly reduced the electron density for the isoalloxazine ring of FMN and induced a conformational change in residues of the FMN-binding pocket that display peptide-bond flipping upon NAD+ binding in proper NADH dehydrogenases.

Carotenoid cleavage dioxygenases (CCDs) use a nonheme Fe(II) cofactor to split alkene bonds of carotenoid and stilbenoid substrates. The iron centers of CCDs are typically five-coordinate in their resting states, with solvent occupying an exchangeable site. The involvement of this iron-bound solvent in CCD catalysis has not been experimentally addressed, but computational studies suggest two possible roles. 1) Solvent dissociation provides a coordination site for O2, or 2) solvent remains bound to iron but changes its equilibrium position to allow O2 binding and potentially acts as a proton source. To test these predictions, we investigated isotope effects (H2O versus D2O) on two stilbenoid-cleaving CCDs, Novosphingobium aromaticivorans oxygenase 2 (NOV2) and Neurospora crassa carotenoid oxygenase 1 (CAO1), using piceatannol as a substrate. NOV2 exhibited an inverse isotope effect (k H/k D ∼ 0.6) in an air-saturated buffer, suggesting that solvent dissociates from iron during the catalytic cycle. By contrast, CAO1 displayed a normal isotope effect (k H/k D ∼ 1.7), suggesting proton transfer in the rate-limiting step. X-ray absorption spectroscopy on NOV2 and CAO1 indicated that the protonation states of the iron ligands are unchanged within pH 6.5-8.5 and that the Fe(II)-aquo bond is minimally altered by substrate binding. We pinpointed the origin of the differential kinetic behaviors of NOV2 and CAO1 to a single amino acid difference near the solvent-binding site of iron, and X-ray crystallography revealed that the substitution alters binding of diffusible ligands to the iron center. We conclude that solvent-iron dissociation and proton transfer are both associated with the CCD catalytic mechanism.

The CTX-M β-lactamases have emerged as the most widespread extended-spectrum β-lactamases (ESBLs) in Gram-negative bacteria. These enzymes rapidly hydrolyze cefotaxime, but not the related cephalosporin, ceftazidime. ESBL variants have evolved, however, that provide enhanced ceftazidime resistance. We show here that a natural variant at a nonactive site, i.e. second-shell residue N106S, enhances enzyme stability but reduces catalytic efficiency for cefotaxime and ceftazidime and decreases resistance levels. However, when the N106S variant was combined with an active-site variant, D240G, that enhances enzyme catalytic efficiency, but decreases stability, the resultant double mutant exhibited higher resistance levels than predicted on the basis of the phenotypes of each variant. We found that this epistasis is due to compensatory effects, whereby increased stability provided by N106S overrides its cost of decreased catalytic activity. X-ray structures of the variant enzymes in complex with cefotaxime revealed conformational changes in the active-site loop spanning residues 103-106 that were caused by the N106S substitution and relieve steric strain to stabilize the enzyme, but also alter contacts with cefotaxime and thereby reduce catalytic activity. We noted that the 103-106 loop conformation in the N106S-containing variants is different from that of WT CTX-M but nearly identical to that of the non-ESBL, TEM-1 β-lactamase, having a serine at the 106 position. Therefore, residue 106 may serve as a "switch" that toggles the conformations of the 103-106 loop. When it is serine, the loop is in the non-ESBL, TEM-like conformation, and when it is asparagine, the loop is in a CTX-M-like, cefotaximase-favorable conformation.

Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) is responsible for the conversion of atmospheric CO2 to organic carbon during photosynthesis, and often acts as a rate limiting step in the later process. Screening the natural diversity of Rubisco kinetics is the main strategy used to find better Rubisco enzymes for crop engineering efforts. Here, we demonstrate the use of Gaussian processes (GPs), a family of Bayesian models, coupled with protein encoding schemes, for predicting Rubisco kinetics from Rubisco large subunit (RbcL) sequence data. GPs trained on published experimentally obtained Rubisco kinetic datasets were applied to over 9000 sequences encoding RbcL to predict Rubisco kinetic parameters. Notably, our predicted kinetic values were in agreement with known trends, e.g. higher carboxylation turnover rates (Kcat) for Rubisco enzymes from C4 or crassulacean acid metabolism (CAM) species, compared with those found in C3 species. This is the first study demonstrating machine learning approaches as a tool for screening and predicting Rubisco kinetics, which could be applied to other enzymes. [ABSTRACT FROM AUTHOR]

Enzymes immobilization has been widely used to increase their shelf life which is essential for the world's industries. Therefore, milk clotting enzyme (MCE) from Bacillus circulans 25 was immobilized by covalent binding, ionic binding and entrapment methods using various carriers. MCE covalently immobilized on activated chitosan polymer with the bifunctional agent glutaraldehyde (Ch-MCE) exhibited highest immobilization yield (74.6 %) and highest retained activity (77 %). The effect of temperature and pH on the enzyme activity was evaluated, and the results showed that Ch-MCE had higher optimum reaction temperature by 10°C and higher optimum pH by 1.0. Compared to the native MCE, Ch-MCE exhibited lower activation energy by 1.4-fold. In addition, Ch-MCE exhibited higher half-life time, lower deactivation rate constant and higher energy for denaturation than the free enzyme. After immobilization, Vmax, KM, specificity constant, turnover number, and catalytic efficiency of the enzyme were significantly changed. Furthermore, thermodynamic parameters for denaturation (enthalpy, entropy and Gibbs free energy) confirmed that the immobilization improved the catalytic properties of MCE. The reusability of Ch-MCE was also assessed, and 90.4% of its activity was retained after 7 catalytic cycles, confirming its suitability for industrial applications. Immobilization helps to overcome the limitations of reducing MCE catalytic activity associated with changes in temperature, pH and inhibitors, which makes it useful in industrial applications and biotechnological processes. [ABSTRACT FROM AUTHOR]

Michaelis–Menten kinetics is an essential model to rationalize enzyme reactions. The quantification of Michaelis–Menten parameters can be very challenging as it is sensitive to even small experimental errors. We here present a quantification of the uncertainty inherent to the experimental determination of kinetic rate parameters for enzymatic reactions. We study the influence of several sources of uncertainty and bias, including the inner filter effect, pipetting errors, number of points in the Michaelis–Menten curve, and flat‐field correction. Using Monte Carlo simulations and analyses of experimental data, we compute typical uncertainties of kcat ${{k}_{cat}}$ , KM ${{K}_{M}}$ , and catalytic efficiency kcat/KM ${{k}_{cat}/{K}_{M}}$. As a salient example, we analyze the extraction of such parameters for CRISPR‐Cas systems. CRISPR diagnostics have recently attracted much interest and yet reports of these enzymatic kinetic rates have been highly unreliable and inconsistent. [ABSTRACT FROM AUTHOR]

Folate derivatives are important cofactors for enzymes in several metabolic processes. Folate-related inhibition and resistance mechanisms in bacteria are potential targets for antimicrobial therapies and therefore a significant focus of current research. Here, we report that the activity of Escherichia coli poly-γ-glutamyl tetrahydrofolate/dihydrofolate synthase (FolC) is regulated by glutamate/glutamine-sensing uridylyltransferase (GlnD), THF-dependent tRNA modification enzyme (MnmE), and UDP-glucose dehydrogenase (Ugd) as shown by direct in vitro protein-protein interactions. Using kinetics analyses, we observed that GlnD, Ugd, and MnmE activate FolC many-fold by decreasing the K half of FolC for its substrate l-glutamate. Moreover, FolC inhibited the GTPase activity of MnmE at low GTP concentrations. The growth phenotypes associated with these proteins are discussed. These results, obtained using direct in vitro enzyme assays, reveal unanticipated networks of allosteric regulatory interactions in the folate pathway in E. coli and indicate regulation of polyglutamylated tetrahydrofolate biosynthesis by the availability of nitrogen sources, signaled by the glutamine-sensing GlnD protein.

A growing number of iron-sulfur (Fe-S) cluster cofactors have been identified in DNA repair proteins. MutY and its homologs are base excision repair (BER) glycosylases that prevent mutations associated with the common oxidation product of guanine (G), 8-oxo-7,8-dihydroguanine (OG) by catalyzing adenine (A) base excision from inappropriately formed OG:A mispairs. The finding of an [4Fe-4S]2+ cluster cofactor in MutY, Endonuclease III, and structurally similar BER enzymes was surprising and initially thought to represent an example of a purely structural role for the cofactor. However, in the two decades subsequent to the initial discovery, purification and in vitro analysis of bacterial MutYs and mammalian homologs, such as human MUTYH and mouse Mutyh, have demonstrated that proper Fe-S cluster coordination is required for OG:A substrate recognition and adenine excision. In addition, the Fe-S cluster in MutY has been shown to be capable of redox chemistry in the presence of DNA. The work in our laboratory aimed at addressing the importance of the MutY Fe-S cluster has involved a battery of approaches, with the overarching hypothesis that understanding the role(s) of the Fe-S cluster is intimately associated with understanding the biological and chemical properties of MutY and its unique damaged DNA substrate as a whole. In this chapter, we focus on methods of enzyme expression and purification, detailed enzyme kinetics, and DNA affinity assays. The methods described herein have not only been leveraged to provide insight into the roles of the MutY Fe-S cluster but have also been provided crucial information needed to delineate the impact of inherited variants of the human homolog MUTYH associated with a colorectal cancer syndrome known as MUTYH-associated polyposis or MAP. Notably, many MAP-associated variants have been found adjacent to the Fe-S cluster further underscoring the intimate relationship between the cofactor, MUTYH-mediated DNA repair, and disease.

Autophosphorylating histidine kinase CheA is central to signaling in bacterial chemotaxis. The kinase donates its phosphoryl group to two response regulators, CheY that controls flagellar rotation and thus motility and CheB, crucial for sensory adaptation. As measured by coupled CheY phosphorylation, incorporation into signaling complexes activates the kinase ∼1000-fold and places it under control of chemoreceptors. By the same assay, receptors modulate kinase activity ∼100-fold as a function of receptor ligand occupancy and adaptational modification. These changes are the essence of chemotactic signaling. Yet, the enzymatic properties affected by incorporation into signaling complexes, by chemoreceptor ligand binding or by receptor adaptational modification are largely undefined. To investigate, we performed steady-state kinetic analysis of autophosphorylation using a liberated kinase phosphoryl-accepting domain, characterizing kinase alone, in isolated core signaling complexes and in small arrays of core complexes assembled in vitro with receptors contained in isolated native membranes. Autophosphorylation in signaling complexes was measured as a function of ligand occupancy and adaptational modification. Activation by incorporation into signaling complexes and modulation in complexes by ligand occupancy and adaptational modification occurred largely via changes in the apparent catalytic rate constant (kcat ). Changes in the autophosphorylation kcat accounted for most of the ∼1000-fold kinase activation in signaling complexes observed for coupled CheY phosphorylation, and the ∼100-fold inhibition by ligand occupancy or modulation by adaptational modification. Our results indicate no more than a minor role in kinase control for simple sequestration of the autophosphorylation substrate. Instead they indicate direct effects on the active site.

This study aimed to produce, characterize and purify a protease from Aspergillus heteromorphus URM0269. After production by solid fermentation of wheat bran performed according to a central composite design, protease was characterized in terms of biochemical, kinetic, and thermodynamic parameters for further purification by chromatography. Proteolytic activity achieved a maximum value of 57.43 U/mL using 7.8 g of wheat bran with 40 % moisture. Protease displayed high stability in the pH and temperature ranges of 5.0–10.0 and 20–30 °C, respectively, and acted optimally at pH 7.0 and 50 °C. The enzyme, characterized as a serine protease, followed Michaelis-Menten kinetics with a maximum reaction rate of 140.0 U/mL and Michaelis constant of 11.6 mg/mL. Thermodynamic activation parameters, namely activation Gibbs free energy (69.79 kJ/mol), enthalpy (5.86 kJ/mol), and entropy (−214.39 J/mol.K) of the hydrolysis reaction, corroborated with kinetic modeling showing high affinity for azocasein. However, thermodynamic parameters suggested a reversible mechanism of unfolding. Purification by chromatography yielded a protease purification factor of 7.2, and SDS-PAGE revealed one protein band with a molecular mass of 14.7 kDa. Circular dichroism demonstrated a secondary structure made up of 45.6 % α-helices. These results show the great potential of this protease for future use in the industrial area. [ABSTRACT FROM AUTHOR]

Histone H3 lysine 4 trimethylation (H3K4me3) and histone H3 lysine 9 trimethylation (H3K9me3) are epigenetic marks with opposing roles in transcription regulation. Whereas colocalization of these modifications is generally excluded in the genome, how this preclusion is established remains poorly understood. Lysine demethylase 4C (KDM4C), an H3K9me3 demethylase, localizes predominantly to H3K4me3-containing promoters through its hybrid tandem tudor domain (TTD) (1, 2), providing a model for how these modifications might be excluded. We quantitatively investigated the contribution of the TTD to the catalysis of H3K9me3 demethylation by KDM4C and demonstrated that TTD-mediated recognition of H3K4me3 stimulates demethylation of H3K9me3 in cis on peptide and mononucleosome substrates. Our findings support a multivalent interaction mechanism, by which an activating mark, H3K4me3, recruits and stimulates KDM4C to remove the repressive H3K9me3 mark, thus facilitating exclusion. In addition, our work suggests that differential TTD binding properties across the KDM4 demethylase family may differentiate their targets in the genome.

We have examined the rapid reaction kinetics and spectroscopic properties of the molybdenum-containing, NAD(+)-dependent FdsABG formate dehydrogenase from Ralstonia eutropha. We confirm previous steady-state studies of the enzyme and extend its characterization to a rapid kinetic study of the reductive half-reaction (the reaction of formate with oxidized enzyme). We have also characterized the electron paramagnetic resonance signal of the molybdenum center in its Mo(V) state and demonstrated the direct transfer of the substrate Cα hydrogen to the molybdenum center in the course of the reaction. Varying temperature, microwave power, and level of enzyme reduction, we are able to clearly identify the electron paramagnetic resonance signals for four of the iron/sulfur clusters of the enzyme and find suggestive evidence for two others; we observe a magnetic interaction between the molybdenum center and one of the iron/sulfur centers, permitting assignment of this signal to a specific iron/sulfur cluster in the enzyme. In light of recent advances in our understanding of the structure of the molybdenum center, we propose a reaction mechanism involving direct hydride transfer from formate to a molybdenum-sulfur group of the molybdenum center.

Background: Fungal saccharification of lignocellulosic biomass occurs concurrently with the secretion of a diverse collection of proteins, together functioning as a catalytic system to liberate soluble sugars from insoluble composite biomaterials. How different fungi respond to different substrates is of fundamental interest to the developing biomass saccharification industry. Among the cornerstones of fungal enzyme systems are the highly expressed cellulases (endo-β-glucanases and cellobiohydrolases). Recently, a cyclophellitol-derived activity-based probe (ABP-Cel) was shown to be a highly sensitive tool for the detection and identification of cellulases. Results: Here we show that ABP-Cel enables endo-β-glucanase profiling in diverse fungal secretomes. In combination with established ABPs for β-xylanases and β-d-glucosidases, we collected multiplexed in-gel fluorescence activity-based protein profiles of 240 secretomes collected over ten days from biological replicates of ten different basidiomycete fungi grown on maltose, wheat straw, or aspen pulp. Our results reveal the remarkable dynamics and unique enzyme fingerprints associated with each species substrate combination. Chemical proteomic analysis identifies significant arsenals of cellulases secreted by each fungal species during growth on lignocellulosic biomass. Recombinant production and characterization of a collection of probe-reactive enzymes from GH5, GH10, and GH12 confirm that ABP-Cel shows broad selectivity towards enzymes with endo-β-glucanase activity. Conclusion: Using small-volume samples with minimal sample preparation, the results presented here demonstrate the ready accessibility of sensitive direct evidence for fungal enzyme secretion during early stages of growth on complex lignocellulosic substrates. [ABSTRACT FROM AUTHOR]

Introduction: Industrially, the use of enzymes has increased over time, as their production processes, stabilization and operating conditions have been optimized. Meanwhile associated with their use are minimized with environmental sustainability. The use of mathematical modeling has been a key factor in this advance, making it an great scientific interest area. Objective: To know the state of the art in this area of knowledge, highlighting the most successful and promising findings at present. Materials and Methods: A systematic search of recent high-impact publications between 2015 and 2021 was carried out in internationally recognized databases. A qualitative/comparative analysis of the approaches and contributions of the selected literature was carried out. Results and Discussion: It was evidenced that most of the mathematical models was developed from the Michaelis-Menten kinetic equation, but the simplifications assumed, the operating conditions and the mathematical methods used to solve these systems define the singularity and complexity of each investigation, which makes complex their comparison or implementation in a standardized way. Conclusions: In all cases, the proposed models were adjusted to experimental results or they agreed when different mathematical resolution methods were used. These results can provide valuable information for processes improvement and for equipment design, minimizing costs and time of experimentation and being more friendly to the environment. [ABSTRACT FROM AUTHOR]

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In this article, photoactive alkyl and aryl α-ketophosphonate derivatives were studied as inhibitors of glutathione S-transferases (GSTs). The α-ketophosphonate monoesters were synthesized by sodium iodide-induced dealkylation of corresponding phosphonate diesters. The compounds being inactive toward the enzyme without UV light were activated by irradiation at 365 nm which caused inhibition of GSTs from equine liver and human placenta with micromolar IC50 values. Hetaryl α-ketophosphonate monoesters can also be potential candidates for the UV-dependent enzyme targeting. Inhibitory potency of the phosphonate monoesters was comparable to that of free phosphonic acid. No effects were observed in case of dialkyl α-ketophosphonates. The light-induced effects of the inhibitors were found to be related to decrease in maximum velocity but not to Michaelis constants of the enzyme-catalyzed reaction. The kinetics of a decrease in enzyme activity was described by pseudo-first order rate constants dependent on inhibitor concentration. The calculated second order rate constants indicated that the alkyl α-ketophosphonate monoesters can exhibit higher potency in comparison with that of aryl or hetaryl phosphonate derivatives. [ABSTRACT FROM AUTHOR]

Starch modification by annealing (ANN) and heat-moisture treatment (HMT) results in a lower crystallinity compared to native but the change of B crystalline type to A type is only observed in HMT starch. All starches possess two different digestion rate constants i.e. k 1 (at rapid phase) and k 2 (at slow phase) which may be linked to the preserved intact starch granule following thermal treatment. HMT starch contains higher content of slowly digestible starch (C 2∞) compared to the C 2∞ of the other starches. The lower enzyme binding to HMT starch (K d value increases from 0.12 mg/mL in native starch to 0.83 mg/mL) may be linked to the increase in the degree of ordered structure of the granule surface (observed from the absorption band ratio of 1000 cm−1/1022 cm−1). The lower affinity may lead to a lower k 1 value. This holds true for ANN and native starch which displays similar k 1 , K d value and degree of ordered to disordered structure. Lower k 2 in HMT starch compared to the corresponding k 2 in the other starches may be linked to the slower enzyme diffusion into the core of starch granule due to the tightly packed structure of A crystalline type in HMT starch. • Starch modified by ANN and HMT exhibits two starch fractions with different digestion reactivity indicated by k 1 and k 2 value • The presence of two digestion rate constants may be linked to the preserved intact starch granule despite thermal treatment • The increase of ordered structure on starch granule surface decreases enzyme affinity and may lead to a decrease of k 1 value • HMT leads to a higher ordered granule structure, lower enzyme affinity and k 1 while ANN does not affect these parameters • More densely packed matrices of A crystalline type in HMT starch may slow enzyme diffusion into the granule hence low k 2 [ABSTRACT FROM AUTHOR]

The role of evolutionary pressure on the chemical step catalyzed by enzymes is somewhat enigmatic, in part because chemistry is not rate-limiting for many optimized systems. Herein, we present studies that examine various aspects of the evolutionary relationship between protein dynamics and the chemical step in two paradigmatic enzyme families, dihydrofolate reductases and alcohol dehydrogenases. Molecular details of both convergent and divergent evolution are beginning to emerge. The findings suggest that protein dynamics across an entire enzyme can play a role in adaptation to differing physiological conditions. The growing tool kit of kinetics, kinetic isotope effects, molecular biology, biophysics, and bioinformatics provides means to link evolutionary changes in structure-dynamics function to the vibrational and conformational states of each protein.

The reaction of the air-tolerant CO dehydrogenase from Oligotropha carboxidovorans with H2 has been examined. Like the Ni-Fe CO dehydrogenase, the enzyme can be reduced by H2 with a limiting rate constant of 5.3 s(-1) and a dissociation constant Kd of 525 μM; both kred and kred/Kd, reflecting the breakdown of the Michaelis complex and the reaction of free enzyme with free substrate in the low [S] regime, respectively, are largely pH-independent. During the reaction with H2, a new EPR signal arising from the Mo/Cu-containing active site of the enzyme is observed which is distinct from the signal seen when the enzyme is reduced by CO, with greater g anisotropy and larger hyperfine coupling to the active site (63,65)Cu. The signal also exhibits hyperfine coupling to at least two solvent-exchangeable protons of bound substrate that are rapidly exchanged with solvent. Proton coupling is also evident in the EPR signal seen with the dithionite-reduced native enzyme, and this coupling is lost in the presence of bicarbonate. We attribute the coupled protons in the dithionite-reduced enzyme to coordinated water at the copper site in the native enzyme and conclude that bicarbonate is able to displace this water from the copper coordination sphere. On the basis of our results, a mechanism for H2 oxidation is proposed which involves initial binding of H2 to the copper of the binuclear center, displacing the bound water, followed by sequential deprotonation through a copper-hydride intermediate to reduce the binuclear center.

This investigation was carried out to study the characterization and kinetics of the partially purified Aspergillusficuumtannase enzyme for commercial scale application in the clarification and detannification of juices like grape. pH, temperature and optimum substrate concentration were determined for the tannase enzyme activity from Aspergillusficuum. Also, the Crude and partial purified enzyme were tested for detannification grape juice quality characteristics. Results evidenced that it was found that the optimum partial purified tannase parameters were: temperature 50 oC, PH 5.5 and substrate concentration 1.6% as a tannic acidwith 6.155 specific activities of partial purified tannase enzyme with 225.46% relative activity higher than its control. The tannase enzyme showed a higher temperature and lower pH optima than the soluble enzyme and showed 81.61% and 66.36 % tannin removal from grape juice by crude enzyme and partial purified enzyme treatment, respectively at 37 oC, which has not been reported earlier. Also, maximum velocity of reaction (Vmax) and Michaeli's constant (Km) values were 0.72 and 1.45 for partially purified tannase enzyme activity, respectively. Overall the quality of grape juice was better in partial pure tannase treated juice compared with untreated and crude enzyme treated juice. The present study exposed thatthis enzyme could demonstrate a valuable tool for a number of biotechnological applications. Also, the application of this enzyme on juice clarification also states that it can be employed in fruit juice processing for removal of tannin efficiently. [ABSTRACT FROM AUTHOR]

Considering the diversified pharmacological importance of thiazole and triazole heterocyclic moieties, a unique series of S-aralkylated bi-heterocyclic hybrids, 7a-l, was synthesized in a convergent manner. The structures of newly synthesized compounds were characterized by ¹H-NMR, 13C-NMR, IR, and EI-MS spectral studies. The structure-activity relationship of these compounds was envisaged by analyzing their inhibitory effects against tyrosinase, whereby all these molecules exhibited potent inhibitory potentials relative to the standard used. The Kinetics mechanism was ascertained by Lineweaver-Burk plots, which revealed that 7g inhibited tyrosinase non-competitively by forming an enzyme-inhibitor complex. The inhibition constants Ki calculated from Dixon plots for this compound was 0.0057µM. These bi-heterocyclic molecules also disclosed good binding energy values (kcal/mol) when assessed computationally. So, these molecules can be considered promising medicinal scaffolds for the treatment of skin disorders. [ABSTRACT FROM AUTHOR]

BackgroundEnamel synthesis is a highly dynamic process characterized by simultaneity of matrix secretion, assembly and processing during apatite mineralization. MMP-20 is the first protease to hydrolyze amelogenin, resulting in specific cleavage products that self-assemble into nanostructures at specific mineral compositions and pH. In this investigation, enzyme kinetics of MMP-20 proteolysis of recombinant full-length human amelogenin (rH174) under different mineral compositions is elucidated.MethodsRecombinant amelogenin was cleaved by MMP-20 under various physicochemical conditions and the products were analyzed by SDS-PAGE and MALDI-TOF MS.ResultsIt was observed that mineral ions largely affect cleavage pattern, and enzyme kinetics of rH174 hydrolysis. Out of the five selected mineral ion compositions, MMP-20 was most efficient at high calcium concentration, whereas it was slowest at high phosphate, and at high calcium and phosphate concentrations. In most of the compositions, N- and C-termini were cleaved rapidly at several places but the central region of amelogenin was protected up to some extent in solutions with high calcium and phosphate contents.ConclusionThese in vitro studies showed that the chemistry of the protein solutions can significantly alter the processing of amelogenin by MMP-20, which may have significant effects in vivo matrix assembly and subsequent calcium phosphate mineralization.General significanceThis study elaborates the possibilities of the processing of the organic matrix into mineralized tissue during enamel development.

Peroxiredoxin 2 (Prdx2) and other typical 2-Cys Prdxs function as homodimers in which hydrogen peroxide oxidizes each active site cysteine to a sulfenic acid which then condenses with the resolving cysteine on the alternate chain. Previous kinetic studies have considered both sites as equally reactive. Here we have studied Prdx2 using a combination of non-reducing SDS-PAGE to separate reduced monomers and dimers with one and two disulfide bonds, and stopped flow analysis of tryptophan fluorescence, to investigate whether there is cooperativity between the sites. We have observed positive cooperativity when H 2 O 2 is added as a bolus and oxidation of the second site occurs while the first site is present as a sulfenic acid. Modelling of this reaction showed that the second site reacts 2.2 ± 0.1 times faster. In contrast, when H 2 O 2 was generated slowly and the first active site condensed to a disulfide before the second site reacted, no cooperativity was evident. Conversion of the sulfenic acid to the disulfide showed negative cooperativity, with modelling of the exponential rise in tryptophan fluorescence yielding a rate constant of 0.75 ± 0.08 s-1 when the alternate active site was present as a sulfenic acid and 2.29 ± 0.08-fold lower when it was a disulfide. No difference in the rate of hyperoxidation at the two sites was detected. Our findings imply that oxidation of one active site affects the conformation of the second site and influences which intermediate forms of the protein are favored under different cellular conditions. Image 1 • Cooperativity exists between the active sites in the peroxiredoxin 2 homodimer. • With bolus H 2 O 2 , the 2nd site is oxidized before the 1st –SOH forms a disulfide and is 2.2-fold more reactive. • With slow H 2 O 2 addition, the 1st -SOH condenses before the 2nd is oxidized and no cooperativity is seen. • Condensation of the 2nd -SOH is 2.4 fold slower when the 1st site is a disulfide than when it is –SOH. [ABSTRACT FROM AUTHOR]

The present study was aimed to explore the ability of six distinct fungi to biotransform the drug clobazam to its metabolites, and the nature of enzymes involved in such fungal biotransformation by performing screening, induction, inhibition and kinetic studies. Among the six organisms, a sample of Aspergillus fumigatus culture showed an extra peak at 3.5 min in the high performance liquid chromatography chromatogram when compared with its controls, indicating the formation of metabolite. The metabolite thus formed was confirmed by mass spectrometry and NMR spectroscopy as 4-hydroxy norclobazam. Enzyme induction and inhibition studies were conducted on the involvement of a CYP3A4-like enzyme in fungal biotransformation. Enzyme kinetic studies were conducted to determine the affinity of the enzyme to the substrate. The study revealed that A. fumigatus can be used as a microbial resource to analyse the complete metabolic profile of clobazam with a maximum concentration 30 µg/ml. [ABSTRACT FROM AUTHOR]

This study is based on two aims firstly, the project is to develop a relation bridge between academic and industry personnel and secondly, in this study, we have evaluated the amount of α-amylase and amyloglucosidase required for effective saccharification of parboiled rice of 18 mesh size. The reason behind the selection of broken rice was its costeffectiveness as well as waste utilization. Another reason behind the selection of broken rice as raw material was its utilization in the industry is on a large scale. The maltodextrin production rate by α-amylase and characterization of α- amylase was also a part of the study. Three unit ratios of α-amylase and amyloglucosidase were chosen i.e. 2:2, 4:4, 6:6. The maximum yield of 85.13 % maltodextrin was obtained by saccharification with a ratio of 6:6 units of α- amylase and amyloglucosidase after 30 minutes of saccharification. The 53.52 % yield of maltodextrin was obtained with 4ml of α-amylase (concentration 1mg/ml) at 120 minutes when α-amylase act alone on rice gelatinized starch. The determined kinetic parameters for α-amylase were Vmax- 33,333 s-1, Km- 446.66 M. The activity of α-amylase was found as 358.15 IU/mg. The kinetic model developed to predict the time perspective maltodextrin production was fitted well. The coefficient of determination (R2) found as0.996 for experimental and predicted values of maltodextrin. [ABSTRACT FROM AUTHOR]

Fungal laccases have great potential as biocatalysts oxidizing a variety of aromatic compounds using oxygen as co-substrate. Here, the crystal structure of 7D5 laccase (PDB 6H5Y), developed in Saccharomyces cerevisiae and overproduced in Aspergillus oryzae , is compared with that of the wild type produced by basidiomycete PM1 (Coriolopsis sp.), PDB 5ANH. SAXS showed both enzymes form monomers in solution, 7D5 laccase with a more oblate geometric structure due to heavier and more heterogeneous glycosylation. The enzyme presents superior catalytic constants towards all tested substrates, with no significant change in optimal pH or redox potential. It shows noticeable high catalytic efficiency with ABTS and dimethyl-4-phenylenediamine, 7 and 32 times better than the wild type, respectively. Computational simulations demonstrated a more favorable binding and electron transfer from the substrate to the T1 copper due to the introduced mutations. PM1 laccase is exceptionally stable to thermal inactivation (t 1/2 70 °C = 1.2 h). Yet, both enzymes display outstanding structural robustness at high temperature. They keep folded during 2 h at 100 °C though, thereafter, 7D5 laccase unfolds faster. Rigidification of certain loops due to the mutations added on the protein surface would diminish the capability to absorb temperature fluctuations leading to earlier protein unfolding. [ABSTRACT FROM AUTHOR]

Advanced glycation end products are the most important species of glycation pathway, and cause disorders such as oxidative stress and diabetes. Sulfonamide compounds, which are generally known as widespread inhibitors, are potential agents used in different drug products, which can readily enter biological matrices. In the present work, the structure and activity of human carbonic anhydrase II studied in the presence of glucose as well as four sulfonamide agents from different views. These included enzyme kinetics, free lysine content, fluorescence spectroscopy, circular dichroism, and ROS measurement. Our results indicated that upon glycation, the structure of HCA II collapses and 8 to 13 lysine residues will be more available based on ligand incubation. Secondary and tertiary structural changes were also observed in the presence and absence of sulfonamide agents using fluorescence and circular dichroism methods, respectively. These spectroscopic data also showed a remarkable increase in hydrophobicity and decrease in α-helix contents during glycation, especially after 35 days of incubation. ROS assay was studied in the presence of glucose and sulfonamide compounds, that demonstrated the role of sulfonamide compounds in ROS formation in the presence of glucose in a synergistic manner. Overall, our data indicated that sulfonamides act as a stimulant factor upon prolonged interaction with HCA II and may intensify the complications of some disorders, such as diabetes and other conformational diseases. • Glycation of proteins leads to changes in structure and function. • The AGEs cause undesirable repercussions and make the human body susceptible to various diseases such as diabetes mellitus. • Sulfonamide inhibitors stimulate ROS formation in presence of glucose • Glycation process affects the availability of lysine residues • Incubation of the enzyme affects K m and V max in presence and absence of glucose. [ABSTRACT FROM AUTHOR]

Enzyme‐mediated catalysis is attributed to enzyme–substrate interactions, with models such as "induced fit" and "conformational selection" emphasizing the role of protein conformational transitions. The dynamic nature of the protein structure, thus, plays a crucial role in molecular recognition and substrate binding. As large‐scale protein motions are coupled to water motions, hydration dynamics play a key role in protein dynamics, and hence, in enzyme catalysis. Here, microfluidic techniques and time‐dependent fluorescence Stokes shift (TDFSS) measurements are employed to elucidate the role of nanoscopic water dynamics in the interaction of an enzyme, α‐Chymotrypsin (CHT), with a substrate, Ala‐Ala‐Phe‐7‐amido‐4‐methylcoumarin (AMC) in the cationic reverse micelles of benzylhexadecyldimethylammonium chloride (BHDC/benzene) and anionic reverse micelles of sodium bis(2‐ethylhexyl)sulfosuccinate (AOT/benzene). The kinetic pathways unraveled from the microfluidic setup are consistent with the "conformational selection" fit for the interaction of CHT with AMC in the cationic reverse micelles, whereas an "induced fit" mechanism is indicated for the anionic reverse micelles. In the cationic reverse micelles of BHDC, faster hydration dynamics (≈550 ps) aid the pathway of "conformational selection", whereas in the anionic reverse micelles of AOT, the significantly slower dynamics of hydration (≈1600 ps) facilitate an "induced fit" mechanism for the formation of the final enzyme–substrate complex. The role of water dynamics in dictating the mechanism of enzyme–substrate interaction becomes further manifest in the neutral reverse micelles of Brij‐30 and Triton X‐100. In the former, the faster water dynamics aid the "conformational selection" pathway, whereas the significantly slower dynamics of water molecules in the latter are conducive to the "induced fit" mechanism in the enzyme–substrate interaction. Thus, nanoscopic water dynamics act as a switch in modulating the pathway of recognition of an enzyme (CHT) by the substrate (AMC) in reverse micelles. [ABSTRACT FROM AUTHOR]

Abstract Regulation of α-glucosidase (EC 3.2.1.20) and its inhibitors is of great interest to researchers due to its clinical relevance as a target enzyme for the treatment of α-glucosidase-mediated diseases, such as type 2 diabetes mellitus and Pompe disease. In this study, we conducted a phloroglucinol-induced inhibition kinetics assay and performed computational molecular dynamics (MD) simulations to assess binding manner in α-glucosidase. The results showed that phloroglucinol reversibly inhibited α-glucosidase in a dose-dependent but non-competitive manner (K i = 2.07 ± 0.16 mM). Interestingly, the maximum peak wavelength and the hydrophobic surface remained unchanged during the inhibition reaction, with computational MD simulations further revealing that phloroglucinol bound in front of the active site pocket rather than in the α-glucosidase active site. Therefore, we speculate that phloroglucinol-specific inhibition is mild and the inhibitor likely binds to a single binding site near but not in the active site. Our study provided insight into the effects and mechanisms associated with a mild inhibitor of α-glucosidase activity and promotes fundamental research and potential applications of inhibitors for treatment of α-glucosidase-mediated clinical disease. [ABSTRACT FROM AUTHOR]

Abstract Simple exponential decaying functions are commonly used for fitting the kinetics of starch digested by amylolytic enzymes. A common assumption is that a sole exponential function can account for the kinetics of the whole digestible starch. Recent studies using logarithm-of-slope (LOS) plots showed that digestion kinetics can exhibit multi-scale behavior, an effect reflecting starch fractions with different digestion characteristics. This work proposed an extension of the widely used Goñi et al.'s model to account for two starch fractions; one fraction linked with fast digestion rate and other with slow digestion rates. The fitting of experimental data was carried out by solving numerically a nonlinear least-squares problem. The estimated parameters have a straightforward interpretation in terms of reaction rates and digestible/resistant starch fractions. Two experimental examples were used for illustrating the performance of the multi-exponential function. Highlights • Enzymatic starch digestion exhibits multi-scale behavior. • A multi-exponential equation was proposed for fitting experimental data. • Classification of digestible starch fractions can be obtained. [ABSTRACT FROM AUTHOR]

The effect of aeration on the stability of glucose oxidase in the reaction of glucose oxidation to gluconic acid was investigated by determining the operational stability decay rate constant in the process conditions. Eupergit C as a porous carrier was chosen for the enzyme immobilization. To evaluate glucose oxidase operational stability during process conditions, experiments of glucose oxidation were carried out in the repetitive batch reactor with and without continuous aeration at different aeration levels. It was found that the decay rate of the free enzyme linearly depended on the air flow rate. Immobilization of glucose oxidase on Eupergit C significantly enhanced enzyme stability at higher aeration rates. Kinetics of the free and immobilized enzyme was also determined. The mathematical model of glucose oxidation catalysed by free and immobilized glucose oxidase in the batch reactor was developed. [ABSTRACT FROM AUTHOR]

Co‐solvents are known to influence the Michaelis constant KM of enzyme‐catalyzed reactions. In the literature, co‐solvent effects on KM are usually explained by interactions between enzyme and co‐solvent. Very recent works replaced substrate concentrations with thermodynamic activities to separate enzyme–co‐solvent from substrate–co‐solvent interactions This yields the thermodynamic‐activity‐based Michalis constant KMa. In this work, this approach was extended to alcohol dehydrogenase (ADH)‐catalyzed reduction of acetophenone (ACP), a two‐substrate reaction. It was experimentally found that polyethylene glycol (PEG) 6000 increased KM of ACP and decreased KM of nicotinamide adenine dinucleotide (NADH). To predict KMa values, non‐covalent interactions between substrates and reaction media were taken into account by electrolyte perturbed‐chain statistical associating fluid theory (ePC‐SAFT) modelling. In contrast to experimental KM values, their activity‐based pendants KMa were independent of co‐solvent. To further verify the approach, the reduction of 2‐pentanone catalyzed by the same ADH was investigated. Interestingly, the addition of PEG caused a decrease of bothKM of 2‐pentanone and KM of NADH. Based on KMa values obtained from KM in co‐solvent‐free conditions and activity coefficients from ePC‐SAFT, the influence of the co‐solvent on KM was quantitatively predicted. Thus, the approach known for pseudo one‐substrate reactions was successfully transferred to two‐substrate reactions. Furthermore, the advantage of thermodynamic activities over concentrations in the field of enzyme kinetics is highlighted. Co‐solvent effect: A thermodynamic‐activity‐based approach renders quantitatively predictable Michaelis constants for enzyme‐catalyzed two‐substrate reactions. Co‐solvent–enzyme interactions were proven to play a minor role in the effect of co‐solvents on Michaelis constants. The approach will help to gain new insights on co‐solvent‐substrate‐enzyme interactions. [ABSTRACT FROM AUTHOR]