Post-translational modification of Rhodococcus R312 and Comamonas NI1 nitrile hydratases

Nitrile hydratases (NHases) are industrially significant iron- and cobalt-containing enzymes used in the large-scale synthesis of acrylamide. Previous reports have shown that the active site peptides of NHases are post-translationally modified by oxidation of cysteine residues, and that these modifications are essential for catalysis. We report mass spectrometric evidence of the oxidation states of the active site cysteines in the iron coordination spheres of two iron-containing nitrile hydratases, namely R312 NHase from Rhodococcus rhodochrous strain R312 and NI1 NHase from Comamonas testosteroni. At least one of these cysteines is oxidised to a sulfinic acid (SO(2)H) and there is also evidence suggesting an additional oxidation to a sulfenic acid (SOH). This is the first evidence for the presence of these oxidation states for full-length NHases and for Fe-NHases from different microorganisms. The presence of these covalent modifications was confirmed by performing mass spectrometry on the active site peptide of R312 NHase, under native, reduced and carboxymethylated conditions. We also show the nitrosylation of the iron by mass spectrometry, as well as the release of NO by photoirradiation.     

Probing the enantioselectivity of a diverse group of purified cobalt-centred nitrile hydratases

In this study a diverse range of purified cobalt containing nitrile hydratases (NHases, EC 4.2.1.84) from Rhodopseudomonas palustris HaA2 (HaA2), Rhodopseudomonas palustris CGA009 (009), Sinorhizobium meliloti 1021 (1021), and Nitriliruptor alkaliphilus (iso2), were screened for the first time for their enantioselectivity towards a broad range of chiral nitriles. Enantiomeric ratios of >100 were found for the NHases from HaA2 and CGA009 on 2-phenylpropionitrile. In contrast, the Fe-containing NHase from the well-characterized Rhodococcus erythropolis AJ270 (AJ270) was practically aselective with a range of different α-phenylacetonitriles. In general, at least one bulky group in close proximity to the α-position of the chiral nitriles seemed to be necessary for enantioselectivity with all NHases tested. Nitrile groups attached to a quaternary carbon atom were only reluctantly accepted and showed no selectivity. Enantiomeric ratios of 80 and >100 for AJ270 and iso2, respectively, were found for the pharmaceutical intermediate naproxennitrile, and 3-(1-cyanoethyl)benzoic acid was hydrated to the corresponding amide by iso2 with an enantiomeric ratio of >100.     

A novel inhibitor for Fe-type nitrile hydratase: 2-cyano-2-propyl hydroperoxide

Nitrile hydratase (NHase) is a non-heme iron or non-corrin cobalt enzyme having two post-translationally modified ligand residues, cysteine-sulfinic acid (alphaCys112-SO(2)H) and -sulfenic acid (alphaCys114-SOH). We studied the interaction between Fe-type NHase and isobutyronitrile (iso-BN) which had been reported as a competitive inhibitor with a K(i) value of 5 microM. From detailed kinetic studies of the inhibitory effect of iso-BN on Fe-type NHase, we found that authentic iso-BN was hydrated normally and that the impurity present in commercially available iso-BN inhibited NHase activity strongly. The inhibitory compound induced significant changes in the UV-vis absorption spectrum of NHase, suggesting its interaction with the iron center. This compound was purified by using reversed-phase HPLC and identified as 2-cyano-2-propyl hydroperoxide (Cpx) by (1)H and PFG-HMBC NMR spectroscopy. Upon addition of a stoichiometric amount of Cpx, NHase was irreversibly inactivated, probably by the oxidation of alphaCys114-SOH to Cys-SO(2)H. This result suggests that the -SOH structure of alphaCys114 is essential for the catalytic activity. The oxygen atom in Cys-SO(2)H is confirmed to come from the solvent H(2)O. The oxidized NHase was found to induce the UV-vis absorption spectral changes by addition of Cpx, suggesting that Cpx strongly interacted with iron(III) in the oxidized NHase to form a stable complex. Thus, Cpx functions as a novel irreversible inhibitor for NHase.     

Proteome analysis of a human heptocellular carcinoma cell line, HCC-M: an update.

Recently, we reported the proteome analysis of a human hepatocellular carcinoma cell line, HCC-M (Electrophoresis 2000, 21, 1787-1813), using two-dimensional gel electrophoresis (2-DE) and matrix assisted laser desorption/ionization-time of flight-mass spectrometry (MALDI-TOF-MS). From a total of 408 unique spots excised from the 2-DE gel, 301 spots yielded good MALDI spectra. Out of these, 272 spots had matches returned from the database search leading to the identification of these proteins. Here, we report the results on the identification of the remaining 29 spots using nanoelectrospray ionization-tandem mass spectrometry (nESI-MS/MS). First, "peptide tag sequencing" was performed to obtain partial amino acid sequences of the peptides to search the SWISS-PROTand NCBI nonredundant protein databases. Spots that were still not able to find any matches from the databases were subjected to de novo peptide sequencing. The tryptic peptide sequences were used to search for homologues in the protein and nucleotide databases with the NCBI Basic Local Alignment Search Tool (BLAST), which was essential for the characterization of novel or post-translationally modified proteins. Using this approach, all the 29 spots were unambiguously identified. Among them, phosphotyrosyl phosphatase activator (PTPA), RNA-binding protein regulatory subunit, replication protein A 32 kDa subunit (RP-A) and N-acetylneuraminic acid phosphate synthase were reported to be cancer-related proteins.     

Influence of sequential thiolate oxidation on a nitrile hydratase mimic probed by multiedge X-ray absorption spectroscopy

Nitrile hydratases (NHases) are Fe(III)- and Co(III)-containing hydrolytic enzymes that convert nitriles into amides. The metal-center is contained within an N(2)S(3) coordination motif with two post-translationally modified cysteinates contained in a cis arrangement, which have been converted into a sulfinate (R-SO(2)(-)) and a sulfenate (R-SO(-)) group. Herein, we utilize Ru L-edge and ligand (N-, S-, and P-) K-edge X-ray absorption spectroscopies to probe the influence that these modifications have on the electronic structure of a series of sequentially oxidized thiolate-coordinated Ru(II) complexes ((bmmp-TASN)RuPPh(3), (bmmp-O(2)-TASN)RuPPh(3), and (bmmp-O(3)-TASN)RuPPh(3)). Included is the use of N K-edge spectroscopy, which was used for the first time to extract N-metal covalency parameters. We find that upon oxygenation of the bis-thiolate compound (bmmp-TASN)RuPPh(3) to the sulfenato species (bmmp-O(2)-TASN)RuPPh(3) and then to the mixed sulfenato/sulfinato speices (bmmp-O(3)-TASN)RuPPh(3) the complexes become progressively more ionic, and hence the Ru(II) center becomes a harder Lewis acid. These findings are reinforced by hybrid DFT calculations (B(38HF)P86) using a large quadruple-ζ basis set. The biological implications of these findings in relation to the NHase catalytic cycle are discussed in terms of the creation of a harder Lewis acid, which aids in nitrile hydrolysis.     

Substrate selectivity and conformational space available to bromoxynil and acrylonitrile in iron nitrile hydratase

Nitrile hydratase (NHase) is used in the commercial conversion of acrylonitrile to acrylamide. There are two main types of NHase: the iron containing and the cobalt containing NHase. They catalyze the conversion of a wide variety of nitriles to their corresponding amides. The Co-NHases are more robust and have wider substrate specificity than the Fe-NHase. We have used dihedral and positional variational Monte Carlo conformational searches to determine the conformational space available to acrylonitrile and bromoxynil bound to the iron in the active site of NHase. Dioxane is an Fe-NHase inhibitor, but has no effect on Co-NHase activity. Our conformational searches showed that although the dioxane restricts the conformational freedom of the iron coordinated acrylonitrile, there is enough room in the active site for both the acrylonitrile and dioxane. A conformational search of dioxane in the active site of Fe-NHase, in the absence of a substrate, revealed that the acrylonitrile and dioxane do not share the same space. We have also shown that if the function of the metal ions in NHases is to activate the nitrile by binding to it and acting as a Lewis acid, then the entrance and channel residues are most likely responsible for Fe-NHase's inability to hydrolize bromoxynil.     

Ising-type magnetic anisotropy in a cobalt(II) nitronyl nitroxide compound: a key to understanding the formation of molecular magnetic nanowires

The compound [Co(hfac)2-(NITPhOMe)2] (2) (hfac = hexafluoroacetylacetonate, NITPhOMe = 4'-methoxyphenyl-4,4,5,5-tetramethylimidazoline-1-oxyl-3-oxide) crystallizes in the triclinic P1 space group, a= 10.870(5), b = 11.520(5), c = 19.749(5) A, alpha = 78.05(5), beta = 84.20(5), gamma = 64.51(5) degrees, Z = 2. It can be considered a model system for studying the nature of the magnetic anisotropy of [Co(hfac)2(NITPhOMe)] (1), which was recently reported to behave as a molecular magnetic wire. The magnetic anisotropy of 2 was investigated by EPR spectroscopy and SQUID magnetometry both in the polycrystalline powder and in a single crystal. The experimental magnetic anisotropy was related to the anisotropy of the central ion and to the exchange interaction between the cobalt(II) ion and the radicals.     

Evidence for a post-translational modification, aspartyl aldehyde, in a photosynthetic membrane protein

In oxygenic photosynthesis, photosystem II (PSII) carries out the oxidation of water and reduction of plastoquinone. Three PSII subunits contain reactive groups that covalently bind amines and phenylhydrazine. It has been proposed that these reactive groups are carbonyl-containing, co- or post-translationally modified amino acids. To identify modified amino acid residues in one of the PSII subunits (CP47), tandem mass spectrometry was performed. Modified residues were affinity-tagged with either biotin-LC-hydrazide or biocytin hydrazide, which are known to label carbonyl groups. The affinity-tagged subunit was isolated by denaturing gel electrophoresis, and tryptic peptides were then subjected to affinity purification and tandem mass spectrometry. This procedure identified a hydrazide-labeled peptide, which has the sequence XKEGR. This result is supported by quantitative results acquired from peptide mapping and methylamine labeling. The gene sequence and these tandem data predict that the first amino acid, X, which is labeled with the hydrazide reagent, is a modified form of aspartic acid. On the basis of these data, we propose that D348 of the CP47 subunit is post- or co-translationally modified to give a novel amino acid side chain, aspartyl aldehyde.     

Trace determination of cobalt ion by using malic acid-malonic acid double substrate oscillating chemical system

A novel kinetic method for determination of trace amounts of cobalt ion was proposed and validated. The method is based on adding malic acid into classical Belousov-Zhabotinskii （B-Z） oscillating chemical system to form a double substrate one. The results showed that when the concentration of cobalt ion was in the range of 5.27× 10^-8 to 5.37 × 10^-12 mol L^-1, the change of the oscillating period was directly proportional to the negative logarithm of cobalt ion concentration. The sensitivity and precision of the developed method were quite satisfactory. The limit of detection was down to 5.20 × 10^-13 mol L^-1 which was a highest sensitivity found for determination of metal ions using oscillating chemical reaction so far. Some factors influencing the determination were also examined. The method has been successfully used to determine cobalt ion in vitamin B12 injection.     

Conductance of a cobalt(II) terpyridine complex based molecular transistor: a computational analysis

A recent experiment, in which a molecular transistor based on the coordination chemistry of cobalt(II) and organic self-assembled monolayers is formed by means of self-aligned lithography,2 is analyzed with a computational approach. The calculations reveal that a complex involving two cobalt(II) ions bridged by acetate ions can effectively span the nanogap. This bridged complex is shown to be both more flexible and more conductive than the alternative structure involving a single cobalt(II) ion. The single cobalt(II) ion complex is the more stable structure in a nonconfined environment (i.e., in solution) but is found to be less effective at connecting the leads of the fabricated gap and is less likely to result in a conductive device.     

A comparative DFT study of substrates and products of industrial enzyme nitrile hydratase

Nitrile hydratase (NHase) is a metalloenzyme used in industrial biotechnology for a large scale production of common chemicals. NHases convert nitriles to the corresponding amides. Although the structures of some forms of NHases containing nonheme low spin Fe(III) or low spin noncorrinoid Co(III) are known, neither a catalytic mechanism nor the reasons of high selectivity towards aromatic ligands are recognized. Optimized geometries, molecular electrostatic potential maps and infrared spectra of commercially important aromatic substrates of the NHase (nicotinonitrile, o‐, m‐, p‐methylbenzonitrile) and the corresponding products (nicotinamide, o‐, m‐, p‐methylbenzamid) were investigated using the density functional theory method with the B3LYP functional and the 6‐31G(d,p) basis set. Calculated hypothetical intrinsic reaction paths indicate that benzimidic acids may be involved as intermediates. This study elucidates differences in the electronic properties of substrates and products of NHases, provides an insight into the molecular basis of the catalytic reaction and helps to explain varying enzymatic activities of microbial NHases. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

A Highly Oxidized Cobalt Porphyrin Dimer: Spin Coupling and Stabilization of the Four‐Electron Oxidation Product

A highly oxidized cobalt porphyrin dimer is reported. Each cobalt(II) ion and porphyrin ring underwent 1e oxidation with iodine as the oxidant to give a 4e‐oxidized cobalt(III) porphyrin π‐cation radical dimer. The bridging ethylene group allows for substantial conjugation of the porphyrin macrocycles, thus leading to a strong antiferromagnetic coupling between the π‐cation radicals and to stabilization of the singlet state. X‐ray crystallography clearly showed that the complex may be considered as a real supramolecule rather than two cobalt(III) porphyrin π‐cation radicals that interact through space.     

Molecular modeling and mutagenesis reveals a tetradentate binding site for Zn2+ in GABA(A) alphabeta receptors and provides a structural basis for the modulating effect of the gamma subunit

Gamma-aminobutyric acid type A receptors (GABA(A)-R) containing alpha1beta2gamma2 subunits are weakly inhibited by Zn2+, whereas receptors containing only the alpha1beta2 subunits are strongly inhibited. We built homology models of the ion pores of alpha1beta2 and alpha1beta2gamma2 GABA(A)-R using coordinates of the nicotinic acetylcholine receptor as a template. Threading the GABA(A)-R beta2 sequence onto this template placed the 17' histidine and the 20' glutamate residues at adjacent locations in the mouth of the pore, such that a nearly ideal tetradentate site for Zn2+ was formed from two histidine and two glutamate residues between adjacent beta subunits in the alpha1beta2 GABA(A)-R. Following optimization with CHARMM, the distance between the alpha-carbons of the adjacent histidine residues was approximately 9.2 A, close to the ideal distance for a Zn2+ binding site. Loss of inhibition by Zn2+ in alpha1beta2gamma2 GABA(A)-R can be explained by the geometry of these residues in the arrangement alpha1beta2gamma2alpha1beta2, in which the nearest C-alpha-C-alpha distance between the histidine residues is 15.5 A, too far apart for an energetically optimal Zn2+ binding site. We then mutated the gamma subunit at the 17' and/or 20' positions. Zn2+ inhibition was not restored in alpha1beta2gamma2 (I282H) receptors. A novel finding is that the modeling shows the native 20' lysine in gamma2 can compete with Zn2+ for binding to the inserted 17' histidine. Sensitivity to Zn2+ was restored in the double mutant receptor, alpha1beta2gamma2 (I282H; K285E), in which the competition with lysine was removed and a more favorable Zn2+ binding site was formed.     

氯化银比浊法测定镍钴锰三元素氢氧化物中氯离子

建立了氯化银比浊法测定镍钴锰三元素氢氧化物中氯离子含量的测定方法。选择了合适的测定波长,并对硝酸用量、沉淀剂用量、稳定时间对测定结果的影响进行了试验,确定了较优的分析条件。样品加标回收率在95%~103.3%,氯离子浓度在0~4μg/mL与浊度值有良好线性关系。方法为控制镍钴锰三元素氢氧化物中氯离子提供了检测依据。     

Theoretical investigation of the first-shell mechanism of nitrile hydratase

The first-shell mechanism of nitrile hydratase (NHase) is investigated theoretically using density functional theory. NHases catalyze the conversion of nitriles to amides and are classified into two groups, the non-heme Fe(III) NHases and the non-corrinoid Co(III) NHases. The active site of the non-heme iron NHase comprises a low-spin iron (S=1/2) with a remarkable set of ligands, including two deprotonated backbone nitrogens and both cysteine-sulfenic and cysteine-sulfinic acids. A widely proposed reaction mechanism of NHase is the first-shell mechanism in which the nitrile substrate binds directly to the low-spin iron in the sixth coordination site. We have used quantum chemical models of the NHase active site to investigate this mechanism. We present potential energy profiles for the reaction and provide characterization of the intermediates and transition-state structures for the NHase-mediated conversion of acetonitrile. The results indicate that the first-shell ligand Cys114-SO- could be a possible base in the nitrile hydration mechanism, abstracting a proton from the nucleophilic water molecule. The generally suggested role of the Fe(III) center as a Lewis acid, activating the substrate toward nucleophilic attack, is shown to be unlikely. Instead, the metal is suggested to provide electrostatic stabilization to the anionic imidate intermediate, thereby lowering the reaction barrier.     

[M + Fe − 5H]2− peptide ion composition verified by Fourier transform mass spectrometry accurate mass and tandem mass spectrometry analyses

Previously, the unusual ion composition [M + Fe - 5H]2- had been proposed as the major species observed when a gamma-carboxy glutamate-containing glyco-peptide was analyzed with electrospray ionization in the negative ionization mode. The sequence assignment of this highly post-translationally modified peptide was based on the mass analysis using a quadrupole ion trap together with information from both Edman and DNA sequencing. Because there was little precedent for the loss of five protons from a ferric cationized peptide, we utilized Fourier transform mass spectrometry accurate mass and tandem mass spectrometry analyses to verify the peptide ion composition.     

Amorphous cobalt silicate nanobelts@carbon composites as a stable anode material for lithium ion batteries

During the past decade, tremendous attention has been given to the development of new electrode materials with high capacity to meet the requirements of electrode materials with high energy density in lithium ion batteries. Very recently, cobalt silicate has been proposed as a new type of high capacity anode material for lithium ion batteries. However, the bulky cobalt silicate demonstrates limited electrochemical performance. Nanostructure engineering and carbon coating represent two promising strategies to improve the electrochemical performance of electrode materials. Herein, we developed a template method for the synthesis of amorphous cobalt silicate nanobelts which can be coated with carbon through the deposition and thermal decomposition of phenol formaldehyde resin. Tested as an anode material, the amorphous cobalt silicate nanobelts@carbon composites exhibit a reversible high capacity of 745 mA h g^–1 at a current density of 100 mA g^–1, and a long life span of up to 1000 cycles with a stable capacity retention of 480 mA h g^–1 at a current density of 500 mA g^–1. The outstanding electrochemical performance of the composites indicates their high potential as an anode material for lithium ion batteries. The results here are expected to stimulate further research into transition metal silicate nanostructures for lithium ion battery applications.     

A simple method for determining water content in organic solvents based on cobalt(Ⅱ)complexes

A method to determine water content in organic solvents was developed based on the color change of cobalt(Ⅱ) nitrate in different solvents.The color-change mechanism and optimal conditions for determining the water content were investigated.The results showed that there was a good linear relationships between the absorbance of cobalt(Ⅱ) complexes in organic solvents and water contents withγin 0.9989～0.9994.This method has the advantages of low cost,good reproducibility,good sensitivity,simple in operation,fast in detection,friendly to the environment and no limitation on linear range for determining water content.It was used to determine water in samples with a satisfactory recovery in 97.81%～101.24%.     

Cyanide-promoted demetalation of TrpyNiNCO: a route to sensitive metallotripyrrins of CoII, FeII, and MnII

Etheral solutions of free base tripyrrins (HTrpy) were prepared by treatment of nickel isocyanate complexes (TrpyNiNCO) with excess cyanide. From these solutions sensitive metallotripyrrins with cobalt(II), iron(II), and manganese(II) ions (TrpyMX) and with a choice of external ligands X could be obtained in pure, crystalline form. Four cobalt and one iron chelate were characterized by X-ray crystallography. Tetracoordinate cobalt(II) species with X = I, NCO, and NCS displayed unstrained tetrahedral coordination geometries, whereas the pentacoordinate TrpyCoNO3 with the O,O-nitrato ligand narrows a trigonal bipyramidal coordination. TrpyFeNCO undergoes a redox-transformation to (TrpyFeNCO)2O upon crystallization and was structurally characterized as this with an almost linear Fe-O-Fe subunit. Donor association was studied by UV-vis spectroscopy employing different solvents and showed that TrpyMnX and TrpyFeX species are very prone to the formation of pentacoordinate species, whereas TrpyCoX compounds have an intermediate tendency to do so. Nevertheless, complex fragments of all three metal ions form 1D coordination polymers with dicyanamido ligands, which were investigated by means of IR and SQUID measurements.     

Heterobimetallic Mn/Co hybrid complexes composed of proximate organometallic and classical coordination sites

A series of highly unsymmetric heterobinuclear Mn/Co complexes is reported, in which an organometallic CpMn(CO)₂ fragment and a classical Werner-type cobalt(II) subunit are arranged in close proximity by means of a bridging pyrazolate. Two ligand scaffolds are employed that differ by the chelate size of the tripodal tetradentate {N4} binding site for cobalt. Molecular structures of three complexes with either nitrate or acetate coligands have been characterized by X-ray crystallography. IR and UV-Vis-spectroelectrochemistry reveals that oxidation of the heterobimetallic systems is highly localized at the organometallic manganese site, while electrochemical reduction occurs at cobalt. Structural and spectroscopic features as well as trends for the redox potentials of the Mn^I/Mn^II couple suggest that changes at the cobalt(II) Werner-type subunit have only minor effects on the properties of the organometallic site.