Active Site (active + site)

Distribution by Scientific Domains
Distribution within Chemistry

Kinds of Active Site

  • enzyme active site
  • putative active site

  • Terms modified by Active Site

  • active site cleft
  • active site geometry
  • active site residue
  • active site serine
  • active site structure

  • Selected Abstracts

    Non-Tethered Organometallic Phosphonate Inhibitors for Lipase Inhibition: Positioning of the Metal Center in the Active Site of Cutinase,,

    Cornelis A. Kruithof
    Abstract Organometallic NCN-pincer complexes, bearing either a p -nitrophenyl phosphonate ester or a phosphonic acid group directly attached to the aromatic ring of the pincer complex, were synthesized. These compounds were tested as covalent inhibitors for the lipase cutinase. In a stoichiometric reaction of the NCN-pincer platinum phosphonate p -nitrophenyl ester 2 with cutinase, a 94,% conversion to the protein,pincer metal complex hybrid was obtained in 48 h. The NCN-pincer metal phosphonic acid derivatives (3, 4) appeared to be inactive as cutinase inhibitors. In contrast to our previous work which entails propyl tethered phosphonate esters connected to pincer metal complexes, the presented strategy allows positioning of metal complexes inside the active site of lipases. This opens up the possibility for fine-tuning the chemical environment (second coordination sphere) around a synthetic metal center inside the pocket of an enzyme for diagnostic and catalytic purposes.(© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2008) [source]

    The Third Hydrogenase: A Ferracyclic Carbamoyl with Close Structural Analogy to the Active Site of Hmd,

    ANGEWANDTE CHEMIE, Issue 41 2010
    Peter J. Turrell
    Der Natur abgeschaut: Die Synthese eines Strukturanalogons des aktiven Zentrums der [Fe]-Hydrogenase wird beschrieben (siehe Struktur; C grau, H dunkelblau, Fe grün, N hellblau, O rot, S gelb). Es wird vermutet, dass das natürliche Enzym den fünfgliedrigen Ferracyclus aufbaut, um den 2-Hydroxypyridinsubstituenten in einer Position auszurichten, in der er die heterolytische Spaltung von Diwasserstoff unterstützt. Das nun verfügbare Analogon kann dazu dienen, diese Annahme zu prüfen. [source]

    Structure and Function Converge To Identify a Hydrogen Bond in a Group,I Ribozyme Active Site,

    ANGEWANDTE CHEMIE, Issue 39 2009
    Marcello Forconi Dr.
    Enzyme nutzen ein ausgefeiltes Netzwerk aus Wechselwirkungen, um Reaktionen zu katalysieren, und die Röntgenbeugung ist eine große Hilfe, um solche Netzwerke sichtbar zu machen. Doch was passiert, wenn unterschiedliche Strukturmodelle (siehe Bild) für denselben Rest unterschiedliche Wechselwirkungen vorschlagen? Funktionsdaten aus Doppelmutantenzyklen können eine Antwort liefern, wie für das Tetrahymena -Gruppe-I-Ribozym gezeigt wurde. [source]

    A New Mechanism for Ethanol Oxidation Mediated by Cytochrome P450 2E1: Bulk Polarity of the Active Site Makes a Difference

    CHEMBIOCHEM, Issue 3 2007
    Yong Wang
    Breaking the habit. A new mechanism, called reversed dual hydrogen abstraction (R-DHA), is presented for ethanol oxidation by cytochrome P450 2E1 (CYP2E1). It is shown that the competition of R-DHA with the consensus mechanism (gem -diol) is modulated by the ethanol population in the enzyme pocket. Thus, as a response to growing blood ethanol level, CYP2E1 adapts its ethanol metabolism by a mechanistic switch from gem -diol to R-DHA. [source]

    Analysis of a Pentacoordinate Iron Dicarbonyl as Synthetic Analogue of the Hmd or Mono-Iron Hydrogenase Active Site,

    Tianbiao Liu
    Abstract Pentacoordinate iron dicarbonyls, (NS)Fe(CO)2P (NS=2-amidothiophenylate, P=PCy3 (4), PPh3, (5), and P(OEt)3 (6)) were prepared as potential biomimetics of the active site of the mono-iron hydrogenase, [Fe]-H2ase. Full characterization including X-ray diffraction, density functional theory (DFT) computations, and Mössbauer studies for complexes 5 and 6 find that, despite similar infrared v(CO) pattern and absorption frequencies as the active site of the [Fe]-H2ase, the geometrical distortions towards trigonal bipyramidal, the negative isomer shift parameters, and the differences in CO-uptake reactivity are due to the "non-innocence" of the NS ligand. Ligand-based protonation with a strong acid, HBF4,Et2O, interrupted the extensive ,-delocalization over Fe and NS ligand of complex 4 and switched on CO uptake (1,bar) to form a CO adduct, mer -[(H-NS)Fe(CO)3(PCy3)]+ or 4(CO)-H+. The extrinsic CO is reversibly removed on deprotonation with Et3N to regenerate complex 4. In a 13CO atmosphere, concomitant CO uptake by 4 -H+ and exchange with intrinsic CO groups provide a facile route to 13C-labeled 4(CO)-H+ and, upon deprotonation, 13C-labeled complex 4. DFT calculations show substantial Fe character in the LUMO of 4 -H+ typical of the d6 FeII in a regular square-pyramidal geometry. Thus, the Lewis acidity of 4 -H+ makes it amenable for CO binding, whereas the dianionic NS ligand renders the iron center of 4 insufficiently electrophilic and largely of FeI character. [source]

    High-Turnover Photochemical Hydrogen Production Catalyzed by a Model Complex of the [FeFe]-Hydrogenase Active Site

    Daniel Streich
    Lifting the diiron curtain: 200,equivalents of H2 per catalyst at a maximum turnover rate of 3.7,H2 per minute can be obtained in a light-driven proton reduction process in near-neutral H2O/DMF (pH,5.5) by using an [FeFe]-hydrogenase active-site model complex as the catalyst (see scheme). [source]

    An Iron(II) Carbonyl Thiolato Complex Bearing 2-Methoxy-Pyridine: A Structural Model of the Active Site of [Fe] Hydrogenase

    Soichiro Tanino Dr.
    Model complex: An FeII complex bearing a thiolate, 2-methoxy-pyridine, and three facially arranged CO ligands was synthesized as a structural analogue of the active site of a CO-inhibited form of [Fe] hydrogenase, from the reaction of [FeBr2(CO)4] with NaS{2,6-(mesityl)2C6H3} and the successive treatment with 2-methoxy-pyridine. [source]

    Dithiolate-Bridged Fe-Ni-Fe Trinuclear Complexes Consisting of Fe(CO)3,n(CN)n (n=0, 1) Components Relevant to the Active Site of [NiFe] Hydrogenase

    Satyanarayan Pal Dr.
    Abstract Step-by-step: A trinuclear Fe-Ni-Fe complex 1 was synthesized from the reaction of [Fe(CO)4I2] with Li2[Ni(norbornane- exo -2,3-dithiolate)2]. The CO ligands in 1 were transformed into CN, upon treatment with ,N(SiMe3)2, and the monocyanide complex 3 and the dicyanide complex 4 were obtained. Complexes 3 and 4 were found to react with protonic acids, whereas 1 is robust. A dithiolate-bridged Fe-Ni-Fe trinuclear carbonyl complex [(CO)3Fe(,-ndt)Ni(,-ndt)Fe(CO)3] (1, ndt=norbornane- exo -2,3-dithiolate) has been synthesized from the reaction of [Fe(CO)4I2] and Li2[Ni(ndt)2]. This reaction was found to occur with concomitant formation of a tetranuclear cluster [Ni3(,-ndt)4FeI] (2). Treatment of 1 with Na[N(SiMe3)2] transforms some of the CO ligands into CN,, and the monocyanide complex (PPh4)[(CO)2(CN)Fe(,-ndt)Ni(,-ndt)Fe(CO)3] (3) and the dicyanide complex (PPh4)2[(CO)2(CN)Fe(,-ndt)Ni(,-ndt)Fe(CO)2(CN)] (4) were isolated. X-ray structural analyses of the trinuclear complexes revealed a Fe-Ni-Fe array in which the metal centers are connected by the ndt sulfur bridges and direct FeNi bonds. Hydrogen bonding between the CN ligand in 3 and cocrystallized ethanol was found in the solid-state structure. The monocyanide complex 3 and dicyanide complex 4 reacted with acids such as HOTf or HCl generating insoluble materials, whereas complex 1 did not react. [source]

    Oxidation of Diiron and Triiron Sulfurdithiolato Complexes: Mimics for the Active Site of [FeFe]-Hydrogenase

    Jochen Windhager
    Abstract The oxidation of the hexacarbonyl(1,3-dithiolato- S,S,)diiron complexes 4a,4c with varying amounts of dimethyldioxirane (DMD) was systematically studied. The chemoselectivity of the oxidation products depended upon the substituent R (R=H, Me, 1/2 (CH2)5). For R=H, four oxidation products, 6a,6d, have been obtained. In the case of R=Me, three products, 7a,7c, were formed, and for R=1/2 (CH2)5, only complex 8 was observed. These observations are due to steric and electronic effects caused by the substituent R. Additionally, oxidation of the triiron complex 5 with DMD was performed to yield the products 9a and 9b. X-Ray diffraction analyses were performed for 6a,6d, 7a, and 7c, as well as for 9a and 9b. The electronic properties were determined by density-functional theory (DFT) calculations. [source]

    Synthesis and Characterization of Hydroxy-Functionalized Models for the Active Site in Fe-Only-Hydrogenases

    Ulf-Peter Apfel
    Abstract The reactions of dl -1,4-disulfanylbutane-2,3-diol and 1,3-disulfanylpropan-2-ol with dodecacarbonyltriiron have been investigated. As main products, the iron complexes 1 and 2 were isolated and characterized by spectroscopic methods, as well as single crystal X-ray analysis. Additionally, the unusually large bond angles in the dithiolato bridge was investigated via density-functional theory (DFT) calculations. Moreover, the electrochemical features have been studied by cyclic voltammetry. [source]

    Construction of the Active Site of Metalloenzyme on Au NC Micelles

    Zhiming ZHANG
    Abstract For developing an efficient nanoenzyme system with self-assembly strategy, gold nanocrystal micelles (Au NC micelles) with inserted catalytic Zn(II) centers were constructed by self-assembly of a catalytic ligand [N,N -bis(2-aminoethyl)- N, -dodecylethylenediamine] Zn(II) complexes (Zn(II)L) on the surface of Au NC via hydrophobic interaction. The functionalized Au NC micelles acted as an excellent nanoenzyme model for imitating ribonuclease. The catalytic capability of the Au NC micelles was evaluated by accelerating the cleavage of 2-hydroxypropyl p -nitrophenyl phosphate (HPNP). These functionalized Au NC micelles exhibited considerable ribonuclease-like activities by a factor of 4.9×104 (kcat/kuncat) for the cleavage of HPNP in comparison to the spontaneous cleavage of HPNP at 37°C. The catalytic capability of the functionalized Au NC micelles can be considerably compared to other models reported previously as nanoenzymes under the comparable conditions. [source]

    Selective Knockout of Gold Active Sites,

    ANGEWANDTE CHEMIE, Issue 17 2010
    Maria Nowicka Dr.
    Radikal-Kur: Die Behandlung der Oberflächen von Goldelektroden mit Hydroxylradikalen senkt die Geschwindigkeitskonstanten ks für den Elektronentransfer bei elektrochemischen Reaktionen mit radikalischen Intermediaten beträchtlich (siehe Bild). Diese Beobachtung lässt sich durch das selektive Ausschalten aktiver Goldzentren mit teilweise gefüllten d-Orbitalen erklären. [source]

    Probing Photocatalytic Active Sites on a Single Titanosilicate Zeolite with a Redox-Responsive Fluorescent Dye,

    ANGEWANDTE CHEMIE, Issue 2 2010
    Takashi Tachikawa Dr.
    Richtig belichtet: Laut In-situ-Fluoreszenzbildgebung einer photokatalytischen Oxidation mit einem redoxempfindlichen Fluoreszenzfarbstoff (siehe Bild, grün) erhöht die Behandlung von Titanosilicat-Einkristallen mit Säure die Adsorptions- und Reaktionseffizienz sowie die Heterogenität der photokatalytischen Aktivität der Kristalle signifikant. Zudem fungieren Kristalldefekte bei der photokatalytischen Reaktion als reaktive Zentren. [source]

    Ab initio Simulation of Lewis Sites in Mordenite and Comparative Study of the Strength of Active Sites via CO Adsorption.

    CHEMINFORM, Issue 45 2004
    L. Benco
    No abstract is available for this article. [source]

    Investigation of Hydrogen Physisorption Active Sites on the Surface of Porous Carbonaceous Materials

    Deyang Qu
    Abstract Hydrogen physisorption in different carbonaceous materials was investigated in liquid nitrogen (77,K). The total hydrogen adsorption was found to have a linear relationship with the surface area of pores <30,Å. The surface area and porosity of the carbon materials were determined by dinitrogen adsorption at 77,K and density function theory (DFT). The active sites for hydrogen adsorption were investigated and found to be related to the edge orientation of defective graphene micro-sheet domains. [source]

    Active site inhibited factor VIIa attenuates myocardial ischemia/reperfusion injury in mice

    S. T. B. G. LOUBELE
    Summary.,Background:,Inhibition of specific coagulation pathways such as the factor VIIa-tissue factor complex has been shown to attenuate ischemia/reperfusion (I/R) injury, but the cellular mechanisms have not been explored. Objectives:,To determine the cellular mechanisms involved in the working mechanism of active site inhibited factor VIIa (ASIS) in the protection against myocardial I/R injury. Methods:,We investigated the effects of a specific mouse recombinant in a mouse model of myocardial I/R injury. One hour of ischemia was followed by 2, 6 or 24 h of reperfusion. Mouse ASIS or placebo was administered before and after induction of reperfusion. Results:,ASIS administration reduced myocardial I/R injury by more than 40% at three reperfusion times. Multiplex ligation dependent probe amplification (MLPA) analysis showed reduced mRNA expression in the ischemic myocardium of CD14, TLR-4, interleukin-1 (IL-1) receptor-associated kinase (IRAK) and I,B, upon ASIS administration, indicative of inhibition of toll-like receptor-4 (TLR-4) and subsequent nuclear factor-,B (NF-,B) mediated cell signaling. Levels of nuclear activated NF-,B and proteins influenced by the NF-,B pathway including tissue factor (TF) and IL-6 that were increased after I/R, were attenuated upon ASIS administration. After 6 and 24 h of reperfusion, neutrophil infiltration into the area of infarction was decreased upon ASIS administration. There was, however, no evidence of an effect of ASIS on apoptosis (Tunel staining and MLPA analysis). Conclusions:,We conclude that the diminished amount of myocardial I/R injury after ASIS administration is primarily due to attenuated inflammation-related lethal I/R injury, probably mediated through the NF-,B mechanism. [source]

    DFT Based Atomic Softness and Its Application in Site Selectivity

    P. Singh
    Abstract Active site of a complex molecule and mechanism of chemical reaction has been studied with the help of atomic softness values derived from calculation based on Density functional theory. The quantum mechanical equation of Klopman has been solved with the help of AM1 calculation by using Win MOPAC7.21 software. On the basis of chemical potential equalization principle, and Koopmans theorem for frontier orbitals a formalism has been developed for the calculation of electron affinity of an atom in a molecule EA. The reliability of the EA values have been tested with electron density (obtained from AM1 calculation) and Fukui function values taken from literature. [source]

    Zinc diethyldithiocarbamate allergenicity: potential haptenation mechanisms

    CONTACT DERMATITIS, Issue 2 2008
    Itai Chipinda
    Background:, Zinc diethyldithiocarbamate (ZDEC) and its disulfide, tetraethylthiuram disulfide (TETD), are rubber accelerators and contact allergens that cross-react in some individuals. Objective:, This study explored potential protein haptenation mechanisms of ZDEC and its oxidation products. Methods:, ZDEC oxidation/reduction products and sites of protein binding were assessed using high-performance liquid chromatography and mass spectrometry. The murine local lymph node assay (LLNA) was employed to probe haptenation mechanisms of ZDEC by examining its allergenicity along with its oxidation products and through elimination of oxidation and chelation mechanisms by substituting cobalt for zinc [cobalt (II) dithiocarbamate, CoDEC]. Results:, Oxidation of ZDEC by hypochlorous acid (bleach, HOCl), iodine, or hydrogen peroxide resulted in production of TETD, tetraethylthiocarbamoyl disulfide, and tetraethyldicarbamoyl disulfide (TEDCD). Albumin thiols reduced TETD with subsequent mixed disulfide formation/haptenation. ZDEC directly chelated the copper ion on the active site of the superoxide dismutase, whereas CoDEC did not bind to Cu proteins or form mixed disulfides with free thiols. ZDEC, sodium diethyldithiocarbamate, TEDCD, and TETD were all positive in the LLNA except CoDEC, which was non-allergenic. Conclusion:, The thiol is the critical functional group in ZDEC's allergenicity, and haptenation is predominantly through chelation of metalloproteins and formation of mixed disulfides. [source]

    Bioelectrochemical Characterization of Horseradish and Soybean Peroxidases

    ELECTROANALYSIS, Issue 21 2009
    Marco Frasconi
    Abstract Heme peroxidase are ubiquitous enzymes catalyzing the oxidation of a broad range of substrates by hydrogen peroxide. In this paper the bioelectrochemical characterization of horseradish peroxidase (HRP) and soybean peroxidase (SBP), belonging to class III of the plant peroxidase superfamily, was studied. The homogeneous reactions between peroxidases and some common redox mediators in the presence of hydrogen peroxide have been carried out by cyclic voltammetry. The electrochemical characterization of the reactions involving enzyme, substrate and mediators concentrations allowed us to calculate the kinetic parameters for the substrate,enzyme reaction (KMS) and for the redox mediator,enzyme reaction (KMM). A full characterization of the direct electron transfer kinetic parameters between the electrode and enzyme active site was also performed by opportunely modeling data obtained from cyclic voltammetry and square wave voltammetry experiments. The experimental data obtained with immobilized peroxidases show enhanced direct electron transfer and excellent electrocatalytical performance for H2O2. Despite the structural similarities and common catalytic cycle, HRP and SBP exhibit differences in their substrate affinity and catalytic efficiency. Basing on our results, it can be concluded that peroxidase from soybean represents an interesting alternative to the classical and largely employed one obtained from horseradish as biorecognition element of electrochemical mediated biosensors. [source]

    Glucose Biosensor Mediated by 1,2-Diferrocenylethane in a Sono-Gel Composite Electrode

    ELECTROANALYSIS, Issue 2-3 2007
    Barbara Ballarin
    Abstract An amperometric glucose biosensor was constructed based on a renewable carbon composite sono-gel matrix incorporating 1,2-diferrocenylethane as electron transfer mediator between the electrode and the active site of glucose oxidase. The enzyme was immobilized on the electrode surface by cross-linking with glutaraldehyde and bovine serum albumin. The process parameters for the fabrication of the biosensor and the influence of various experimental conditions (i.e., pH, temperature, operating potential) were investigated. Cyclic voltammetry and amperometric measurements were used to study the response of the glucose sensor, which displayed fast response time and good reproducibility. The analytical performances and the apparent Michaelis-Menten constant of the biosensor were evaluated. [source]

    Capillary electrophoresis versus differential scanning calorimetry for the analysis of free enzyme versus enzyme-ligand complexes: In the search of the ligand-free status of cholinesterases

    ELECTROPHORESIS, Issue 2 2006
    Daniel Rochu Dr.
    Abstract Cholinesterases (ChEs) are highly efficient biocatalysts whose active site is buried in a deep, narrow gorge. The talent of CE to discover inhibitors in the gorge of highly purified preparations has fairly altered the meaning of a ChE ligand-free status. To attempt at a description of this one, we investigated the stability of Bungarus fasciatus acetylcholinesterase (AChE), alone or complexed with different inhibitors. Determination of midtransition temperature for thermal denaturation, using differential scanning calorimetry (DSC) and CE, provided conflicting results. Discrepancies strongly question the reality of a ligand-free AChE state. DSC allowed estimation of the stability of AChE-ligands complexes, and to rank the stabilizing effect of different inhibitors. CE acted as a detector of hidden ligands, provided that they were charged, reversibly bound, and thus dissociable upon action of electric fields. Then, CE allowed quantification of the stability of ligand-free AChE. CE and DSC providing each fractional and nonredundant information, cautious attention must be paid for actual estimation of the conformational stability of ChEs. Because inhibitors used in purification of ChEs by affinity chromatography are charged, CE remains a leading method to estimate enzyme stability and detect the presence of bound hidden ligands. [source]

    Novel DNA repair alkyltransferase from Caenorhabditis elegans

    Sreenivas Kanugula
    Abstract O6 -Alkylguanine DNA-alkyltransferase (AGT) is a widely distributed DNA repair protein that protects living organisms from endogenous and exogenous alkylation damage to DNA at the O6 -position of guanine. The search of the C. elegans genome database for an AGT protein revealed the presence of a protein (cAGT-2) with some similarity to known AGTs in addition to the easily recognized cAGT-1 protein. The predicted protein sequence of cAGT-2 contains the amino acid sequence ,ProCysHisPro, at the presumed active site of the protein, whereas all other known AGTs have ,ProCysHisArg,. A truncated version of the cAGT-2 protein was expressed in E. coli. This purified recombinant protein was able to repair O6 -methylguanine and O4 -methylthymine adducts in DNA in vitro and also reacted with the bulky benzyl adduct in O6 -benzylguanine. This fragment of cAGT-2 (104 amino acids) is the smallest protein possessing AGT activity yet described. The full-length cAGT-2 protein (274 amino acids) totally lacks the N-terminal domain present in all other known AGTs but has a long C-terminal extension that has significant homology to histone 1C. Expression of cAGT-2 in an E. coli strain lacking endogenous AGT activity provided modest but statistically significant resistance to the toxicity of N -methyl- N,-nitro- N -nitrosoguanidine, confirming that cAGT-2 is an alkyltransferase. Environ. Mol. Mutagen. 38:235,243, 2001. © 2001 Wiley-Liss, Inc. [source]

    Diversity of the cadmium-containing carbonic anhydrase in marine diatoms and natural waters

    Haewon Park
    Summary A recent report of a novel carbonic anhydrase (CDCA1) with Cd as its metal centre in the coastal diatom Thalassiosira weissflogii has led us to search for the occurrence of this Cd enzyme (CDCA) in other marine phytoplankton and in the environment. Using degenerate primers designed from the published sequences from T. weissflogii and a putative sequence in the genome of Thalassiosira pseudonana, we show that CDCA is widespread in diatom species and ubiquitous in the environment. All detected genes share more than 64% amino acid identity with the CDCA of T. pseudonana. Analysis of the amino acid sequence of CDCA shows that the putative Cd binding site resembles that of beta-class carbonic anhydrases (CAs). The prevalence of CAs in diatoms that presumably contain Cd at their active site probably reflects the very low concentration of Zn in the marine environment and the difficulty in acquiring inorganic carbon for photosynthesis. The cdca primers developed in this study should be useful for detecting cdca genes in the field, and studying the conditions under which they are expressed. [source]

    Microbial succession of nitrate-reducing bacteria in the rhizosphere of Poa alpina across a glacier foreland in the Central Alps

    K. Deiglmayr
    Summary Changes in community structure and activity of the dissimilatory nitrate-reducing community were investigated across a glacier foreland in the Central Alps to gain insight into the successional pattern of this functional group and the driving environmental factors. Bulk soil and rhizosphere soil of Poa alpina was sampled in five replicates in August during the flowering stage and in September after the first snowfalls along a gradient from 25 to 129 years after deglaciation and at a reference site outside the glacier foreland (> 2000 years deglaciated). In a laboratory-based assay, nitrate reductase activity was determined colorimetrically after 24 h of anaerobic incubation. In selected rhizosphere soil samples, the community structure of nitrate-reducing microorganisms was analysed by restriction fragment length polymorphism (RFLP) analysis using degenerate primers for the narG gene encoding the active site of the membrane-bound nitrate reductase. Clone libraries of the early (25 years) and late (129 years) succession were constructed and representative clones sequenced. The activity of the nitrate-reducing community increased significantly with age mainly due to higher carbon and nitrate availability in the late succession. The community structure, however, only showed a small shift over the 100 years of soil formation with pH explaining a major part (19%) of the observed variance. Clone library analysis of the early and late succession pointed to a trend of declining diversity with progressing age. Presumably, the pressure of competition on the nitrate reducers was relatively low in the early successional stage due to minor densities of microorganisms compared with the late stage; hence, a higher diversity could persist in this sparse environment. These results suggest that the nitrate reductase activity is regulated by environmental factors other than those shaping the genetic structure of the nitrate-reducing community. [source]

    A molecular modeling analysis of polycyclic aromatic hydrocarbon biodegradation by naphthalene dioxygenase

    Kristine H. Wammer
    Abstract A theoretical analysis was performed to examine the role of naphthalene dioxygenase(NDO) enzymes in determining differences in biodegradability and biodegradation rates of two- to four-ring polycyclic aromatic hydrocarbons (PAHs) via oxygenation and desaturation reactions. Investigation of the thermodynamics of PAH biodegradation reactions catalyzed by NDO revealed that enthalpies of reaction can explain reaction patterns or regioselectivity of the enzyme in limited cases. Molecular modeling analysis of the size and shape constraints of PAH-enzyme interactions suggests that PAHs bigger than approximately four rings and compounds with , substituents or other structural features contributing to increased width at the end of the substrate near the active site are expected to have binding difficulties. This explains some regioselectivity observations, in that thermody-namically favorable sites on some PAH molecules cannot be positioned correctly to be oxidized at the active site. The enzyme fit analysis also suggests that slower biodegradation rates are expected for compounds with larger widths because of the unique positioning that is required for reaction to occur. An inverse relationship between a molecular descriptor of compound width and previously obtained biodegradation rates suggests that this descriptor may be valuable for predicting relative biodegradation rates of PAHs with dioxygenases other than NDO. [source]

    Effects of Anabaena spiroides (cyanobacteria) aqueous extracts on the acetylcholinesterase activity of aquatic species

    José María Monserrat
    Abstract The effects of aqueous extracts from a cyanobacteria species, Anabaena spiroides, on fish (Odontesthes argentinensis), crab (Callinectes sapidus), and purified eel acetylcholinesterase (AChE) activity were studied. In vitro concentrations of A. spiroides aqueous extract that inhibited 50% of enzyme activity (IC50) were 23.0, 17.2, and 45.0 mg/L of lyophilized cyanobacteria for eel, fish, and crab AChE, respectively. Eel AChE inhibition follows pseudo-first-order kinetics, the same expected for organophosphorus pesticides. Inhibition of purified eel AChE using mixtures of bioxidized malathion and aqueous extract of A. spiroides showed a competitive feature (p < 0.05), suggesting that the toxin(s) could be structurally similar to an organophosphorus pesticide and that toxins present in the aqueous extract inhibit the active site of the enzyme. The inhibition recovery assays using 2-PAM (0.3 mM) showed that (1) bioxidized malathion inhibited 27.0 ± 1.1% of crab and 36.5 ± 0.1% of eel AChE activities; (2) with bioxidized malathion + 2-PAM the registered inhibition was 13.2 ± 2.1% and 3.7 ± 0.5% in crab and eel AChE, respectively; (3) the aqueous extract from A. spiroides inhibited 17.4 ± 2.2% and 59.9 ± 0.5% of crab and eel AChE activity, respectively; and (4) aqueous extract + 2-PAM inhibited 22.3 ± 2.6 and 61.5 ± 0.2% of crab and eel AChEs. The absence of enzyme activity recovery after 2-PAM exposure could imply that the enzyme aging process was extremely quick. [source]

    [FeFe]-Hydrogenase Models: Overpotential Control for Electrocatalytic H2 Production by Tuning of the Ligand ,-Acceptor Ability

    Fengwei Huo
    Abstract In the search for synthetic competitive catalysts that function with hydrogenase-like capability, a series of (Pyrrol-1-yl)phosphane-substituted diiron complexes [(,-pdt)Fe2(CO)5L] [pdt = propanedithiolate, L = Ph2PPyr (2), PPyr3 (4); Pyr = pyrrolyl] and [(,-pdt)Fe2(CO)4L2] [L = Ph2PPyr (3), PPyr3 (5)] were prepared as functional models for the active site of Fe-only hydrogenase. The structures of these complexes were fully characterized by spectroscopy and X-ray crystallography. In the IR spectra the CO bands for complexes 2,5 are shifted to higher energy relative to those of complexes with "traditional" phosphane ligands, such as PPh3, PMe3, and PTA (1,3,5-triaza-7-phosphaadamantane), indicating that (pyrrol-1-yl)phosphanes are poor ,-donors and better ,-acceptors. The electrochemical properties of complexes 2,5 were studied by cyclic voltammetry in CH3CN in the absence and presence of the the weak acid HOAc. The reduction potentials of these complexes show an anodic shift relative to other phosphane-substituted derivatives. All of the complexes can catalyze proton reduction from HOAc to H2 in CH3CN at their respective FeIFe0 level. Complex 4 is the most effective electrocatalyst, which catalytically generates H2 from HOAc at ,1.66 V vs. Fc+/Fc with only ca. 0.2 V overpotential in CH3CN. [source]

    Non-Tethered Organometallic Phosphonate Inhibitors for Lipase Inhibition: Positioning of the Metal Center in the Active Site of Cutinase,,

    Cornelis A. Kruithof
    Abstract Organometallic NCN-pincer complexes, bearing either a p -nitrophenyl phosphonate ester or a phosphonic acid group directly attached to the aromatic ring of the pincer complex, were synthesized. These compounds were tested as covalent inhibitors for the lipase cutinase. In a stoichiometric reaction of the NCN-pincer platinum phosphonate p -nitrophenyl ester 2 with cutinase, a 94,% conversion to the protein,pincer metal complex hybrid was obtained in 48 h. The NCN-pincer metal phosphonic acid derivatives (3, 4) appeared to be inactive as cutinase inhibitors. In contrast to our previous work which entails propyl tethered phosphonate esters connected to pincer metal complexes, the presented strategy allows positioning of metal complexes inside the active site of lipases. This opens up the possibility for fine-tuning the chemical environment (second coordination sphere) around a synthetic metal center inside the pocket of an enzyme for diagnostic and catalytic purposes.(© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2008) [source]

    Mechanism-Based Inactivation of Coenzyme B12 -Dependent 2-Methyleneglutarate Mutase by (Z)-Glutaconate and Buta-1,3-diene-2,3-dicarboxylate

    Wolfgang Buckel
    Abstract In the presence of holo 2-methyleneglutarate mutase, buta-1,3-diene-2,3-dicarboxylate and (Z)-glutaconate [(Z)-pent-2-ene-1,5-dicarboxylate], but not (E)-glutaconate, each induced homolysis of the Co,C bond of coenzyme B12 to afford cob(II)alamin and the 5,-deoxyadenosyl radical. The latter probably added to the double bond in (Z)-glutaconate and one of the double bonds in buta-1,3-diene-2,3-dicarboxylate to afford a corresponding "radical adduct". The formation of new radicals and cob(II)alamin was diagnosed by UV/Visible and EPR spectroscopy. (Z)-Glutaconate rapidly inactivated the mutase with formation of aquocobalamin, which was possibly derived by electron transfer from cob(II)alamin to the radical adduct. In contrast, buta-1,3-diene-2,3-dicarboxylate was a much slower inactivator. In this case, the spectroscopic data revealed a relatively stable complex of the radical adduct with cob(II)alamin in the active site of the enzyme. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2006) [source]

    An Investigation of the Reactivity of [(diimine)(dithiolato)M] Complexes Using the Fukui Functions Concept

    Christodoulos Makedonas
    Abstract Fukui functions are widely used when investigating the reactivity of organic molecules, but rarely with metal complexes. Here, we investigate the reactivity of [(diimine)(dithiolato)M] complexes with different types of reagents and upon oxidation employing this concept. Mixed-ligand complexes of this type have a peculiar electronic description due to the mixed-metal-ligand-to-ligand charge-transfer band, which is why they are considered as very promising candidates for non-linear optical (NLO) materials and molecular photochemical devices (MPD). As a result, their reactivity is of crucial importance for their potential applications. The obtained results of f+ and f, for the neutral [(diimine)(dithiolato)M] complexes (M = Pd, Ni and Pt) not only predict that the sulfur atom is the preferable active site for electrophilic attack but also reveal the different tunability of these complexes when they are subjected to an oxidation process, in agreement with experimental results. Under the framework of the Fukui indices we also provide an alternative explanation for crystal packing that could find widespread application. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2006) [source]