In silico structural and functional analysis of Mesorhizobium ACC deaminase

Nodulation is one of the very important processes of legume plants as it is the initiating event of fixing nitrogen. Although ethylene has essential role in normal plant metabolism but it has also negative impact on plants particularly in nodule formation in legume plants. It is also produced due to a variety of biotic or abiotic stresses. 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase is a rhizobial enzyme which cleaves ACC (immediate precursor of ethylene) into α-ketobutyrate and ammonia. As a result, the level of ethylene from the plant cells is decreased and the negative impact of ethylene on nodule formation is reduced. ACC deaminase is widely studied in several plant growth promoting rhizobacterial (PGPR) strains including many legume nodulating bacteria like Mesorhizobium sp. It is an important symbiotic nitrogen fixer belonging to the class – alphaproteobacteria under the order Rhizobiales. ACC deaminase has positive role in Legume-rhizobium symbiosis. Rhizobial ACC deaminase has the potentiality to reduce the adverse effects of ethylene, thereby triggering the nodulation process. The present study describes an in silico comparative structural (secondary structure prediction, homology modeling) and functional analysis of ACC deaminase from Mesorhizobium spp. to explore physico-chemical properties using a number of bio-computational tools. M. loti was selected as a representative species of Mesorhizobium genera for 3D modelling of ACC deaminase protein. Correlation by the phylogenetic relatedness on the basis of both ACC deaminase enzymes and respective acdS genes of different strains of Mesorhizobium has also studied.     

Ethylene biosynthesis by 1-aminocyclopropane-1-carboxylic acid oxidase: a DFT study

The reaction catalyzed by the plant enzyme 1-aminocyclopropane-1-carboxylic acid oxidase (ACCO) was investigated by using hybrid density functional theory. ACCO belongs to the non-heme iron(II) enzyme superfamily and carries out the bicarbonate-dependent two-electron oxidation of its substrate ACC (1-aminocyclopropane-1-carboxylic acid) concomitant with the reduction of dioxygen and oxidation of a reducing agent probably ascorbate. The reaction gives ethylene, CO(2), cyanide and two water molecules. A model including the mononuclear iron complex with ACC in the first coordination sphere was used to study the details of O-O bond cleavage and cyclopropane ring opening. Calculations imply that this unusual and complex reaction is triggered by a hydrogen atom abstraction step generating a radical on the amino nitrogen of ACC. Subsequently, cyclopropane ring opening followed by O-O bond heterolysis leads to a very reactive iron(IV)-oxo intermediate, which decomposes to ethylene and cyanoformate with very low energy barriers. The reaction is assisted by bicarbonate located in the second coordination sphere of the metal.     

Spectroscopic studies of 1-aminocyclopropane-1-carboxylic acid oxidase: molecular mechanism and CO(2) activation in the biosynthesis of ethylene

1-Aminocyclopropane-1-carboxylic acid (ACC) oxidase (ACCO) catalyzes the last step in the biosynthesis of the gaseous plant hormone ethylene, which is involved in development, including germination, fruit ripening, and senescence. ACCO is a mononuclear non-heme ferrous enzyme that couples the oxidation of the cosubstrate ascorbate to the oxidation of substrate ACC by dioxygen. In addition to substrate and cosubstrate, ACCO requires the activator CO(2) for continuous turnover. NIR circular dichroism and magnetic circular dichroism spectroscopies have been used to probe the geometric and electronic structure of the ferrous active site in ACCO to obtain molecular-level insight into its catalytic mechanism. Resting ACCO/Fe(II) is coordinatively saturated (six-coordinate). In the presence of CO(2), one ferrous ligand is displaced to yield a five-coordinate site only when both the substrate ACC and cosubstrate ascorbate are bound to the enzyme. The open coordination position allows rapid O(2) activation for the oxidation of both substrates. In the absence of CO(2), ACC binding alone converts the site to five-coordinate, which would react with O(2) in the absence of ascorbate and quickly deactivate the enzyme. These studies show that ACCO employs a general strategy similar to other non-heme iron enzymes in terms of opening iron coordination sites at the appropriate time in the reaction cycle and define the role of CO(2) as stabilizing the six-coordinate ACCO/Fe(II)/ACC complex, thus preventing the uncoupled reaction that inactivates the enzyme.     

Determination of 1-aminocyclopropane-1-carboxylic acid in apple extracts by capillary electrophoresis with laser-induced fluorescence detection

A rapid and sensitive method for the determination of 1-aminocyclopropane-1-carboxylic acid (ACC) in apple tissues has been described. This method is based on the derivatization of ACC with 3-(2-furoyl)quinoline-2-carboxaldehyde (FQ), and separation and quantification of the resulting FQ-ACC derivative by capillary electrophoresis coupled to laser-induced fluorescence detection (CE-LIF). Our results indicated that ACC derivatized with FQ could be well separated from other interfering amino acids using 20 mM borate buffer (pH 9.35) containing 40 mM sodium dodecyl sulfate and 10 mM Brij 35. The linearity of ACC was determined in the range from 0.05 to 5 microM with a correlation of 0.9967. The concentration detection limit for ACC was 10 nM (signal-to-noise = 3). The sensitivity and selectivity of this described method allows the analysis of ACC in crude apple extracts without extra purification and enrichment procedure.     

Extraction and quantitative analysis of 1-aminocyclopropane-1-carboxylic acid in plant tissue by gas chromatography coupled to mass spectrometry

We developed a new method for the determination of the ethylene precursor 1-aminocyclopropane-1-carboxylic acid (ACC) using quantitative GC-negative chemical ionisation MS as a detection and quantification system, in combination with isotope dilution using [2H4]ACC and an off-line solid-phase extraction. By derivatisation with pentafluorobenzyl bromide, ACC could easily be detected with m/z 280 being the most abundant ion. Determination of this component resulted in a detection limit of 10 fmol and a linear fit in the 100 fmol-100 pmol range. The combination of a rapid, high yield purification method with a stable derivatisation procedure and a sensitive detection method allowed the detection of ACC in samples as low as 100 mg fresh mass.     

Determination of 1-aminocyclopropane-1-carboxylic acid and its structural analogue by liquid chromatography and ion spray tandem mass spectrometry

Liquid chromatography coupled to ion spray tandem mass spectrometry was developed as a method for the simultaneous analysis of the amino acid 1-aminocyclopropane-1-carboxylic acid (ACC) and its structural analogue, cyclopropane-1,1-dicarboxylic acid (CDA). ACC and CDA fragmentation as well as optimization of MS parameters were investigated in positive ion mode. In selective reaction monitoring mode the protonated molecule [M+H]+ was selected as parent ion for both ACC and CDA, while the immonium ion from ACC and the [M+H-H2O]+ ion from CDA were selected, respectively, as product ions. In spite of the high selectivity of MS/MS among the 20 protein amino acids potentially present with ACC and CDA in the plant material analyzed, Glu and Thr can interfere with the signal of ACC. As a result, their chromatographic separation is necessary. This was achieved in less than 4 min by ion-pair reversed-phase chromatography with nonafluoropentanoic acid as ion-pair reagent. A linear response within a concentration range of 1-5 mg l(-1) was observed for this LC method and the detection limit was found to be 20 pmol for ACC and 150 pmol for CDA (using a 20-microl loop). This methodology was successfully applied to the detection of ACC in apple tissue.     

Free energy perturbation calculations on models of active sites: Applications to adenosine deaminase inhibitors

Free energy perturbation calculations were performed to determine the free energy of binding associated with the presence of perhaps an unusual hydroxyl group in the transition state analog of nebularine, an inhibitor of the enzyme adenosine deaminase. The presence of a single hydroxyl group in this inhibitor has been found to contribute ?9.8 kcal/mol to the free energy of binding, with a 10⁸-fold increase in the binding affinity by the enzyme. In this work, we calculate the difference in solvation free energy for the 1,6-dihydropurine complex versus that of the 6-hydroxyl-1,6-dihydropurine complex to determine if this marked increase in binding affinity is attributed to an unusually hydrophobic hydroxyl group. The calculated ΔG associated for the solvation free energy is ?11.8 kcal/mol. This large change in the solvation free energy suggests that this hydroxyl is instead unusually hydrophilic and that the difference in free energy of interaction for the two inhibitors to the enzyme must be at least ca. 20 kcal/mol. Although the crystal structure for adenosine deaminase is currently not known, we attempt to mimic the nature of the active site by constructing models which simulate the enzyme-inhibitor complex. We present a first attempt at determining the change in free energy of binding for a system in which structural data for the enzyme is incomplete. To do this, we construct what we believe is a minimal model of the binding between adenosine deaminase and an inhibitor. The active site is simulated as a single charged carboxyl group which can form a hydrogen bond with the hydroxyl group of the analog. Two different carboxyl anion models are used. In the first model, the association is modeled between an acetic acid anion and the modified inhibitor. The second model consists of a hydrophobic amino acid pocket with an interior Glu residue in the active site. From these models we calculate the change in free energy of association and the overall change in free energy of binding. We calculate the free energies of interaction both in the absence and presence of water. We conclude from this that the presence of a single suitably placed-CO^?₂ group probably cannot explain the binding effect of the-OH group and that additional interactions will be found in the adenosine deaminase active site.     

Identification of a copper(I) intermediate in the conversion of 1-aminocyclopropane carboxylic acid (ACC) into ethylene by Cu(II)-ACC complexes and hydrogen peroxide

Several Cu(II) complexes with ACC (=1-aminocyclopropane carboxylic acid) or AIB (=aminoisobutyric acid) were prepared using 2,2'-bipyridine, 1,10-phenanthroline, and 2-picolylamine ligands: [Cu(2,2'-bipyridine)(ACC)(H2O)](ClO4) (1a), [Cu(1,10-phenanthroline)(ACC)](ClO4) (2a), [Cu(2-picolylamine)(ACC)](ClO4) (3a), and [Cu(2,2'-bipyridine)(AIB)(H2O)](ClO4) (1b). All of the complexes were characterized by X-ray diffraction analysis. The Cu(II)-ACC complexes are able to convert the bound ACC moiety into ethylene in the presence of hydrogen peroxide, in an "ACC-oxidase-like" activity. A few equivalents of base are necessary to deprotonate H2O2 for optimum activity. The presence of dioxygen lowers the yield of ACC conversion into ethylene by the copper(II) complexes. During the course of the reaction of Cu(II)-ACC complexes with H2O2, brown species (EPR silent and lambda max approximately 435 nm) were detected and characterized as being the Cu(I)-ACC complexes that are obtained upon reduction of the corresponding Cu(II) complexes by the deprotonated form of hydrogen peroxide. The geometry of the Cu(I) species was optimized by DFT calculations that reveal a change from square-planar to tetrahedral geometry upon reduction of the copper ion, in accordance with the observed nonreversibility of the redox process. In situ prepared Cu(I)-ACC complexes were also reacted with hydrogen peroxide, and a high level of ethylene formation was obtained. We propose Cu(I)-OOH as a possible active species for the conversion of ACC into ethylene, the structure of which was examined by DFT calculation.     

New Efficient Synthesis of 1-Aminocyclopropanecarboxylic Acid (ACC)

A new efficient synthesis of 1-aminocyclopropanecarboxylic acid (ACC) from methyl 2-diphenylmethyleneaminoacrylate in nearly quantitative yield has been developed. The key step in the synthesis is the removal of both protecting groups in mild conditions and in quantitative yield to afford ACC.     

Inhibition effects of gangliosides G(M1), G(D1a) and G(T1b) on base-catalyzed isomerization of prostaglandin A(2)

Micellar inhibition effect of gangliosides on a degradation of drug was investigated, where ganglioside G(M1) (GM1), G(D1a) (GD1a) and G(T1b) (GTlb) whose sialic acid residue is one, two and three, respectively, were used. The base-catalyzed isomerization of prostaglandin A(2) (PGA(2)) to prostaglandin B(2) (PGB(2)) was chosen as a model experiment. The rate for the isomerization of PGA(2) was determined by measuring the concentration of PGA(2) (and PGB(2)) with a high-performance liquid chromatography. Gangliosides micelles inhibited the isomerization of PGA(2). The inhibition effect of GT1b micelles was larger than that of GD1a micelles. This result would be due to the larger absolute value of surface potential of GT1b micelles, which brings about a larger electrostatic repulsion between micellar surface and OH(-). The terminal sialic acid residue of ganglioside was effective to inhibit the isomerization of PGA(2). GM1 micelles without terminal sialic acid residue but with large aggregation number exhibited a superior steric shielding effect rather than an electrostatically repulsive effect. The inhibition effect of GM1 micelles was enhanced by the mixed micellization with the other ganglioside with a terminal sialic acid residue. GM1-GD1a or GM1-GT1b mixed micelles remarkably inhibited the isomerization of PGA(2). The physiological activity of PGs in the biological membranes containing gangliosides was also discussed.     

Y443F mutation in the substrate-binding domain of extracellular PHB depolymerase enhances its PHB adsorption and disruption abilities

Extracellular poly[(R)-3-hydroxybutyrate] (PHB) depolymerase (PhaZ_RpiT1) from Ralstonia pickettii T1 adsorbs to the PHB surface via its substrate-binding domain (SBD) and cleaves the PHB chain using its catalytic domain. Our previous study (Biomacromolecules 2010; 11: 113-119) has suggested that the hydrophobic interaction between the amino acid residues at positions 441, 443, and 445 in the SBD and the PHB surface plays a crucial role in facilitating the association phase of the enzyme adsorption process. In the present study, in order to improve PhaZ_RpiT1 for effective PHB degradation, we targeted Tyr at position 443 for substitution with a more highly hydrophobic amino acid residue because its hydrophobicity shows medium to high degree compared to those of general naturally occurring amino acid residues. We designed a mutant enzyme with an amino acid substitution at this position, taking the following factors into consideration: (1) to achieve higher hydrophobicity than the original residue, (2) to retain the β-sheet structure, and (3) to change as little as possible the volume of the amino acid residue after the substitution. As a result, the substitution of Tyr443 with Phe (Y443F) was considered to be appropriate. The purified Y443F enzyme showed identical CD spectrum and hydrolysis activity for a water-soluble substrate with the wild type, indicating that the mutation had no influence on the structure and the ester bond cleavage activity. In contrast, the Y443F enzyme had higher PHB degradation activity than the wild type. Kinetic analysis of PHB degradation suggests that this amino acid substitution promoted not only the adsorption of the mutant enzyme to PHB, but also the disruption of the PHB surface to enhance the hydrolysis of the PHB polymer chain.     

IMP synthesis using immobilized adenosine (Phosphate) deaminase

Inosinic acid (IMP) has been prepared by the deamination of adenosine monophosphate (AMP) with an immobilized adenosine (phosphate) deaminase extracted from the snail Biomphalaria glabrata. The enzyme has been immobilized in polyacrylamide beads. The preparation and characterization of this system are described.     

Determination of plasma cytidine deaminase activity by HPLC

Cytidine deaminase is an enzyme of nucleic acid metabolism, the measurement of which has been proposed as a useful test for the early detection of pre-eclamptic toxaemia in pregnancy. The enzyme converts the nucleoside cytidine to uridine, with the release of ammonia, and it is the measurement of this latter compound that forms the basis of the conventional methods for the assay of cytidine deaminase. The low activity of the enzyme requires long incubation times, which in turn increase the possibility of contamination by exogenous ammonia. We have developed a new method for determining cytidine deaminase activity, utilising high performance liquid chromatography to measure the production of uridine. This method uses much shorter incubation times and is unaffected by ammonia contamination. This paper describes the development of the method and its comparison with the established assay. The relative merits of each are discussed. Finally, the adaptation of incubation and chromatographic conditions, in order to measure other enzymes of nucleic acid metabolism which are of clinical interest, is briefly mentioned.     

Thermodynamic investigation of the binary and ternary complexes involving 1-aminocyclopropane carboxylic acid with reference to plant hormone

Complex formation equilibria of 1-aminocyclopropane carboxylic acid (ACC) and 3,3-bis(1-methylimidazol-2-yl) propionic acid (BIMP) with metal ions Cu²⁺, Ni²⁺, Co²⁺, Zn²⁺, Mn²⁺ and Fe²⁺ were investigated. ACC forms 1:1 and 1:2 complexes in addition to the hydrolysed form of the 1:1 complex, except in the case of Mn²⁺ and Fe²⁺, where the hydrolysed complex is not formed. BIMP forms 1:1 and 1:2 complexes in addition to the hydrolsed form of the 1:1 complex in the case of Mn²⁺ and Cu²⁺, however the hydrolysed complex is not detected for Ni²⁺, Co²⁺, Zn²⁺ and Fe²⁺. The concentration distribution diagrams of the complexes were determined. The Fe²⁺-complex with BIMP is exothermic and the thermodynamic parameters were calculated. The effect of organic solvent on the acid dissociation constants of 1-aminocyclopropane carboxylic acid (ACC) and 3,3-bis(1-methylimidazol-2-yl) propionic acid (BIMP) and the formation constants of Fe²⁺ complexes were investigated. Fe²⁺ forms a mixed-ligand complex with ACC and BIMP with stoichiometric coefficients 1:1:1. The formation constant was determined. The ternary complex is enhanced by back donation from the negatively charged 1-aminocyclopropane carboxylate to the π-system of BIMP. From the concentration distribution diagram, the ternary complex prevails in the physiological pH range.      

In vitro germination of Striga hermonthica and Striga aspera seeds by 1-aminocyclopropane-1-carboxylic acid

Treatment of conditioned seeds of four isolates of Striga hermonthica and one isolate of Striga aspera with various concentrations of the ethylene precursor, 1-aminocyclopropane-1-carboxylic acid (ACC), caused complex stimulation of germination patterns. GR 24, the strigol analogue served as a positive control and its stimulatory activity was comparable to that of ACC. When conditioned Striga seeds were treated with negative control that did not contain ACC, the stimulatory effect was lost. Overall, the germination data suggested a hormonal mode of action by ACC, which involves indirect stimulation of biosynthesis of ethylene that then triggers seed germination. The various mechanisms that have been proposed for the chemical and biological oxidation of ACC to generate ethylene are discussed.     

A Novel Synthesis of 1-Aminocyclopropane-1-carboxylic Acid (ACC)

A novel synthetic route of 1-aminocyclopropane-1-carboxylic acid (ACC) has been built via cyclopropanedicarboxylic acid monohydrazide III in moderation to good yield.     

Determination of 1-aminocyclopropane-1-carboxylic Acid in Apple and Peach Extracts by High Performance Liquid Chromatography Coupled to a Fluorescence Detector

A new, sensitive, and simple HPLC method was described for the determination of 1-aminocyclopropane-1-carboxylic acid (ACC) in apple and peach extracts. The method was based on the derivatization of ACC with fluorescamine in borate buffer systems of pH 8.0 to yield a highly fluorescent product. The experimental parameters affecting the derivatization reaction efficiency were optimized by fluorimetric analysis. Under optimum derivatization conditions, the derivative product of ACC in apple and peach extracts without extra purification was successfully chromatographed on a C-18 column by HPLC coupled to fluorescence detection. The derivative product of ACC with fluorescamine could be well separated from other concomitant substances or their derivatives that might interfere with the determination of ACC. The linearity of ACC was measured in the range of 23.82–238.82 µg · L^?1 with a good correlation coefficient of 0.9997. Based on signal-to-noise ratio of 3, a low detection limit of 5.0 µg · L^?1 could be reached. The proposed method was applied successfully to the determination of ACC in the crude apple and peach extracts without extra purification with low RSDs of 0.19–1.9% and good recoveries of 90.89–104.4%. The sensitive HPLC quantitative method is of great significance for the investigations of ACC metabolism in plants.     

Effect of organotin compounds on trout AMP‐deaminases

The comparative toxicity of the organotin compounds tributyltin chloride (TBTC), dibutylin dichloride (DBTC) and monobutyltin trichloride (MBTC) was investigated on 5′ adenylic acid deaminase (AMP‐deaminase) purified from trout skeletal muscle and heart. Treatment with TBTC of both enzymatic forms of AMP‐deaminase rapidly decreases the enzyme activity, and the organotin derivatives DBTC and MBTC have a significant minor inhibitory effect. Differences were observed in TBTC inhibition rate between trout muscle and heart purified enzymes that could be related to the different cellular localization of the two AMP‐deaminases. Copyright © 2001 John Wiley & Sons, Ltd.     

Characterization of covalently inhibited extracellular lipase from Streptomyces rimosus by matrix-assisted laser desorption/ionization time-of-flight and matrix-assisted laser desorption/ionization quadrupole ion trap reflectron time-of-flight mass spectrometry: localization of the active site serine

A chemical modification approach combined with matrix-assisted laser desorption/ionization (MALDI) mass spectrometry was used to identify the active site serine residue of an extracellular lipase from Streptomyces rimosus R6-554W. The lipase, purified from a high-level overexpressing strain, was covalently modified by incubation with 3,4-dichloroisocoumarin, a general mechanism-based serine protease inhibitor. MALDI time-of-flight (TOF) mass spectrometry was used to probe the nature of the intact inhibitor-modified lipase and to clarify the mechanism of lipase inhibition by 3,4-dichloroisocoumarin. The stoichiometry of the inhibition reaction revealed that specifically one molecule of inhibitor was bound to the lipase. The MALDI matrix 2,6-dihydroxyacetophenone facilitated the formation of highly abundant [M + 2H](2+) ions with good resolution compared to other matrices in a linear TOF instrument. This allowed the detection of two different inhibitor-modified lipase species. Exact localization of the modified amino acid residue was accomplished by tryptic digestion followed by low-energy collision-induced dissociation peptide sequencing of the detected 2-(carboxychloromethyl)benzoylated peptide by means of a MALDI quadrupole ion trap reflectron TOF instrument. The high sequence coverage obtained by this approach allowed the confirmation of the site specificity of the inhibition reaction and the unambiguous identification of the serine at position 10 as the nucleophilic amino acid residue in the active site of the enzyme. This result is in agreement with the previously obtained data from multiple sequence alignment of S. rimosus lipase with different esterases, which indicated that this enzyme exhibits a characteristic Gly-Asp-Ser-(Leu) motif located close to the N-terminus and is harboring the catalytically active serine residue. Therefore, this study experimentally proves the classification of the S. rimosus lipase as GDS(L) lipolytic enzyme.     

Spectroscopic and computational studies of α-keto acid binding to Dke1: understanding the role of the facial triad and the reactivity of β-diketones

The O(2) activating mononuclear nonheme iron enzymes generally have a common facial triad (two histidine and one carboxylate (Asp or Glu) residue) ligating Fe(II) at the active site. Exceptions to this motif have recently been identified in nonheme enzymes, including a 3His triad in the diketone cleaving dioxygenase Dke1. This enzyme is used to explore the role of the facial triad in directing reactivity. A combination of spectroscopic studies (UV-vis absorption, MCD, and resonance Raman) and DFT calculations is used to define the nature of the binding of the α-keto acid, 4-hydroxyphenlpyruvate (HPP), to the active site in Dke1 and the origin of the atypical cleavage (C2-C3 instead of C1-C2) pattern exhibited by this enzyme in the reaction of α-keto acids with dioxygen. The reduced charge of the 3His triad induces α-keto acid binding as the enolate dianion, rather than the keto monoanion, found for α-keto acid binding to the 2His/1 carboxylate facial triad enzymes. The mechanistic insight from the reactivity of Dke1 with the α-keto acid substrate is then extended to understand the reaction mechanism of this enzyme with its native substrate, acac. This study defines a key role for the 2His/1 carboxylate facial triad in α-keto acid-dependent mononuclear nonheme iron enzymes in stabilizing the bound α-keto acid as a monoanion for its decarboxylation to provide the two additional electrons required for O(2) activation.