Interaction of purified alternative oxidase from thermogenic Arum maculatum with pyruvate

Plant alternative oxidase (AOX) activity in isolated mitochondria is regulated by carboxylic acids, but reaction and regulatory mechanisms remain unclear. We show that activity of AOX protein purified from thermogenic Arum maculatum spadices is sensitive to pyruvate and glyoxylate but not succinate. Rapid, irreversible AOX inactivation occurs in the absence of pyruvate, whether or not duroquinol oxidation has been initiated, and is insensitive to duroquinone. Our data indicate that pyruvate stabilises an active conformation of AOX, increasing the population of active protein in a manner independent of reducing substrate and product, and are thus consistent with an exclusive effect of pyruvate on the enzyme’s apparent V_max.     

Development of thermostable Candida antarctica lipase B through novel in silico design of disulfide bridge

Lipase B from Candida antarctica (CalB) is a versatile biocatalyst for various bioconversions. In this study, the thermostability of CalB was improved through the introduction of a new disulfide bridge. Analysis of the B‐factors of residue pairs in CalB wild type (CalB‐WT) followed by simple flexibility analysis of residues in CalB‐WT and its designated mutants using FIRST server were newly proposed to enhance the selective power of two computational tools (MODIP and DbD v1.20) to predict the possible disulfide bonds in proteins for the enhancement of thermostability. Five residue pairs (A162‐K308, N169‐F304, Q156_‐L163, S50‐A273, and S239C‐D252C) were chosen and the respective amino acid residues were mutated to cysteine. In the results, CalB A162C‐K308C showed greatly improved thermostability while maintaining its catalytic efficiency compared to that of CalB‐WT. Remarkably, the temperature at which 50% of its activity remained after 60‐min incubation (T) of CalB A162C_K308C was increased by 8.5°C compared to that of CalB‐WT (55 and 46.5°C, respectively). Additionally, the half‐life at 50°C of CalB A162C‐K308C was 4.5‐fold higher than that of CalB‐WT (220 and 49 min, respectively). The improvement of thermostability of CalB A162C‐K308C was elucidated at the molecular level by molecular dynamics (MD) simulation. Biotechnol. Bioeng. 2012; 109:867–876. © 2011 Wiley Periodicals, Inc.     

Inhibition of extracellular lipase from Streptomyces rimosus with 3,4-dichloroisocoumarin

Kinetic characterization of lipase inhibition was performed by activity measurement and mass spectrometry (MS), for the first time with serine-protease inhibitor 3,4-dichloroisocoumarin (DCI). Inhibition of Streptomyces rimosus extracellular lipase (SrLip), a member of the SGNH superfamily, by means of DCI follows the mechanism of two-step irreversible inhibition. The dissociation constant of the noncovalent E?I complex and first-order rate constant for inactivation were determined by incubation (K_i* = 26.6?±?2.8 µM, k₂ = 12.2?±?0.6 min–1) or progress curve (K_i* = 6.5?±?1.5 µM, k₂ = 0.11?±?0.01 min–1) method. Half-times of reactivation for lipase inhibited with 10-fold molar excess of DCI were determined by activity measurement (t_1/2 = 11.3?±?0.2?h), matrix-assisted laser desorption/ionization (MALDI, t_1/2 = 13.5?±?0.4?h), and electro-spray ionization (ESI, t_1/2 = 12.2?±?0.5?h) MS. The active SrLip concentration was determined by incubating the enzyme with near equimolar concentrations of DCI, followed by activity and MS measurement.     

Expression of functional Candida antarctica lipase B in a cell‐free protein synthesis system derived from Escherichia coli

This article reports the cell‐free expression of functional Lipase B from Candida antarctica (CalB) in an Escherichia coli extract. Although most of the cell‐free synthesized CalB was insoluble under conventional reaction conditions, the combined use of molecular chaperones led to the soluble expression of CalB. In addition, the functional enzyme was generated by applying the optimal redox potential. When examined using p‐nitrophenyl palmitate as a substrate, the specific activity of the cell‐free synthesized CalB was higher than that of the reference protein produced in Pichia pastoris. These results highlight the potential of cell‐free protein synthesis technology as a powerful platform for the rapid expression, screening and analysis of industrially important enzymes. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2009     

Immobilization to prevent enzyme incompatibility with proteases

Abstract

Enzyme incompatibility is a problem in multi-enzyme processes that involve a non-specific protease, such as Alcalase. An example is the one-pot enzymatic synthesis of peptides catalyzed by a lipase and a protease. The incompatibility between lipase B from Candida antarctica (CalB) and Alcalase was studied. To what extent immobilization of both or either CalB or Alcalase onto macroporous beads helps to prevent hydrolysis of CalB by Alcalase was evaluated. The rate of activity loss of native and immobilized CalB in the absence and presence of native and immobilized Alcalase was calculated from the rate of triacetin hydrolysis. Immobilization of both or either CalB or Alcalase onto macroporous beads was found to be effective in largely preventing hydrolysis of CalB by Alcalase.     

Reversible and irreversible inactivation of cellular nitrogenase upon oxygen stress in Azotobacter vinelandii growing in oxygen controlled continuous culture

Azotobacter vinelandii growing in oxygen controlled chemostat culture was subjected to sudden increases of ambient oxygen concentrations (oxygen stress) after adaptation to different oxygen concentrations adjustable with air (100% air saturation corresponds to 225±14 M O₂). Inactivations of cellular nitrogenase during stress (switch off) as well as after release of stress (switch on) were evaluated in vivo as depending on stress duration and stress height (pO₂). Switch off was at its final extent within 1 min of stress. The extent of switch off, however, increased with stress height and was complete at pO₂ between 8–10% air saturation irrespective of different oxygen concentrations the organisms were adapted to before stress, indicating that switch off is adaptable. Inactivation of nitrogenase measurable after switch on represents irreversible loss of activity. Irreversible inactivation was at its characteristic level within less than 3 min of stess and at a pO₂ of less than 1% air saturation. The level of irreversible inactivation increased linearly with the oxygen concentration the organisms were adapted to before stress. Thus adaptation of cells to increased oxygen concentrations did not prevent increased susceptibility of nitrogenase to irreversible inhibition during oxygen stress. The fast response of irreversible inactivation at low stress heights suggests that it takes place already during stress. Thus switch off comprised both a reversible and an irreversible phase. The data showed that reversible inactivation of nitrogenase was less susceptible to oxygen stress than irreversible inactivation. A basic pre-requisite of the hypothesis of respiratory protection of nitrogenase, i.e. the proposed relationship between respiratory activities and the protection of nitrogenase from irreversible inhibition by oxygen, was not supported by the results of this report.     

Structural modification of proteins by direct electric current from low voltage

The interaction of direct electric current (dc) and proteins is a little explored topic. We had reported that exposure of Crotalus atrox venom to dc caused irreversible inactivation of phospholipase A₂ and metalloprotease and that the eukaryote adenylate kinases (AK) precipitate in nondenaturing gel electrophoresis. AK1 displays an elevated percent difference of CHarged versus POlar amino acid content (CH‐PO 14). Commercial AK1 and other 17 enzymes with various CH‐PO values were exposed in solution to dc (0–0.7 mA) from low voltage (0–10 V), then enzymatic activity was assayed. The enzymes with CH‐PO higher than 10.0 were irreversibly inactivated by current exposure; those with CH‐PO between +3 and ?5 were not. Inactivation was dependent on the ionic strength of the medium and not on the net charge of the protein. Circular dichroic spectroscopy showed a structural modification in some of the inactivated enzymes. CH‐PO could be a crucial, although rough, parameter for predicting protein inactivation by low‐voltage exposure. The observed effect seems due to the current density. Enzymatic activity maybe a more accurate sensor of conformational changes than circular dichroism spectroscopy. A better understanding of efficacy of many electrical devices utilized in medical practice may follow. © 2009 Wiley Periodicals, Inc. J Biochem Mol Toxicol 23:309–317, 2009; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/jbt.20293     

Functional expression of Candida antarctica lipase B in the Escherichia coli cytoplasm—a screening system for a frequently used biocatalyst

In this paper, we report for the first time the functional expression of lipase B from the yeast Candida antarctica (CalB) in the Escherichia coli cytoplasm. The enzyme possessing three disulfide bonds was functionally expressed in the strain Origami B. Expression under the control of a lac promoter yielded 2 U mg⁻¹, whereas expression of a thioredoxin–CalB fusion protein yielded 17 U mg⁻¹. The native enzyme was most efficiently expressed under control of the cspA promoter (11 U mg⁻¹). Coexpression of different chaperones led to a strong increase in active protein formation (up to 61 U mg⁻¹). A codon-optimized synthetic variant of calb did not show significant effects on functional protein yield. Functional CalB expression was not only achieved in shake flasks but also in microtiter plate scale. Therefore, this CalB expression system is suitable for high-throughput applications, including the screening of large gene libraries as those derived from directed evolution experiments.     

Kinetic analysis of the inhibition of sulfate transport in human red blood cells by isothiocyanates

Summary A kinetic analysis of anion self-exchange in human red blood cells, in the presence of an irreversible inhibitor, is presented and applied to the study of the inactivation of sulfate transport by three isothiocyanates: 3-isothiocyano-1,5-naphthalenedisulfonic acid, disodium salt (INDS), 1-isothiocyano-4-naphthalene sulfonic acid, sodium salt, monohydrate (INS), and 1-isothiocyano-4-benzenesulfonic acid, sodium salt, monohydrate (IBS). The time dependence of the inhibition of sulfate transport by the isothiocyanates used could be described by a single exponential and could be shown to contain a reversible and an irreversible component. In each case a portion of sulfate efflux was found to be resistant to inactivation. The residual portion of the sulfate efflux varied with inhibition: 4% for INS, 16% for INDS, and 34% for IBS. INS showed the largest reversible inhibitory effect (12% of the flux remaining at 0.2mm inhibitor concentration), while INDS showed the weakest effect (92% of the flux remaining at 0.3mm inhibitor concentration). IBS had the highest rate of inactivation while INDS had the lowest. The kinetic analysis further suggests that all three isothiocyanates bind reversibly to an inhibitory site on the membrane before they bind covalently, and therefore irreversibly, to the same site on the membrane. The equilibrium constant for the dissociation of the reversibly-bound complex,K _i, and the rate of irreversible inactivation after all membrane sites are reversibly bound,k _max, have been computed for all three inhibitors: INDS (K _i=420m,k _max=5.04 hr^–1), INS (K _i=148 m,k _max=6.48 hr^–1), and IBS (K _i=208 m,k _max=8.11 hr^–1).     

Partial purification of two proteins (100 kDa and 67 kDa) cooperating in the ATP-dependent inactivation of spinach leaf nitrate reductase

Using a three-step purification procedure, two protein fractions which catalyzed the ATP-dependent in-activation of nitrate reductase (NR) were obtained from spinach (Spinacia oleracea L.) leaf extracts. Purification involved ammonium-sulfate fractionation, anion-exchange chromatography and size-exclusion chromatography. The capacity of the fractions to inactivate NR by preincubation with ATP was examined by using as target either a crude NR-ammonium sulfate precipitate or partially purified NR (ppNR). The fractions were also examined for protein-kinase activity by measuring the phosphorylation of histone III S (or casein) with-[³²P]ATP as substrate, and subsequent SDS-PAGE, autoradiography and liquid scintillation counting of cut-off histone bands. The two proteins had apparent molecular weights in the 67-kDa and 100-kDa region (termed P₆₇ and P₁₀₀, respectively). Neither P₆₇ nor P₁₀₀ alone was able to inactivate ppNR by preincubation with ATP. However, when P₁₀₀ and P₆₇ were added together to ppNR, ATP-dependent inactivation was observed, with a half-time of about 10 min. The P₆₇, but not P₁₀₀ had histone-kinase activity (casein was not phosphorylated). Using the partially purified system, various compounds were examined as possible effectors of NR inactivation. Sugar phosphates had little effect on the inactivation of NR. Addition of AMP at very high concentrations (5 mM), and removal of Mg²⁺ by excess EDTA also prevented the inactivation.Abbreviations AS ammonium sulfate - DTT dithiothreitol - NR NADH-nitrate reductase - NRA nitrate reductase activity - ppNR partially purified nitrate reductase     

Affinity labeling of oxaloacetate decarboxylase by novel dichlorotriazine linked alpha-ketoacids

The 4-aminophenyloxanilic acid and -mercaptopyruvic acid linked to the reactive diclorotriazine ring, were studied as active site-direct affinity labels towards oxaloacetate decarboxylase (EC 4.1.1.3, OXAD). Oxaloacetate decarboxylase when incubated with 4-aminophenyloxanilic-diclorotriazine (APOD) or -mercaptopyruvic-diclorotriazine (MPD) at pH 7.0 and 25°C shows a time-dependent and concentration-dependent loss of enzyme activity. The inhibition was irreversible and activity cannot be recovered either by extensive dialysis or gel-filtration chromatography. The enzyme inactivation following the Kitz & Wilson kinetics for time-dependent irreversible inhibition. The observed rate of enzyme inactivation (k _obs) exhibits a non-linear dependence on APOD or MPD concentration with maximum rate of inactivation (k ₃) of 0.013 min^–1 and 0.0046 min^–1 and K _D equal to 20.3 and 156 M respectively. The inactivation of oxaloacetate decarboxylase by APOD and MPD is competitively inhibited by OXAD substrate and inhibitors, such as oxaloacetate, ADP and oxalic acid whereas Mn⁺² enhances the rate of inactivation. The rate of inactivation of OXAD by APOD shows a pH dependence with an inflection point at 6.8, indicating a possible histidine derivatization by the label. These results show that APOD and MPD demonstrate the characteristics of an active-site probe towards the oxaloacetate binding site of oxaloacetate decarboxylase.     

Cloning and high-level production of a chitinase from <Emphasis Type="Italic">Chromobacterium</Emphasis> sp. and the role of conserved or nonconserved residues on its catalytic activity

A gene encoding an alkaline (pI of 8.67) chitinase was cloned and sequenced from Chromobacterium sp. strain C-61. The gene was composed of 1,611 nucleotides and encoded a signal sequence of 26 N-terminal amino acids and a mature protein of 510 amino acids. Two chitinases of 54 and 52 kDa from both recombinant Escherichia coli and C-61 were detected on SDS-PAGE. Maximum chitinase activity was obtained in the culture supernatant of recombinant E. coli when cultivated in TB medium for 6 days at 37°C and was about fourfold higher than that from C-61. Chi54 from the culture supernatants could be purified by a single step based on isoelectric point. The purified Chi54 had about twofold higher binding affinity to chitin than to cellulose. The chi54 encoded a protein that included a type 3 chitin-binding domain belonging to group A and a family 18 catalytic domain belonging to subfamily A. In the catalytic domain, mutation of perfectly conserved residues and highly conserved residues resulted in loss of nearly all activity, while mutation of nonconserved residues resulted in enzymes that retained activity. In this process, a mutant (T218S) was obtained that had about 133% of the activity of the wild type, based on comparison of K _cat values.     

Understanding the effect of tert-butanol on Candida antarctica lipase B using molecular dynamics simulations

The use of organic solvents as reaction media for enzymatic reactions has many advantages. Several organic solvents have been proposed as reaction media, especially for transesterifications using Candida antarctica lipase B (CalB). Among organic solvents, tert-butanol is associated with an enhanced conversion rate in bio-diesel production. Thus, it is necessary to understand the effect of tert-butanol on CalB to explain the high-catalytic efficiency compared with the reaction in other hydrophilic organic solvents. In this study, the effects of tert-butanol on the structure of CalB were investigated by MD simulations. The overall flexibility was increased in the presence of tert-butanol. The substrate entrance and the binding pocket size of CalB in tert-butanol were maintained as in TIP3P water. The distance between the catalytic residues of CalB in tert-butanol indicated a higher likelihood of forming hydrogen bonds. These structural analyses could be useful for understanding the effect of tert-butanol on lipase transesterification.     

Turnover of Brain Monoamine Oxidase Measured In Vivo by Positron Emission Tomography Using l-[11C]Deprenyl

The distribution of carbon-11-labeled L-deprenyl, an irreversible inhibitor of monoamine oxidase type B (MAO-B), was determined in the baboon brain by positron emission tomography. The irreversible blood-to-brain transfer constant (influx constant, K_i) was measured using a complete metabolite-corrected arterial plasma concentration curve. This influx constant was used as a measure of functional enzyme activity for sequential determinations of MAO-B recovery following a single high dose of unlabeled l -deprenyl. The half-life for turnover of MAO-B was thus determined to be 30 days. Using appropriate irreversible inhibitors, this procedure should be generally useful for determining enzyme turnover rates in any organ in vivo and can be applied to some human studies as well.     

Suppression of isotope scrambling in cell-free protein synthesis by broadband inhibition of PLP enymes for selective 15N-labelling and production of perdeuterated proteins in H2O

Selectively isotope labelled protein samples can be prepared in vivo or in vitro from selectively labelled amino acids but, in many cases, metabolic conversions between different amino acids result in isotope scrambling. The best results are obtained by cell-free protein synthesis, where metabolic enzymes are generally less active, but isotope scrambling can never be suppressed completely. We show that reduction of E. coli S30 extracts with NaBH₄ presents a simple and inexpensive way to achieve cleaner selective isotope labelling in cell-free protein synthesis reactions. The purpose of the NaBH₄ is to inactivate all pyridoxal-phosphate (PLP) dependent enzymes by irreversible reduction of the Schiff bases formed between PLP and lysine side chains of the enzymes or amino groups of free amino acids. The reduced S30 extracts retain their activity of protein synthesis, can be stored as well as conventional S30 extracts and effectively suppress conversions between different amino acids. In addition, inactivation of PLP-dependent enzymes greatly stabilizes hydrogens bound to α-carbons against exchange with water, minimizing the loss of α-deuterons during cell-free production of proteins from perdeuterated amino acids in H₂O solution. This allows the production of highly perdeuterated proteins that contain protons at all exchangeable positions, without having to back-exchange labile deuterons for protons as required for proteins that have been synthesized in D₂O.     

Studies of Specificity and Inhibition of Human Cerebrospinal Fluid Dynorphin Converting Enzyme

Abstract

Dynorphin-converting activity was recently discovered in human cerebrospinal fluid.¹ This enzyme (hCSF-DCE) cleaves dynorphin A, dynorphin B and alpha-neoendorphin to release Leu-enkephalin-Arg⁶. To characterize the enzyme further we used several protease inhibitors, including N-peptidyl-O-acyl hydroxylamines which are known to act as potent irreversible inhibitors of serine and cysteine proteinases.^2-4

No irreversible inactivation occurred but strong, reversible effects on the dynorphin-converting activity by some of the inhibitors tested could be observed. Although, hCSF-DCE binds its substrates (dynorphin A and B) in the μM-mM concentration range, it exhibits high specificity in recognizing and cleaving the linkage between the two basic amino acids in the substrate sequence.     

Enzymatic activity and thermal stability of PEG-α-chymotrypsin conjugates

α-Chymotrypsin was chemically modified with methoxypoly(ethylene glycol) (PEG) of different molecular weights (700, 2,000, and 5,000 Da) and the amount of polymer attached to the enzyme was varied systematically from 1 to 9 PEG molecules per enzyme molecule. Upon PEG conjugation, enzyme catalytic turnover (k _cat) decreased by 50% and substrate affinity was lowered as evidenced by an increase in the K _M from 0.05 to 0.19 mM. These effects were dependent on the amount of PEG bound to the enzyme but were independent of the PEG size. In contrast, stabilization toward thermal inactivation depended on the PEG molecular weight with conjugates with the larger PEGs being more stable.     

The reactions of pyridoxal 5′-phosphate with the M4 and H4 isoenzymes of pig lactate dehydrogenase

The H₄ and M₄ isoenzymes of pig lactate dehydrogenase are both inactivated by reaction with pyridoxal 5′-phosphate. In the early stages, inactivation is largely reversible by the addition of lysine in excess, but may be made irreversible by reduction with borohydride. This indicates that modification of lysine residues probably causes the initial inactivation. Both isoenzymes also undergo a slower process of irreversible inactivation which becomes more evident with increasing concentrations of pyridoxal 5′-phosphate and higher temperature. Although coenzymes give only partial protection of enzyme activity, they nevertheless completely prevent irreversible inactivation. Neither pyruvate nor lactate alone gives any protection. With the M₄ isoenzyme, complete protection against inactivation by pyridoxal 5′-phosphate may be achieved in ternary complexes, but no conditions have been found for complete protection of the H₄ isoenzyme. In the course of irreversible inactivation of H₄ lactate dehydrogenase, complete loss of activity can be correlated with the loss of approximately two free thiol groups per subunit. Present findings with regard to the importance of temperature and reagent concentration in determining the outcome of the chemical modification appear to resolve earlier controversy.     

Identification of two forms of the maltose transport system in Saccharomyces cerevisiae and their regulation by catabolite inactivation

The maltose transport system of Saccharomyces cerevisiae exists in two forms with K_m values of approx. 4 mM and 70 mM, respectively. The V_max of the high-K_m form is about 4-fold greater than the V_max of the low one. A rapid and irreversible inactivation of both forms is detected on protein synthesis impairment. This inactivation is stimulated by the catabolism of fermentable sugars and prevented during ethanol catabolism. It is concluded that both forms of the maltose transport system are regulated by catabolite inactivation.