A study of some thiol ester hydrolyses as models for the deacylation step of papain-catalysed hydrolyses

1. The self-catalysed hydrolyses of the thiol esters, S-hippurylthioglycollic acid and S-ethyl monothiolsuccinate, have been shown to be slower than the deacylation step for the papain-catalysed hydrolysis of hippuric esters, by a factor approx. 10⁵. This difference in rate constants largely reflects a difference in activation energy, which together with other evidence drawn from the literature make it unlikely that a carboxylate ion could be the nucleophile responsible for the deacylation of acyl-papain. 2. The imidazole-catalysed hydrolysis of S-hippurylthioglycollic acid and ethyl thiolacetate have activation energies similar to that for the deacylation step in papain-catalysed hydrolyses. This, together with other evidence drawn from the literature, suggests that the imidazole of a histidine residue is the nucleophile responsible for the deacylation of acyl-papain.     

The kinetics of papain- and ficin-catalysed hydrolyses in the presence of alcohols

1. The maximum rate of production of p-nitrophenol (V_max.) for both papain- and ficin-catalysed hydrolyses of p-nitrophenyl hippurate is independent of methanol concentration up to 2m for papain and 1·5m for ficin. 2. The observed catalytic constant (k₀) for the production of hippuric acid for both papain- and ficin-catalysed hydrolyses of methyl hippurate decreases with increasing methanol concentration, 1/k₀ being linearly dependent on the methanol concentration. The k_MeOH/k_H2O ratio is determined. 3. These results provide strong evidence against general base catalysis for the rate-determining step in the deacylation of hippuryl-papain and hippuryl-ficin and probably for other specific acyl-papains and acyl-ficins. 4. The rate-determining step for the deacylation of the non-specific trans-cinnamoyl-papain appears to be different from that for the specific hippuryl-papain, and is probably subject to general base catalysis. It is possible, however, to accommodate all these observations in a single four-step reaction pathway. 5. Propan-2-ol did not influence the rate of production of hippuric acid for the papain-catalysed hydrolysis of methyl hippurate. A similar result has previously been reported for the ficin-catalysed hydrolysis of methyl hippurate. Ethanol and of course methanol (see 2) decrease the rate of production of hippuric acid for both papain- and ficin-catalysed hydrolyses of methyl hippurate. It is suggested that the secondary alcohol is incapable for structural reasons of approaching the bond to be hydrolysed.     

Direct evidence for an acylated thiol as an intermediate in papain- and ficin-catalysed hydrolyses

1. Methyl thionohippurate was prepared and shown to be a specific substrate for both papain and ficin. 2. The ultraviolet-absorption properties of the acyl-enzyme intermediate for both papain and ficin with methyl thionohippurate was that expected of an acyl-thiol. The possibility that other functional groups present in papain or ficin might be the site of acylation has been excluded. 3. The change in extinction at the absorption maximum with time was as expected for the acyl-enzyme on the basis of the known Michaelis–Menten parameters for methyl thionohippurate. 4. The variation of extinction with initial substrate concentration for both papain and ficin was that expected from the Michaelis–Menten parameters. 5. The extinction of the absorption maximum of the thionohippuryl-enzyme intermediate was suppressed by the addition of methyl hippurate to the extent predicted from the Michaelis–Menten parameters. 6. The decay of the extinction for the acyl-enzyme was arrested by adjusting the pH of the solution to 2·5. 7. These experiments provide compelling evidence that the acylation by substrate of both papain and ficin takes place through a thiol residue.     

Characterisation of the DNA-dependent ATPase activity of human DNA topoisomerase IIbeta: mutation of Ser165 in the ATPase domain reduces the ATPase activity and abolishes the in vivo complementation ability

We report for the first time an analysis of the ATPase activity of human DNA topoisomerase (topo) IIβ. We show that topo IIβ is a DNA-dependent ATPase that appears to fit Michaelis–Menten kinetics. The ATPase activity is stimulated 44-fold by DNA. The k_cat for ATP hydrolysis by human DNA topo IIβ in the presence of DNA is 2.25 s^–1. We have characterised a topo IIβ derivative which carries a mutation in the ATPase domain (S165R). S165R reduced the k_cat for ATP hydrolysis by 7-fold, to 0.32 s^–1, while not significantly altering the apparent K_m. The specificity constant for the interaction between ATP and topo IIβ (k_cat/K_mapp) showed a 90% reduction for βS165R. The DNA binding affinity and ATP-independent DNA cleavage activity of the enzyme are unaffected by this mutation. However, the strand passage activity is reduced by 80%, presumably due to reduced ATP hydrolysis. The mutant enzyme is unable to complement ts yeast topo II in vivo. We have used computer modelling to predict the arrangement of key residues at the ATPase active site of topo IIβ. Ser165 is predicted to lie very close to the bound nucleotide, and the S165R mutation could thus influence both ATP binding and ADP dissociation.     

Kinetics of Avibactam Inhibition against Class A,C, and D β-Lactamases

Avibactam is a non-β-lactam β-lactamase inhibitor with a spectrum of activity that includes β-lactamase enzymes of classes A, C, and selected D examples. In this work acylation and deacylation rates were measured against the clinically important enzymes CTX-M-15, KPC-2, Enterobacter cloacae AmpC, Pseudomonas aeruginosa AmpC, OXA-10, and OXA-48. The efficiency of acylation (k₂/K_i) varied across the enzyme spectrum, from 1.1 × 10¹ m⁻¹s⁻¹ for OXA-10 to 1.0 × 10⁵ for CTX-M-15. Inhibition of OXA-10 was shown to follow the covalent reversible mechanism, and the acylated OXA-10 displayed the longest residence time for deacylation, with a half-life of greater than 5 days. Across multiple enzymes, acyl enzyme stability was assessed by mass spectrometry. These inhibited enzyme forms were stable to rearrangement or hydrolysis, with the exception of KPC-2. KPC-2 displayed a slow hydrolytic route that involved fragmentation of the acyl-avibactam complex. The identity of released degradation products was investigated, and a possible mechanism for the slow deacylation from KPC-2 is proposed.     

Stimulation of human 8-oxoguanine-DNA glycosylase by AP-endonuclease: potential coordination of the initial steps in base excision repair

8-Oxoguanine-DNA glycosylase 1 (OGG1), with intrinsic AP lyase activity, is the major enzyme for repairing 7,8-dihydro-8-oxoguanine (8-oxoG), a critical mutagenic DNA lesion induced by reactive oxygen species. Human OGG1 excised the damaged base from an 8-oxoG·C-containing duplex oligo with a very low apparent k_cat of 0.1 min^–1 at 37°C and cleaved abasic (AP) sites at half the rate, thus leaving abasic sites as the major product. Excision of 8-oxoG by OGG1 alone did not follow Michaelis–Menten kinetics. However, in the presence of a comparable amount of human AP endonuclease (APE1) the specific activity of OGG1 was increased ~5-fold and Michaelis–Menten kinetics were observed. Inactive APE1, at a higher molar ratio, and a bacterial APE (Nfo) similarly enhanced OGG1 activity. The affinity of OGG1 for its product AP·C pair (K_d ~ 2.8 nM) was substantially higher than for its substrate 8-oxoG·C pair (K_d ~ 23.4 nM) and the affinity for its final β-elimination product was much lower (K_d ~ 233 nM). These data, as well as single burst kinetics studies, indicate that the enzyme remains tightly bound to its AP product following base excision and that APE1 prevents its reassociation with its product, thus enhancing OGG1 turnover. These results suggest coordinated functions of OGG1 and APE1, and possibly other enzymes, in the DNA base excision repair pathway.     

The effect of systematic error on the accuracy of Michaelis constants and maximum velocities estimated by using the integrated Michaelis–Menten equation (Short Communication)

Systematic errors in initial substrate concentration (s₀), product concentration and reaction time give much larger errors in the Michaelis–Menten parameters unless s₀ is treated as an unknown parameter. These errors are difficult to detect because the fitted curve deviates little from the data. The effect of non-enzymic reaction is also examined.     

Partial purification and kinetics of oestriol 16α-glucuronyltransferase from the cytosol fraction of human liver

An enzyme that conjugates the 16α-hydroxyl group of oestriol with glucuronic acid was found in the cytosol fraction of human liver. The enzymic activity could not be sedimented when the cytosol fraction was centrifuged at 158000g_av. for 120min. The oestriol 16α-glucuronyltransferase was purified 100-fold by 0–30% saturation of the cytosol fraction with ammonium sulphate followed by filtration of the precipitate through Sephadex G-200. The activity was eluted at the void volume. The product of the reaction, oestriol 16α-monoglucuronide, was identified by paper chromatography and by crystallization of radioactive product to constant specific radioactivity. The optimum temperature was 37°C, and the activation energy was calculated to be 11.1kcal/mol. The apparent Michaelis–Menten constants for oestriol and UDP-glucuronic acid were 13.3 and 100μm respectively. Cu²⁺, Zn²⁺ and Hg²⁺ inhibited, whereas Mg²⁺, Mn²⁺ and Fe²⁺ stimulated the enzyme. Substrate-specificity studies indicated that the amount of oestradiol-17β, oestradiol-17α and oestrone conjugated was not more than about 5% of that found for oestriol. Oestriol 16α-monoglucuronide, a product of the reaction, did not inhibit the 16α-oestriol glucuronyltransferase; in contrast, UDP, another product of the reaction, inhibited the enzyme competitively with respect to UDP-glucuronic acid as the substrate, and non-competitively with respect to oestriol as the substrate. ATP and UDP-N-acetylglucosamine did not affect the oestriol 16α-glucuronyltransferase. 17-Epioestriol acted as a competitive inhibitor and 16-epioestriol as a non-competitive inhibitor of the glucuronidation of oestriol. 5α-Pregnane-3α,20α-diol also inhibited the enzyme non-competitively. It is most likely that the oestriol 16α-glucuronyltransferase described here is bound to the membranes of the endoplasmic reticulum.     

AMPHOTERIC BEHAVIOR OF COMPLEX SYSTEMS : IV. NOTE ON THE ISOELECTRIC POINT AND IONIZATION CONSTANTS OF SULFANILIC ACID.

From the solubility minimum the value of the basic ionization constant of sulfanilic acid is shown to lie probably between the values 1.7 x 10^–15 and 3.2 x 10^–15. From solubility measurements the value of this same constant is shown to lie probably between 2.0 and 2.2 x 10^–15, and the isoelectric point of sulfanilic acid is thus at a cH of 0.056 or a pH of 1.25. From conductivity ratios the acid ionization constant of sulfanilic acid is shown to be 7.05 x 10^–4 at room temperature (21°C.). Calculations are made, from data published in preceding papers, of the ionization constants of glycine, K_a being 2.3 x 10^–10, and K_b being 2.2 x 10^–12.     

Kinetics and thermodynamics of activation by pretreatment with guanosine 5′-[β-imido]triphosphate of smooth-muscle adenylate cyclase

Catalytic subunits (C) of uterine smooth-muscle adenylate cyclase were activated (C*) by incubating the enzyme with the GTP analogue guanosine 5′-[βγ-imido]triphosphate (p[NH]ppG), followed by treatment with GTP and washing at 2°C. Activation (C→C*) proceeded in a time- and temperature-dependent manner as disclosed by subsequent assay of the pretreated particles at 37°C. The properties of the activated subunits were a function of the pretreatment temperature and not those of the enzyme assay performed at 37°C. Over the range 6–24°C, activation by pretreatment with p[NH]ppG followed simple Michaelis–Menten kinetics, and increase in temperature increased the concentration of catalytic subunits in the C* state and decreased K_m for the guanosine nucleotide. Characterization of the temperature-dependent effects of pretreatment with p[NH]ppG suggested that activation of the catalytic subunit at the temperature in situ (37°C) was moderately endergonic (ΔH⁰ ~8kJ·mol⁻¹) and accompanied by an increase in entropy (ΔS⁰ ~146J·mol⁻¹·K⁻¹). The β-adrenergic catecholamine receptor, reflected by isoproterenol's effect on activation by pretreatment with p[NH]ppG, increased the concentration of catalytic subunits in the C* state but had an insignificant (P>0.05) effect on the K_m at every temperature. This result suggested that formation of the receptor–hormone complex produced an increase in the first-order rate constant without an appreciable effect on the actual catalytic-subunit activation step. The primary function of the β-adrenergic catecholamine receptor under these conditions appeared to be regulation of the concentration of activation sites available for binding of p[NH]ppG.     

Activation of brain hexokinase by magnesium ions and by magnesium ion–adenosine triphosphate complex

1. An alternative explanation for the kinetic data obtained by Bachelard (1971) for the brain hexokinase reaction is presented. 2. Apparently sigmoidal saturation curves for MgATP²⁻ based upon Bachelard's (1971) studies can be corrected to hyperbolic curves by use of a stability constant for MgATP²⁻ complex formation. 3. A number of other effects related to the concentration-dependent stability of the MgATP²⁻ complex and to the presence of the inhibitory free uncomplexed ATP⁴⁻ concentration are also explained in terms of a non-allosteric role for either Mg²⁺ or MgATP²⁻ fully consistent with a number of previous reports on this enzyme. 4. A brief discussion of the validity of Hill plots in studies of multisubstrate co-operative enzymes is presented. 5. A simple model is presented that demonstrates how enzymes obeying Michaelis–Menten kinetics can demonstrate sigmoidal velocity responses if the true substrate of the reaction is the metal–substrate complex.     

Improved model simulation of soil carbon cycling by representing the microbially derived organic carbon pool

During the decomposition process of soil organic carbon (SOC), microbial products such as microbial necromass and microbial metabolites may form an important stable carbon (C) pool, called microbially derived C, which has different decomposition patterns from plant-derived C. However, current Earth System Models do not simulate this microbially derived C pool separately. Here, we incorporated the microbial necromass pool to the first-order kinetic model and the Michaelis–Menten model, respectively, and validated model behaviors against previous observation data from the decomposition experiments of ¹³C-labeled necromass. Our models showed better performance than existing models and the Michaelis–Menten model was better than the first-order kinetic model. Microbial necromass C was estimated to be 10–27% of total SOC in the study soils by our models and therefore should not be ignored. This study provides a novel modification to process-based models for better simulation of soil organic C under the context of global changes.Subject terms: Biogeochemistry, Theoretical ecology, Microbial ecology, Stable isotope analysis     

A comparison of acylation, phosphorylation and binding in related substrates and inhibitors of serum cholinesterase

1. The K_m and catalytic-centre activities for human serum cholinesterase and methyl, ethyl, n-propyl and n-butyl butyrate substrates were determined and compared with the related inhibition constants of a similarly substituted organophosphate inhibitor series based on malaoxon. The results indicated that the catalytic-centre activities approximated to k_+2(a), the acylation rate constant, and that K_m approximated to the equilibrium binding constant. The inhibition constants measured were K_a, the equilibrium binding constant, and k_+2(p), the phosphorylation rate constant. 2. The effects of the alkyl substituents on k_+2(p) and k_+2(a) were closely parallel, and the decreasing order in each case was: n-butyl; methyl; n-propyl; ethyl. The Taft constants did not follow this order, suggesting that alkyl substituents did not primarily effect acylation or phosphorylation by electron induction. 3. For comparable homologues, the k_+2(a) values were on average 435 times the k_+2(p) values. The k_+2(p) values at 25° and pH7·6 ranged from 6·6min.⁻¹ for the diethyl member to 22·6min.⁻¹ for the di-n-butyl member. 4. The effect of the alkyl substituents on K_a and K_m were closely paralleled. The increasing order in each case was: n-butyl; n-propyl; ethyl; methyl. The K_a values were about 100 times less than the comparable K_m values. 5. Consideration of the binding energies suggested that only one of the two alkyl groups on the malaoxon homologues bound to the active site. 6. The possibility that malaoxon acted as a substrate as well as an inhibitor for cholinesterase was also investigated, but no evidence of a substrate reaction was found.     

Nucleoside diphosphate kinase from Mycobacterium tuberculosis cleaves single strand DNA within the human c-myc promoter in an enzyme-catalyzed reaction

The reason for secretion of nucleoside diphosphate kinase (NdK), an enzyme involved in maintaining the cellular pool of nucleoside triphosphates in both prokaryotes and eukaryotes, by Mycobacterium tuberculosis is intriguing. We recently observed that NdK from M.tuberculosis (mNdK) localizes within nuclei of HeLa and COS-1 cells and also nicks chromosomal DNA in situ (A. K. Saini, K. Maithal, P. Chand, S. Chowdhury, R. Vohra, A. Goyal, G. P. Dubey, P. Chopra, R. Chandra, A. K. Tyagi, Y. Singh and V. Tandon (2004) J. Biol. Chem., 279, 50142–50149). In the current study, using a molecular beacon approach, we demonstrate that the mNdK catalyzes the cleavage of single strand DNA. It displays Michaelis–Menten kinetics with a k_cat/K_M of 9.65 (±0.88) × 10⁶ M⁻¹ s⁻¹. High affinity (K_d ≈ K_M of ~66 nM) and sequence-specific binding to the sense strand of the nuclease hypersensitive region in the c-myc promoter was observed. This is the first study demonstrating that the cleavage reaction is also enzyme-catalyzed in addition to the enzymatic kinase activity of multifunctional NdK. Using our approach, we demonstrate that GDP competitively inhibits the nuclease activity with a K_I of ~1.9 mM. Recent evidence implicates mNdK as a potent virulence factor in tuberculosis owing to its DNase-like activity. In this context, our results demonstrate a molecular mechanism that could be the basis for assessing in situ DNA damage by secretory mNdK.     

A hydrogen peroxide biosensor based on the direct electrochemistry of hemoglobin modified with quantum dots

Direct electron transfer of hemoglobin modified with quantum dots (QDs) (CdS) has been performed at a normal graphite electrode. The response current is linearly dependent on the scan rate, indicating the direct electrochemistry of hemoglobin in that case is a surface-controlled electrode process. UV–vis spectra suggest that the conformation of hemoglobin modified with CdS is little different from that of hemoglobin alone, and the conformation changes reversibly in the pH range 3.0–10.0. The hemoglobin in a QD film can retain its bioactivity and the modified electrode can work as a hydrogen peroxide biosensor because of its peroxidase-like activity. This biosensor shows an excellent response to the reduction of H₂O₂ without the aid of an electron mediator. The catalytic current shows a linear dependence on the concentration of H₂O₂ in the range 5 × 10⁻⁷–3 × 10⁻⁴ M with a detection limit of 6 × 10⁻⁸ M. The response shows Michaelis–Menten behavior at higher H₂O₂ concentrations and the apparent Michaelis–Menten constant is estimated to be 112 μM.     

Metabolic response to point mutations reveals principles of modulation of in vivo enzyme activity and phenotype

The relationship between sequence variation and phenotype is poorly understood. Here, we use metabolomic analysis to elucidate the molecular mechanism underlying the filamentous phenotype of E. coli strains that carry destabilizing mutations in dihydrofolate reductase (DHFR). We find that partial loss of DHFR activity causes reversible filamentation despite SOS response indicative of DNA damage, in contrast to thymineless death (TLD) achieved by complete inhibition of DHFR activity by high concentrations of antibiotic trimethoprim. This phenotype is triggered by a disproportionate drop in intracellular dTTP, which could not be explained by drop in dTMP based on the Michaelis–Menten‐like in vitro activity curve of thymidylate kinase (Tmk), a downstream enzyme that phosphorylates dTMP to dTDP. Instead, we show that a highly cooperative (Hill coefficient 2.5) in vivo activity of Tmk is the cause of suboptimal dTTP levels. dTMP supplementation rescues filamentation and restores in vivo Tmk kinetics to Michaelis–Menten. Overall, this study highlights the important role of cellular environment in sculpting enzymatic kinetics with system‐level implications for bacterial phenotype.     

Kinetic study of the cellobiase activity of Trichoderma reesei cellulase complex at high substrate concentrations

At high cellobiose concentrations, the cellobiase activity of a Trichoderma reesei cellulase preparation does not follow Michaelis–Menten kinetics and shows substrate inhibition. Several rate equations were fitted to the initial rate-cellobiose concentration data. The best fit is obtained for a rate equation corresponding to partial substrate inhibition of cellobiase. In this case, the K_m, V_max and K_I values obtained are 1.1 mM, 16 IU ml^–1 and 26 mM, respectively.     

Performance of three pilot-scale immobilized-cell biotrickling filters for removal of hydrogen sulfide from a contaminated air steam

Hydrogen sulfide (H₂S) is a major malodorous compound emitted from wastewater treatment plants. In this study, the performance of three pilot-scale immobilized-cell biotrickling filters (BTFs) spacked with combinations of bamboo charcoal and ceramsite in different ratios was investigated in terms of H₂S removal. Extensive tests were performed to determine the removal characteristics, pressure drops, metabolic products, and removal kinetics of the BTFs. The BTFs were operated in continuous mode at low loading rates varying from 0.59 to 5.00 g H₂S m⁻³ h⁻¹ with an empty bed retention time (EBRT) of 25 s. The removal efficiency (RE) for each BTF was >99% in the steady-state period, and high standards were met for the exhaust gas. It was found that a multilayer BTF had a slight advantage over a perfectly mixed BTF for the removal of H₂S. Furthermore, an impressive amount >97% of the H₂S was eliminated by 10% of packing materials near the inlet of the BTF. The modified Michaelis–Menten equation was adopted to describe the characteristics of the BTF, and K_s and V_m values for the BTF with pure bamboo charcoal packing material were 3.68 ppmv and 4.26 g H₂S m⁻³ h⁻¹, respectively. Both bamboo charcoal and ceramsite demonstrated good performance as packing materials in BTFs for the removal of H₂S, and the results of this study could serve as a guide for further design and operation of industrial-scale systems.     

Chitosan–SiO2–multiwall carbon nanotubes nanocomposite: A novel matrix for the immobilization of creatine amidinohydrolase

A matrix made up of chitosan–SiO₂–multiwall carbon nanotubes (CHIT–SiO₂–MWCNTs) nanocomposite was fabricated to investigate the immobilization of creatine amidinohydrolase (CAH). CAH enzyme was covalently immobilized with the CHIT–SiO₂–MWCNTs matrix using glutaraldehyde as a linker. The resulting CAH/CHIT–SiO₂–MWCNTs biomatrix was characterized with Fourier transform infrared spectroscopy (FTIR), scanning electron microscopy (SEM) and cyclic voltammetry (CV) taking CHIT–SiO₂–MWNTs as a reference. The influence of various parameters on CAH enzyme activity within the matrix was investigated including pH, temperature, and time. The Michaelis–Menten constant and apparent activities for the CAH enzyme were calculated to be 0.58 mM and 83.16 mg/cm², respectively; indicating CHIT–SiO₂–MWCNTs nanocomposite matrix has a high affinity to immobilize CAH enzyme.