Oxidation of methionine residues in aqueous solutions: free methionine and methionine in granulocyte colony-stimulating factor

The free energy barriers and a mechanism of the oxidation of the amino acid methionine in water and in granulocyte colony-stimulating factor (G-CSF) are analyzed via combined quantum mechanical and molecular mechanical (QM/MM) methods, constrained molecular dynamics, and committor probability calculations. The computed free energy barrier of free methionine amino acid is very close to the measured value (14.7 +/- 1.2 versus 15.5 +/- 0.02 kcal/mol). The reaction coordinate was found to be the difference between the O-O bond of H2O2 and the S-O bond, where the S is the sulfur atom of the methionine residue. It was confirmed by computing the committor probability distribution and the distribution of constrained forces that this coordinate is not coupled to the activation of other degrees of freedom. The computed free energies of the oxidation of methionine residues in G-CSF indicate that the protein environment has insignificant effects on the reaction barriers of oxidation. This result further validates our proposal that the access of solvent to methionine sites, as measured by the two-shell water coordination number, governs the kinetics of the oxidation reaction of methionine groups in a protein molecule. We also found that the number of hydrogen bonds between the distal oxygen of H2O2 and the water molecules near the methionine increases along the reaction coordinate as oxidation progresses, indicating that the charge separation developed during the oxidation by H2O2 is stabilized by specific interactions with water molecules, such as hydrogen bonding.     

Reduction mechanism in class A methionine sulfoxide reductases: a theoretical chemistry investigation

Ab initio calculations at the B3LYP/6–311 ++G(2df,2p) and B3LYP/6–31G(d) level have been carried out to investigate the reaction mechanism of methionine sulfoxide reductases of class A. These enzymes reduce oxidized methionine in vivo and therefore play an important role in repairing protein damage caused by the oxidative stress. Our calculations have been carried out for a model reaction in a model active site. Several reaction mechanisms have been explored that can roughly be described as (2H⁺ + 2e⁻) or (H⁺ + e⁻). The results suggest that the actual reaction mechanism is of the (2H⁺ + 2e⁻) type corresponding to a more or less asynchronous-concerted double-proton transfer reaction leading to the formation of methionine (dimethylthioether in our model) and a sulfenic acid Cys-SOH. The Michaelis complex would involve one deprotonated Cys and one protonated Glu residues in the active site, this protonation state being mandatory to stabilize the sulfoxide substrate. Then, proton transfer from Glu to the substrate takes place, followed by proton transfer from one Tyr residue and fast reorganization of the system. The overall activation energy barrier is estimated to fall in the range 7–9 kcal/mol, much lower than the predicted barrier in DMSO solution (29.6 kcal/mol) reported before.     

Stereospecific electrophoretically mediated microanalysis assay for methionine sulfoxide reductase enzymes

An electrophoretically mediated microanalysis assay (EMMA) for the determination of the stereoselective reduction of l-methionine sulfoxide diastereomers by methionine sulfoxide reductase enzymes was developed using fluorenylmethyloxycarbonyl (Fmoc)-l-methionine sulfoxide as substrate. The separation of the diastereomers of Fmoc-l-methionine sulfoxide and the product Fmoc-l-methionine was achieved in a successive multiple ionic-polymer layer-coated capillary using a 50 mM Tris buffer, pH 8.0, containing 30 mM sodium dodecyl sulfate as background electrolyte and an applied voltage of 25 kV. 4-Aminobenzoic acid was employed as internal standard. An injection sequence of incubation buffer, enzyme, substrate, enzyme, and incubation buffer was selected. The assay was optimized with regard to mixing time and mixing voltage and subsequently applied for the analysis of stereoselective reduction of Fmoc-l-methionine-(S)-sulfoxide by human methionine sulfoxide reductase A and of the Fmoc-l-methionine-(R)-sulfoxide by human methionine sulfoxide reductase B. The Michaelis–Menten constant, K _m, and the maximum velocity, v _max, were determined. Essentially identical data were determined by the electrophoretically mediated microanalysis assay and the analysis of the samples by CE upon offline incubation. Furthermore, it was shown for the first time that Fmoc-methionine-(R)-sulfoxide is a substrate of human methionine sulfoxide reductase B.

The preparation of99mTc-labelled methionine

^99mTc-labelled methionine was prepared by ligand substitution reaction. Methionine was reacted with^99mTc-citrate under physiological conditions, to form a radiochemically pure, neutral Tc complex. Labelling parameters involving incubation period of methionine in^99mTc-citrate solution were studied by paper and thin-layer chromatography.     

Zinc-homocysteine binding in cobalamin-dependent methionine synthase and its role in the substrate activation: DFT, ONIOM, and QM/MM molecular dynamics studies

Cobalamin-dependent methionine synthase (MetH) is an important metalloenzyme responsible for the biosynthesis of methionine. It catalyzes methyl transfer from N(5)-methyl-tetrahydrofolate to homocysteine (Hcy) by using a zinc ion to activate the Hcy substrate. Density functional theory (B3LYP) calculations on the active-site model in gas phase and in a polarized continuum model were performed to study the Zn coordination changes from the substrate-unbound state to the substrate-bound state. The protein effect on the Zn(2+) coordination exchange was further investigated by ONIOM (B3LYP:AMBER)-ME and EE calculations. The Zn(2+)-coordination exchange is found to be highly unfavorable in the gas phase with a high barrier and endothermicity. In the water solution, the reaction becomes exothermic and the reaction barrier is drastically decreased to about 10.0 kcal/mol. A considerable protein effect on the coordination exchange was also found; the reaction is even more exothermic and occurs without barrier. The enzyme was suggested to constrain the zinc coordination sphere in the reactant state (Hcy-unbound state) more than that in the product state (Hcy-bound state), which promotes ligation of the Hcy substrate. Molecular dynamics simulations using molecular mechanics (MM) and PM3/MM potentials suggest a correlation between the flexibility of the Zn(2+)-binding site and regulation of the enzyme function. Directed in silico mutations of selected residues in the active site were also performed. Our studies support a dissociative mechanism starting with the Zn-O(Asn234) bond breaking followed by the Zn-S((Hcy)) bond formation; the proposed associative mechanism for the Zn(2+)-coordination exchange is not supported.     

Regulation of c-Src nonreceptor tyrosine kinase activity by bengamide A through inhibition of methionine aminopeptidases

Methionine aminopeptidases (MetAPs) remove the N-terminal initiator methionine during protein synthesis, a prerequisite step for N-terminal myristoylation. N-myristoylation of proto-oncogene c-Src is essential for its membrane association and proper signal transduction. We used bengamides, a family of general MetAP inhibitors, to understand the downstream physiological functions of MetAPs. c-Src from bengamide A-treated cells retained its N-terminal methionine and suffered a decrease in N-terminal myristoylation, which was accompanied by a shift of its subcellular distribution from the plasma membrane to the cytosol. Furthermore, bengamide A decreased the tyrosine kinase activities of c-Src both in vitro and in vivo and eventually delayed cell-cycle progression through G(2)/M. Thus, c-Src is a physiologically relevant substrate for MetAPs whose dysfunction is likely to account for the cell-cycle effects of MetAP inhibitors including bengamide A.     

Synthesis and properties of aliphatic oligoamides containing methionine fragment

Oligoamides were prepared from dimerized fatty acid, hexamethylenediamine, and an amino acid (methionine). The effect of methionine on the course of polycondensation and properties of the reaction products was examined. New thermoplastic adhesive compounds based on these products were developed.     

Pyrolysis mass spectrometry of methionine

The mechanisms of some fragmentation of methionine upon Curie-point pyrolysis have been studied by the use of deuterium labelling. They lead to products having the same nominal mass but essentially different elemental compositions compared with ions generated by electron impact on methionine. For exaple, upon pyrolysis the product with mass 116 is due to a 1,2 elimination of hydroxylamine from the title compound, whereas upon electron impact the ion with m/e 116 is generated by successive loss of a molecule of water and of a methyl radical from the molecular ion; the generated of product m/e 101 proceeds via successive loss of a molecule of water, carbon monoxide and of hydrogen upon pyrolysis, but via a one-step elimination of methanethiol upon electron impact. No evidence has been found for a diketopiperazine formation by a bimolecular process upon pyrolysis, although this type of reaction is well known for α-amino acids.     

Kinetic resolution of phenyl methyl sulfoxides by mammalian methionine sulfoxide reductase A

Chiral sulfoxides are widely used in organic synthesis as chiral auxiliaries. There are numerous strategies for the preparation of enantiomerically pure sulfoxides, based either on the enantioselective oxidation of sulphides or the enantiospecific reduction of sulfoxides. For both cases, bioconversion techniques have been developed and proposed for large-scale synthesis. Methionine sulfoxide reductase enzymes (MsrA and MsrB) catalyse the stereoselective conversion of methionine sulfoxide to methionine. MsrA can also catalyse the reduction of other exogenous sulfoxides, including p-tolyl methyl sulfoxide. However, the stereoselectivity towards this type of substrate is not yet well characterized. The activity and enantioselectivity of MsrA toward several aryl methyl sulfoxides is presented in this paper.     

Investigation of the metal binding site in methionine aminopeptidase by density functional theory

All methionine aminopeptidases exhibit the same conserved metal binding site. The structure of this site with either Co²⁺ions or Zn²⁺ions was investigated using density functional theory. The calculations showed that the structure of the site was not influenced by the identity of the metal ions. This was the case for both of the systems studied; one based on the X-ray structure of the human methionine aminopeptidase type 2 (hMetAP-2) and the other based on the X-ray structure of the E. colimethionine aminopeptidase type 1 (eMetAP-1). Another important structural issue is the identity of the bridging oxygen, which is part of either a water molecule or a hydroxide ion. Within the site of hMetAP-2 the results strongly indicate that a hydroxide ion bridges the metal ions. By contrast, the nature of the oxygen bridging the metal ions within the metal binding site of eMetAP-1 cannot be determined based on the results here, due to the similar structural results obtained with a bridging water molecule and a bridging hydroxide ion.     

A simple spectrophotometric method for the microdetermination of methionine

Summary A simple spectrophotometric method for the determination of methionine is described. The method is based on the inhibitory activity of methionine on the reaction of lactic acid withp-hydroxydiphenyl. The method was developed with mixtures containing known amounts of lactic acid in concentrated sulphuric acid to which increasing amounts of methionine were added. The intensity of colour obtained decreased in proportion to the amount of methionine added (in the range 5–45g). The method is recommended for analysis of samples which contain methionine in the presence of different amino-acids.

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Zusammenfassung Ein einfaches spektrophotometrisches Verfahren zur Bestimmung von Methionin wurde beschrieben. Es beruht auf der hemmenden Wirkung des Methionins auf die Reaktion von Milchsäure mitp-Hydroxydiphenyl. Die Methode wurde mit Gemischen bekannter Milchsäuremengen in konz. Schwefelsäure ausgearbeitet, denen steigende Mengen Methionin zugesetzt wurden. Die Farbintensität nimmt proportional der Menge zugesetzten Methionins (5–45g) ab. Das Verfahren wurde zur Analyse von Proben empfohlen, die Methionin in Gegenwart verschiedener anderer Aminosäuren enthalten.

     

Mechanistic Insights into the Radical S‐adenosyl‐l‐methionine Enzyme NosL From a Substrate Analogue and the Shunt Products

The radical S‐adenosyl‐l ‐methionine (SAM) enzyme NosL catalyzes the transformation of l ‐tryptophan into 3‐methyl‐2‐indolic acid (MIA), which is a key intermediate in the biosynthesis of a clinically interesting antibiotic nosiheptide. NosL catalysis was investigated by using the substrate analogue 2‐methyl‐3‐(indol‐3‐yl)propanoic acid (MIPA), which can be converted into MIA by NosL. Biochemical assays with different MIPA isotopomers in D₂O and H₂O unambiguously indicated that the 5′‐deoxyadenosyl (dAdo)‐radical‐mediated hydrogen abstraction is from the amino group of l ‐tryptophan and not a protein residue. Surprisingly, the dAdo‐radical‐mediated hydrogen abstraction occurs at two different sites of MIPA, thereby partitioning the substrate into different reaction pathways. Together with identification of an α,β‐unsaturated ketone shunt product, our study provides valuable mechanistic insight into NosL catalysis and highlights the remarkable catalytic flexibility of radical SAM enzymes.     

Decomposition of methionine by low energy electrons

In this work, we present the results from low energy (<12 eV) electron impact on isolated methionine, Met. We show that dissociative electron attachment is the operative mechanism for the sulfur content amino-acid fragmentation. The two most dominant fragments are attributed to the (Met-H)(-) and (C(4)NOH(5))(-) ions that are formed at energy below 2 eV. The formation of the latter anion is accompanied by the loss of neutral counterparts, which are most likely a water molecule and highly toxic methanethiol, CH(3)SH. Further fragments are associated with the damage at the sulfur end of the amino acid, producing the methyl sulfide anion CH(3)S(-) or sulfur containing neutrals. In the context of radiation induced damage to biological material at the nano-scale level, the present interest of methionine arises from the implication of the molecule in biological processes (e.g., S-adenosyl methionine for the stimulation of DNA methyltransferase reactions or protein synthesis).     

Boron doped diamond and glassy carbon electrodes comparative study of the oxidation behaviour of cysteine and methionine

The electrochemical oxidation behaviour at boron doped diamond and glassy carbon electrodes of the sulphur-containing amino acids cysteine and methionine, using cyclic and differential pulse voltammetry over a wide pH range, was compared. The oxidation reactions of these amino acids are irreversible, diffusion-controlled pH dependent processes, and occur in a complex cascade mechanism. The amino acid cysteine undergoes similar three consecutive oxidation reactions at both electrodes. The first step involves the oxidation of the sulfhydryl group with radical formation, that undergoes nucleophilic attack by water to give an intermediate species that is oxidized in the second step to cysteic acid. The oxidation of the sulfhydryl group leads to a disulfide bridge between two similar cysteine moieties forming cysteine. The subsequent oxidation of cystine occurs at a higher potential, due to the strong disulfide bridge covalent bond. The electro-oxidation of methionine at a glassy carbon electrode occurs in two steps, corresponding to the formation of sulfoxide and sulfone, involving the adsorption and protonation/deprotonation of the thiol group, followed by electrochemical oxidation. Methionine undergoes a one-step oxidation reaction at boron doped diamond electrodes due to the negligible adsorption, and the oxidation also leads to the formation of methionine sulfone.     

Gas-phase basicity of methionine

Proton affinity and protonation entropy of methionine (Met) were determined by the extended kinetic method from ESI-Q-TOF tandem mass spectrometry experiments. The values, PA(Met) = 937.5 +/- 2.9 kJ mol(-1) and Delta(p)S degrees (Met) = - 22 +/- 5 J mol(-1) K(-1), lead to gas-phase basicity GB(Met) = 898.2 +/- 3.2 kJ.mol(-1). Quantum chemical calculations using density functional theory confirm that the proton affinity of Met is indeed in the 940 kJ mol(-1) range and that a significant entropy loss, of at least - 25 J mol(-1) K(-1), occurs upon protonation. This last point is evidenced here for the first time and suggests revision of the tabulated protonation thermochemistry of Met. A comparison with previous experimental data allows us to propose the following evaluated thermochemical values: PA(Met) = 943 +/- 4 kJ mol(-1) and Delta(p)S degrees (Met) = - 35 +/- 15 J mol(-1) K(-1) and GB(Met) = 900 +/- 2 kJ mol(-1).     

Direct determination of methionine sulfoxide in milk proteins by enzyme hydrolysis/high-performance liquid chromatography

A direct and simultaneous HPLC/UV determination of methionine and methionine sulfoxide in enzyme-hydrolyzed milk proteins is described. Protein hydrolysis is accomplished by a three-enzyme (pronase, leucine aminopeptidase, prolidase) 20-h/37 degrees C digestion. A gradient elution reversed-phase HPLC system with UV detection at 214 nm and 280 nm is then used to determine the quantitative releases of methionine sulfoxide, methionine, tyrosine, and tryptophan. The ease of methionine oxidation by a wide variety of oxidants, coupled with the quantitative release of both methionine and its sulfoxide by the three-enzyme hydrolysis, renders the approach valuable for identifying oxidized milk proteins. The relatively simple method proved accurate and precise in its application to commercial milk products, finding methionine sulfoxide levels as high as 74% of the total methionine.     

Conversion of methionine into homocysteic acid in heavily oxidized proteomics samples

Analysis of protein oxidation is necessary in numerous areas of biochemistry, including hydroxyl radical surface mapping, oxidative stress assays, and pharmaceutical stability testing. Mass spectrometry is one of the tools most often used to identify protein oxidation products, and previous studies have attempted to identify and characterize all of the major oxidation products detected by mass spectrometry for each amino acid residue. In this note, we present evidence that in heavily oxidized protein samples, such as those produced by hydroxyl radical surface mapping, a major oxidation product of methionine is homocysteic acid. The formation of homocysteic acid from methionine was previously unrecognized in other mass spectrometric analyses, and has important implications for the analysis of oxidized samples, as well as potential implications as to the functional consequences of methionine oxidation. Copyright © 2010 John Wiley & Sons, Ltd.     

The kinetics and mechanism of the oxidation of seleno-DL- methionine by potassium ferrate

The kinetics of the reaction of seleno-DL-methionine with potassium ferrate were investigated under pseudo first-order conditions. The oxidation to the selenoxide is complete within the timeframe of 7.5ms to 2s. The kinetics are first-order in each of the hydrogen ion, selenomethionine and ferrate ion concentrations over the pH range 8.53 to 10.13, but zeroth-order in hydrogen ion concentration at lower pH values. The results are very similar for methionine, except that the overall rate constant is over two orders of magnitude lower. The proposed mechanism involves a rate- determining step between selenomethionine and the protonated ferrate ion.     

Estimation of methionine and its metal complexes by oxidation with chloramine-T and dichloramine-T

A simple method for the estimation of methionine (HMt) in aqueous solution has been developed, based on its oxidation with chloramine-T and dichloramine-T at room temperature. The direct titration, with visual or potentiometric end-point involves a two-electron change, corresponding to the formation of methionine sulphoxide. Most amino-acids do not interfere, but cysteine, glutathione and thiourea are oxidized under these conditions. A back-titration procedure in which methionine is oxidized in 0.1M sodium hydroxide by excess of chloramine-T with a four-electron change corresponding to the formation of methionine sulphone has also been developed. Methionine is oxidized to the respective nitrile, however, with excess of dichloramine-T. The methods have also been employed in estimating methionine in two of its soluble complexes, [NiMt]ClO(4) and Na[AgMt(2)].     

Direct determination of free methionine in soy-based infant formula

A method was developed for the direct determination of free methionine in soy-based infant formula, with analyte separation and quantitation by reversed-phase liquid chromatography (LC), and UV absorbance at 214 nm, respectively. Sample preparation required only dilution with mobile phase and syringe filtration. Using a 0.02M KH2PO4 mobile phase (pH adjusted to 2.9 with 85% o-phosphoric acid) and 0.7 mL/min flow rate, methionine eluted at approximately 8 min, and total run time was 14 min after column regeneration with acetonitrile-water. System linearity was demonstrated as peak area versus analyte concentration, ranging from 80 to 120% of the formula specification for free methionine (r > 0.999, and all residuals < 0.45%). Intermediate precision relative standard deviation values were < 1.5% for ready-to-feed and reconstituted powder samples, and recoveries ranged from 98.0 to 103.5% for inter-method comparison with an amino acid analyzer method. The limit of quantitation was 3 mg methionine/L in the "as fed" infant formula. Despite the relatively weak UV absorptivity of methionine, the 214 nm signal was sufficiently intense in the 30-65 mg/L (201-436 microM) range to afford quantitation by peak area proportionation versus a 2-point external standard calibration. This direct UV detection after reversed-phase LC separation provides a simple and accurate method for determining free methionine without derivatization.