Enzyme Isomerization Research Articles

Detection of an enzyme isomechanism by means of the kinetics of covalent inhibition

Turnover of substrates by many enzymes involves free enzyme forms that differ from the stable form of the enzyme in the absence of substrate. These enzyme species, known as isoforms, have, in general, different physical and chemical properties than the native enzymes. They usually occur only in small concentrations under steady state turnover conditions and thus are difficult to detect. We show in this paper that in one particular case of an enzyme (a class C β-lactamase) with specific substrates (cephalosporins) the presence of an enzyme isoform (E′) can be detected by means of its different reactivity than the native enzyme (E) with a class of covalent inhibitors (phosphonate monoesters). Generation of E′ from E arises either directly from substrate turnover or by way of a branched path from an acyl-enzyme intermediate. The relatively slow spontaneous restoration of E from E′ is accelerated by certain small molecules in solution, for example cyclic amines such as imidazole and salts such as sodium chloride. Solvent deuterium kinetic isotope effects and the effect of methanol on cephalosporin turnover showed that for both E and E′, kcat is limited by deacylation of an acyl-enzyme intermediate rather than by enzyme isomerization.

Kinetic solvent viscosity effects reveal a protein isomerization in the reductive half-reaction of Neurospora crassa class II nitronate monooxygenase

Nitronate monooxygenase from Neurospora crassa (NcNMO) is an FMN-dependent enzyme that oxidizes nitronates. The enzyme belongs to Group H of flavin monooxygenases. Previous biochemical and mechanistic studies on the enzyme showed that NcNMO oxidizes both anionic nitronates and neutral nitroalkanes, a feature distinguishing NcNMO from bacterial and other fungal NMOs which are active exclusively on nitronates. Recently, NMOs have been shown to oxidize propionate 3-nitronate (P3N), a toxic nitro acid present in legumes, fungi, and leaf beetles; P3N is an irreversible inhibitor of succinate dehydrogenase causing anywhere from neurological disorders to death in livestock and humans. In this study, we report the first kinetic investigation of NcNMO with P3N and its conjugated acid 3-nitropropionic acid (3NPA), and a mechanistic investigation with 3NPA using kinetic solvent viscosity effects. The kcat value with P3N (300 s−1) was 7-times larger than with 3NPA and the kcat/KP3N value (1,700,000 M−1s−1) was ~500-times larger than the kcat/K3NPA value, consistent with P3N being a faster and better substrate than 3NPA. The normalized kcat and kcat/K3NPA values showed inverse hyperbolic dependences on the relative solvent viscosity, consistent with an internal isomerization of the enzyme-substrate complex. A similar inverse hyperbolic pattern of the normalized kred value for the rate constant of flavin reduction determined anaerobically in a stopped-flow spectrophotometer suggested that the internal enzyme isomerization occurs before the flavin reduction step in the reductive half-reaction.

Supramolecular Rare Sugar

We introduce rare sugars including their derivatives and supramolecular rare sugars, that have been actively researched at Kagawa University, Japan. Although the rare sugars are special sugars which hardly exist in nature, we has succeeded in mass synthesis of the rare sugars by utilizing biological enzyme isomerization reaction. In addition, the rare sugars have various functions such as blood sugar level suppressing function, cancer cell growth suppressing function, and antibacterial action. In addition, since rare sugars have a large number of hydroxyl groups, they have a possibility for using as devices for expressing various functions by employing them as ligands of transition metal complexes. In recent years, it is successful that we have synthesized the suplamolecular rare sugars (SRSs) from the different types of rare sugars, that is not as simple mixtures but as single crystals having supralattice structure, that can be freely controlled optical rotation. It has been found that the crystal structures of these SRSs mostly follow the Wallach rule, but do not satisfy the Wallach rule especially in the case of D, L-psicose. Therefore, we have investigated the single crystal X-ray structural analyses of SRSs, obtaining the detailed crystal structure data, and analyzed the intermolecular interaction between their sugar molecules in the crystal by means of the DV-Xα molecular orbital calculation. According to our detailed analysis of the research, calculating the intermolecular interaction revealed that the stability of the intermolecular interaction in the crystal can not be explained only by following the simple Wallach rule. Specifically, for example in the case of D, L-psicose, the total energy in a crystal can be stabilized by aligning the polarization vectors of the molecules, and as a result, we have clarified that the SRSs crystal structure can be stabilized, even if it does not follow the simple Wallach rule.

Crowding-Induced Uncompetitive Inhibition of Lactate Dehydrogenase: Role of Entropic Pushing.

The cell is an extremely complex environment, notably highly crowded, segmented, and confining. Overall, there is overwhelming and ever-growing evidence that to understand how biochemical reactions proceed in vivo, one cannot separate the biochemical actors from their environment. Effects such as excluded volume, obstructed diffusion, weak nonspecific interactions, and fluctuations all team up to steer biochemical reactions often very far from what is observed in ideal conditions. In this paper, we use Ficoll PM70 and PEG 6000 to build an artificial crowded milieu of controlled composition and density in order to assess how such environments influence the biocatalytic activity of lactate dehydrogenase (LDH). Our measurements show that the normalized apparent affinity and maximum velocity decrease in the same fashion, a behavior reminiscent of uncompetitive inhibition, with PEG resulting in the largest reduction. In line with previous studies on other enzymes of the same family, and in agreement with the known role of a surface loop involved in enzyme isomerization and regulation of access to the active site, we suggest that the crowding matrix interferes with the conformational ensemble of the enzyme. This likely results in both impaired enzyme-complex isomerization and thwarted product release. Molecular dynamics simulations confirm that excluded-volume effects lead to an entropic force that effectively tends to push the loop closed, thereby effectively shifting the conformational ensemble of the enzyme in favor of a more stable complex isoform. Overall, our study substantiates the idea that most biochemical kinetics cannot be fully explained without including the subtle action of the environment where they take place naturally, in particular accounting for important factors such as excluded-volume effects and also weak nonspecific interactions when present, confinement, and fluctuations.

Competitive protein tyrosine phosphatase 1B (PTP1B) inhibitors, prenylated caged xanthones from Garcinia hanburyi and their inhibitory mechanism

Protein tyrosine phosphatase 1B (PTP1B) plays important role in diabetes, obesity and cancer. The methanol extract of the gum resin of Garcinia hanburyi (G. hanburyi) showed potent PTP1B inhibition at 10µg/ml. The active compounds were identified as prenylated caged xanthones (1–9) which inhibited PTP1B in dose-dependent manner. Carboxybutenyl group within caged motif (A ring) was found to play a critical role in enzyme inhibition such as 1–6 (IC50s=0.47–4.69µM), whereas compounds having hydroxymethylbutenyl 7 (IC50=70.25µM) and methylbutenyl 8 (IC50>200µM) showed less activity. The most potent inhibitor, gambogic acid 1 (IC50=0.47µM) showed 30-fold more potency than ursolic acid (IC50=15.5µM), a positive control. In kinetic study, all isolated xanthones behaved as competitive inhibitors which were fully demonstrated with Km, Vmax and Kik/Kiv ratio. It was also proved that inhibitor 1 operated under the enzyme isomerization model having k5=0.0751µM−1S−1, k6=0.0249µM−1S−1 and Kiapp=0.499µM. To develop a pharmacophore model, we explored the binding sites of compound 1 and 7 in PTP1B. These modeling results were in agreement with our findings, which revealed that the inhibitory activities are tightly related to caged motif and prenyl group in A ring.

Kinetic and Thermodynamic Rationale for Suberoylanilide Hydroxamic Acid Being a Preferential Human Histone Deacetylase 8 Inhibitor As Compared to the Structurally Similar Ligand, Trichostatin A

Of the different hydroxamate-based histone deacetylase (HDAC) inhibitors, suberoylanilide hydroxamic acid (SAHA) has been approved by the Food and Drug Administration for the treatment of T-cell lymphoma. Interestingly, a structurally similar inhibitor, trichostatin A (TSA), which has a higher in vitro inhibitory potency against HDAC8, reportedly shows poor efficacy in clinical settings. To gain molecular insight into this discriminatory feature, we performed transient kinetic and isothermal titration calorimetric studies for the interaction of SAHA and TSA with the recombinant form of human HDAC8. The transient kinetic data revealed that the binding of both inhibitors to the enzyme showed biphasic profiles, which represented an initial encounter of the enzyme with the inhibitor followed by the isomerization of the transient enzyme-inhibitor complexes. The temperature-dependent transient kinetic studies with these inhibitors revealed that the bimolecular process is primarily dominated by favorable enthalpic changes, as opposed to the isomerization step, which is solely contributed by entropic changes. The standard binding enthalpy (ΔH°) of SAHA, deduced from the transient kinetic as well as the isothermal titration calorimetric experiments, was 2-3 kcal/mol higher than that of TSA. The experimental data presented herein suggest that SAHA serves as a preferential (target-specific and -selective) HDAC8 inhibitor as compared to TSA. Arguments that the detailed kinetic and thermodynamic studies may guide the rational design of HDAC inhibitors as therapeutic agents are presented.

Tanshinones as selective and slow-binding inhibitors for SARS-CoV cysteine proteases

In the search for anti-SARS-CoV, tanshinones derived from Salvia miltiorrhiza were found to be specific and selective inhibitors for the SARS-CoV 3CLpro and PLpro, viral cysteine proteases. A literature search for studies involving the seven isolated tanshinone hits showed that at present, none have been identified as coronaviral protease inhibitors. We have identified that all of the isolated tanshinones are good inhibitors of both cysteine proteases. However, their activity was slightly affected by subtle changes in structure and targeting enzymes. All isolated compounds (1–7) act as time dependent inhibitors of PLpro, but no improved inhibition was observed following preincubation with the 3CLpro. In a detail kinetic mechanism study, all of the tanshinones except rosmariquinone (7) were identified as noncompetitive enzyme isomerization inhibitors. However, rosmariquinone (7) showed a different kinetic mechanism through mixed-type simple reversible slow-binding inhibition. Furthermore, tanshinone I (5) exhibited the most potent nanomolar level inhibitory activity toward deubiquitinating (IC50=0.7μM). Additionally, the inhibition is selective because these compounds do not exert significant inhibitory effects against other proteases including chymotrysin, papain, and HIV protease. These findings provide potential inhibitors for SARS-CoV viral infection and replication.

Identification of the Key Residues Determining the Product Specificity of Isomerohydrolase

The efficient recycling of the chromophore of visual pigments, 11-cis-retinal, through the retinoid visual cycle is an essential process for maintaining normal vision. RPE65 is the isomerohydrolase in retinal pigment epithelium and generates predominantly 11-cis-retinol (11cROL) and a minor amount of 13-cis-retinol (13cROL), from all-trans-retinyl ester (atRE). We recently identified and characterized novel homologues of RPE65, RPE65c, and 13-cis-isomerohydrolase (13cIMH), which are expressed in the zebrafish inner retina and brain, respectively. Although these two homologues have 97% identical amino acid sequences, they exhibit distinct product specificities. Under the same assay conditions, RPE65c generated predominantly 11cROL, similar to RPE65, while 13cIMH generated exclusively 13cROL from atRE substrate. To study the impacts of the key residues determining the isomerization product specificity of RPE65, we replaced candidate residues by site-directed mutagenesis in RPE65c and 13cIMH. Point mutations at residues Tyr58, Phe103, and Leu133 in RPE65c resulted in significantly altered isomerization product specificities. In particular, our results showed that residue 58 is a primary determinant of isomerization specificity, because the Y58N mutation in RPE65c and its reciprocal N58Y mutation in 13cIMH completely reversed the respective enzyme isomerization product specificities. These findings will contribute to the elucidation of molecular mechanisms underlying the isomerization reaction catalyzed by RPE65.

Role of Induced Fit in Limiting Discrimination against AZT by HIV Reverse Transcriptase

Single turnover kinetic studies were conducted using fluorescently labeled HIV reverse transcriptase (RT) to evaluate the role of nucleotide-induced changes in enzyme structure in the selectivity against AZT in order to explore why AZT-resistant forms of the enzyme fail to significantly discriminate against AZT. Fluorescent labeling of HIV RT provided a signal to monitor the isomerization from "open" to "closed" states following nucleotide binding. We measured the rate constants governing nucleotide binding and enzyme isomerization for TTP and AZT-triphosphate by the wild-type and AZT-resistant forms of the enzyme containing the thymidine analogue mutations (TAMs). We show that the TAMs alter the kinetics of AZT incorporation by weakening ground-state nucleotide binding and decreasing the rate of chemistry relative to the wild-type enzyme. However, the slower rate of incorporation of AZT by the TAMs HIV RT is counterbalanced a lower K(m), resulting from the equilibration of the conformational change step. In contrast, the K(m) for the wild-type enzyme reflects the balance between rates of binding and incorporation so the conformational change step does not come to equilibrium. These data once again demonstrate that the rate of substrate release, limited by the reverse of the substrate-induced conformational change, is the key determinant of the role of induced fit in enzyme specificity. Mutations leading to slower rates of incorporation have the unfortunate consequence of lowering the K(m) value by allowing the conformational change step to come to equilibrium.

Constitutive expression, purification and characterization of a phosphoglucomutase from Fusarium oxysporum

The phosphoglucomutase gene from a wild type Fusarium oxysporum strain (F3), was homologously expressed, under the control of the constitutive promoter of gpdA of Aspergillus nidulans. The transformant produced elevated levels of phosphoglucomutase activity compared to the wild type, a fact that facilitated the subsequent purification procedure. The enzyme (FoPGM) was purified to homogeneity applying three anion exchange and one gel filtration chromatography steps. The native enzyme revealed a monomeric structure with a molecular mass of 60kDa, while the isoelectric point was 3.5. FoPGM was active in pH ranged from 6.0 to 8.0, with an optimum using 3-(N-morpholino)propanesulfonic acid buffer at 7.0, while loss of activity was observed when phosphate buffer was used in the above mentioned pH range. The optimal temperature for activity was 45°C but the enzyme became unstable at temperatures above 40°C. FoPGM requires the presence of a divalent cation for its function with maximum activity being obtained with Co2+. The apparent Km for Co2+ was found to be 10μM. The enzyme was also active with other divalent metal ions such as Mn2+, Mg2+, Ni2+ and Ca2+ but to a lesser extent. The following kinetic constants were determined: vmax, 0.74μmolmgprotein−1min−1; kcat, 44.2min−1; Km(G1P), 0.10mM; Km(G1,6diP), 1.03μM; kcat/Km(G1P), 443mM−1min−1 and kcat/Km(G1,6diP), 42,860mM−1min−1. The enzyme was considered to follow a Ping Pong substituted enzyme or enzyme isomerization mechanism.

Kinetic Model for the Reversible Hydration of Carbon Dioxide Catalyzed by Human Carbonic Anhydrase II

Four variants of the two-step Ping Pong mechanism for the reversible hydration of carbon dioxide to bicarbonate catalyzed by free human carbonic anhydrase II (HCA II) in solutions were derived and their goodness-of-fit to match measured initial hydration rates tested. The pseudo (i.e., no central complex) random Quad Quad Iso Ping Pong mechanism with one transitory complex was retained which implied a possible competitive intermolecular proton transfer step by the CO2/HCO3− pair with respect to external buffer. The model suggests this role could be emphasized in product inhibition conditions at high bicarbonate/buffer concentration ratios. A 4-parameter kinetic model was derived to complement the existing single- (intra- or intermolecular) limiting-step models for HCA II catalyzed hydration of CO2 in which were accounted for altogether the enzyme isomerization and CO2/HCO3− proton transfer via a [CO2]·[HCO3−] coupling, the CO2/HCO3− proton transfer via [HCO3−]2 and [CO2]·[HCO3−]2 couplings, and an enzyme−...

Xanthones with neuraminidase inhibitory activity from the seedcases of Garcinia mangostana

This study was designed to gain deeper insights into the molecular properties of natural xanthones as neuraminidase inhibitors. A series of xanthones 1– 12 was isolated from the seedcases of Garcinia mangostana and evaluated for bacteria neuraminidase inhibitory activity. Compounds 11 and 12 emerged to be new xanthones (mangostenone F, mangostenone G) which we fully spectroscopically characterized. The IC 50 values of compounds 1– 12 were determined to range between 0.27–65.7 μM. The most potent neuraminidase inhibitor 10 which has an IC 50 of 270 nM features a 5,8-diol moiety on the B ring. Interestingly, structure–activity studies reveal that these xanthones show different kinetic inhibition mechanisms depending upon the arrangement of hydroxyl groups in the B ring. Compound 6 possessing a 6,7-diol motif on the B-ring operated under the enzyme isomerization model ( k 5 = 0.1144 μM −1 s −1, k 6 = 0.001105 s −1, and K i app = 7.41 μM), whereas compound 10 possessing a 5,8-diol unit displayed simple reversible slow-binding inhibition ( k 3 = 0.02294 μM −1 s −1, k 4 = 0.001025 s −1, and K i app = 0.04468 μM).

Characteristic of neuraminidase inhibitory xanthones from Cudrania tricuspidata

Natural polyphenolic compounds generally transpire to show relatively low inhibition against glycosidase including neuraminidase. In addition the inhibition modes of such compounds are rarely competitive. In this manuscript, a series of xanthone derivatives from Cudrania tricuspidata are shown to display nanomolar inhibitor activity against neuraminidase (EC 3.2.1.18) as well as competitive inhibition modes. Compound 8 bearing vicinal dihydroxy group on the A-ring displays nanomolar activity (IC 50 = 0.08 ± 0.01 μM), a 200-fold increase in activity relative to that of the first reported xanthone-derived neuraminidase inhibitor, mangiferin (IC 50 = 16.2 ± 4.2 μM). The 6,7-vicinal dihydroxy group plays a crucial role for inhibitory activity because compound 4, which has one of these hydroxyl groups prenylated was inactive (33% at 200 μM), whereas other compounds ( 1– 3 and 6– 8) showed nanomolar activity (0.08–0.27 μM) and competitive inhibition modes. Interestingly all inhibitors manifested enzyme isomerization inhibition against neuraminidase. The most potent inhibitor, compound 8 showed similar interaction with a transition-state analogue of neuraminic acid in active site.

Tyrosinase Inhibitory Polyphenols from Roots ofMorus lhou

Twelve polyphenols (1-12) possessing tyrosinase inhibitory properties were isolated from the methanol (95%) extract of Morus lhou. The isolated compounds consisted of four flavanones (1-4), four flavones (5-8), and four phenylbenzofuranes (9-12). Moracin derivative 12 proved to be new a compound which was fully characterized. Compounds 1-12 were evaluated for both monophenolase and diphenolase (the two steps catalyzed by tyrosinase) inhibition to identify the structural characteristics required for mushroom tyrosinase inhibition. We observed that all parent compounds (1, 5, and 9) possessing an unsubstituted resorcinol group were highly effective inhibitors of monophenolase activity (IC(50) values of 1.3, 1.2, and 7.4 microM). The potency of the inhibitors diminished with alkyl substitution on either the aromatic ring or the hydroxyl functions. Interestingly, flavone 5 was shown to possess only monophenolase inhibitory activity, but flavanone 1 and phenylbenzofuran 9 inhibited diphenolase as well as monophenolase significantly. The inhibitory mode of these species was also dependent upon the skeleton: phenylbenzofuran 9 manifested a simple competitive inhibition mode for monophenolase and diphenolase; on the other hand flavanone 1 (monophenolase, k(3) = 0.1966 min(-1) microM(-1), k(4) = 0.0082 min(-1), and K(i)(app) = 0.0468 microM; diphenolase, k(3) = 0.0014 min(-1) microM(-1), k(4) = 0.0013 min(-1), and K(i)(app) = 0.8996 microM) and flavone 5 both showed time-dependent inhibition against monophenolase. Compound 1 operated according to the simple reversible slow binding model whereas compound 5 operated under the enzyme isomerization model.

The Reopening Rate of the Fingers Domain Is a Determinant of Base Selectivity for RB69 DNA Polymerase

Two divalent metal ions are required for nucleotide incorporation by DNA polymerases. Here we use the bacteriophage RB69 DNA polymerase (RB69 pol) and the metal ion exchange-inert nucleotide analogue rhodium(III) deoxythymidine triphosphate (Rh.dTTP) to investigate the requirements of metal binding to the "A" site and to the "B" site, independently. We show that while binding of a metal ion to the A site is required for the nucleotidyl transfer reaction to occur, this metal binding is insufficient to initiate the prechemistry enzyme isomerization that has been observed with this polymerase. Moreover, we show that binding of a deoxynucleoside triphosphate (dNTP), in the absence of a catalytic metal ion, is sufficient to induce this conformational change. In this report, we also present several lines of evidence (from pulse-chase, rapid chemical quench-flow, and stopped-flow fluorescence experiments) for the reverse rate of the enzyme isomerization, closed to open, of a DNA polymerase complex. The implications of these data for the fidelity of DNA polymerization by RB69 pol are discussed.

Amino Acids Allosterically Regulate the Thiamine Diphosphate-dependent α-Keto Acid Decarboxylase from Mycobacterium tuberculosis

The gene rv0853c from Mycobacterium tuberculosis strain H37Rv codes for a thiamine diphosphate-dependent alpha-keto acid decarboxylase (MtKDC), an enzyme involved in the amino acid degradation via the Ehrlich pathway. Steady state kinetic experiments were performed to determine the substrate specificity of MtKDC. The mycobacterial enzyme was found to convert a broad spectrum of branched-chain and aromatic alpha-keto acids. Stopped-flow kinetics showed that MtKDC is allosterically activated by alpha-keto acids. Even more, we demonstrate that also amino acids are potent activators of this thiamine diphosphate-dependent enzyme. Thus, metabolic flow through the Ehrlich pathway can be directly regulated at the decarboxylation step. The influence of amino acids on MtKDC catalysis was investigated, and implications for other thiamine diphosphate-dependent enzymes are discussed.

Inhibitory effects on mushroom tyrosinase by flavones from the stem barks of Morus lhou (S.) Koidz

Five flavones displaying tyrosinase inhibitory activity were isolated from the stem barks of Morus lhou (S.) Koidz., a cultivated edible plant. The isolated compounds were identified as mormin (1), cyclomorusin (2), morusin (3), kuwanon C (4), and norartocarpetin (5). Mormin (1) was characterized as a new flavone possesing a 3-hydroxymethyl-2-butenyl at C-3. The inhibitory potencies of these flavonoids toward monophenolase activity of mushroom tyrosinase were investigated. The IC50 values of compounds 1–5 for monophenolase activity were determined to be 0.088, 0.092, 0.250, 0.135 mM, and 1.2 μM, respectively. Mormin (1), cyclomorusin (2), kuwanon C (4) and norartocarpetin (5) exhibited competitive inhibition characteristics. Interestingly norartocarpetin (5) showed a time–dependent inhibition against oxidation of l–tyrosine: it also operated under the enzyme isomerization model (k5 = 0.8424 min− 1, k6 = 0.0576 min− 1, = 1.354 μM).

Kinetic Conformational Analysis of Human 8-Oxoguanine-DNA Glycosylase

7,8-dihydro-8-oxoguanine (8-oxoG) is one of the major DNA lesions formed by reactive oxygen species that can result in transversion mutations following replication if left unrepaired. In human cells, the effects of 8-oxoG are counteracted by OGG1, a DNA glycosylase that catalyzes excision of 8-oxoguanine base followed by a much slower beta-elimination reaction at the 3'-side of the resulting abasic site. Many features of OGG1 mechanism, including its low beta-elimination activity and high specificity for a cytosine base opposite the lesion, remain poorly explained despite the availability of structural information. In this study, we analyzed the substrate specificity and the catalytic mechanism of OGG1 acting on various DNA substrates using stopped-flow kinetics with fluorescence detection. Combining data on intrinsic tryptophan fluorescence to detect conformational transitions in the enzyme molecule and 2-aminopurine reporter fluorescence to follow DNA dynamics, we defined three pre-excision steps and assigned them to the processes of (i) initial encounter with eversion of the damaged base, (ii) insertion of several enzyme residues into DNA, and (iii) enzyme isomerization to the catalytically competent form. The individual rate constants were derived for all reaction stages. Of all conformational changes, we identified the insertion step as mostly responsible for the opposite base specificity of OGG1 toward 8-oxoG:C as compared with 8-oxoG:T, 8-oxoG:G, and 8-oxoG:A. We also investigated the kinetic mechanism of OGG1 stimulation by 8-bromoguanine and showed that this compound affects the rate of beta-elimination rather than pre-excision dynamics of DNA and the enzyme.

Biochemical Basis of Glucokinase Activation and the Regulation by Glucokinase Regulatory Protein in Naturally Occurring Mutations

Glucokinase (GK) has several known polymorphic activating mutations that increase the enzyme activity by enhancing glucose binding affinity and/or by alleviating the inhibition of glucokinase regulatory protein (GKRP), a key regulator of GK activity in the liver. Kinetic studies were undertaken to better understand the effect of these mutations on the enzyme mechanism of GK activation and GKRP regulation and to relate the enzyme properties to the associated clinical phenotype of hypoglycemia. Similar to wild type GK, the transient kinetics of glucose binding for activating mutations follows a general two-step mechanism, the formation of an enzyme-glucose complex followed by an enzyme conformational change. However, the kinetics for each step differed from wild type GK and could be grouped into specific types of kinetic changes. Mutations T65I, Y214C, and A456V accelerate glucose binding to the apoenzyme form, whereas W99R, Y214C, and V455M facilitate enzyme isomerization to the active form. Mutations that significantly enhance the glucose binding to the apoenzyme also disrupt the protein-protein interaction with GKRP to a large extent, suggesting these mutations may adopt a more compact conformation in the apoenzyme favorable for glucose binding. Y214C is the most active mutation (11-fold increase in k(cat)/K(0.5)(h)) and exhibits the most severe clinical effects of hypoglycemia. In contrast, moderate activating mutation A456V nearly abolishes the GKRP inhibition (76-fold increase in K(i)) but causes only mild hypoglycemia. This suggests that the alteration in GK enzyme activity may have a more profound biological impact than the alleviation of GKRP inhibition.

Biochemical characterization of a low molecular weight aspartic protease inhibitor from thermo-tolerant Bacillus licheniformis: Kinetic interactions with Pepsin

The present article reports a low molecular weight aspartic protease inhibitor, API, from a newly isolated thermo-tolerant Bacillus licheniformis. The inhibitor was purified to homogeneity as shown by rp-HPLC and SDS-PAGE. API is found to be stable over a broad pH range of 2–11 and at temperature 90 °C for 2 1/2 h. It has a Mr (relative molecular mass) of 1363 Da as shown by MALDI-TOF spectra and 1358 Da as analyzed by SDS-PAGE .The amino acid analysis of the peptide shows the presence of 12 amino acid residues having Mr of 1425 Da. The secondary structure of API as analyzed by the CD spectra showed 7% α-helix, 49% β-sheet and 44% aperiodic structure. The Kinetic studies of Pepsin–API interactions reveal that API is a slow-tight binding competitive inhibitor with the IC 50 and K i values 4.0 nM and (3.83 nM–5.31 nM) respectively. The overall inhibition constant K i⁎ value is 0.107 ± 0.015 nM. The progress curves are time-dependent and consistent with slow-tight binding inhibition: E + I ⇄ ( k 4, k 5) EI ⇄ ( k 6, k 7) EI⁎. Rate constant k 6 = 2.73 ± 0.32 s − 1 reveals a fast isomerization of enzyme–inhibitor complex and very slow dissociation as proved by k 7 = 0.068 ± 0.009 s − 1 . The Rate constants from the intrinsic tryptophanyl fluorescence data is in agreement with those obtained from the kinetic analysis; therefore, the induced conformational changes were correlated to the isomerization of EI to EI⁎.