Science.gov

Sample records for active catalytic site

  1. Ionizable Side Chains at Catalytic Active Sites of Enzymes

    PubMed Central

    Jimenez-Morales, David; Liang, Jie

    2012-01-01

    Catalytic active sites of enzymes of known structure can be well defined by a modern program of computational geometry. The CASTp program was used to define and measure the volume of the catalytic active sites of 573 enzymes in the Catalytic Site Atlas database. The active sites are identified as catalytic because the amino acids they contain are known to participate in the chemical reaction catalyzed by the enzyme. Acid and base side chains are reliable markers of catalytic active sites. The catalytic active sites have 4 acid and 5 base side chains, in an average volume of 1072 Å3. The number density of acid side chains is 8.3 M (in chemical units); the number density of basic side chains is 10.6 M. The catalytic active site of these enzymes is an unusual electrostatic and steric environment in which side chains and reactants are crowded together in a mixture more like an ionic liquid than an ideal infinitely dilute solution. The electrostatics and crowding of reactants and side chains seems likely to be important for catalytic function. In three types of analogous ion channels, simulation of crowded charges accounts for the main properties of selectivity measured in a wide range of solutions and concentrations. It seems wise to use mathematics designed to study interacting complex fluids when making models of the catalytic active sites of enzymes. PMID:22484856

  2. Resonant active sites in catalytic ammonia synthesis: A structural model

    NASA Astrophysics Data System (ADS)

    Cholach, Alexander R.; Bryliakova, Anna A.; Matveev, Andrey V.; Bulgakov, Nikolai N.

    2016-03-01

    Adsorption sites Mn consisted of n adjacent atoms M, each bound to the adsorbed species, are considered within a realistic model. The sum of bonds Σ lost by atoms in a site in comparison with the bulk atoms was used for evaluation of the local surface imperfection, while the reaction enthalpy at that site was used as a measure of activity. The comparative study of Mn sites (n = 1-5) at basal planes of Pt, Rh, Ir, Fe, Re and Ru with respect to heat of N2 dissociative adsorption QN and heat of Nad + Had → NHad reaction QNH was performed using semi-empirical calculations. Linear QN(Σ) increase and QNH(Σ) decrease allowed to specify the resonant Σ for each surface in catalytic ammonia synthesis at equilibrium Nad coverage. Optimal Σ are realizable for Ru2, Re2 and Ir4 only, whereas other centers meet steric inhibition or unreal crystal structure. Relative activity of the most active sites in proportion 5.0 × 10- 5: 4.5 × 10- 3: 1: 2.5: 3.0: 1080: 2270 for a sequence of Pt4, Rh4, Fe4(fcc), Ir4, Fe2-5(bcc), Ru2, Re2, respectively, is in agreement with relevant experimental data. Similar approach can be applied to other adsorption or catalytic processes exhibiting structure sensitivity.

  3. Isolated metal active site concentration and stability control catalytic CO2 reduction selectivity.

    PubMed

    Matsubu, John C; Yang, Vanessa N; Christopher, Phillip

    2015-03-01

    CO2 reduction by H2 on heterogeneous catalysts is an important class of reactions that has been studied for decades. However, atomic scale details of structure-function relationships are still poorly understood. Particularly, it has been suggested that metal particle size plays a unique role in controlling the stability of CO2 hydrogenation catalysts and the distribution of active sites, which dictates reactivity and selectivity. These studies often have not considered the possible role of isolated metal active sites in the observed dependences. Here, we utilize probe molecule diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS) with known site-specific extinction coefficients to quantify the fraction of Rh sites residing as atomically dispersed isolated sites (Rhiso), as well as Rh sites on the surface of Rh nanoparticles (RhNP) for a series of TiO2 supported Rh catalysts. Strong correlations were observed between the catalytic reverse water gas shift turn over frequency (TOF) and the fraction of Rhiso sites and between catalytic methanation TOF and the fraction of RhNP sites. Furthermore, it was observed that reaction condition-induced disintegration of Rh nanoparticles, forming Rhiso active sites, controls the changing reactivity with time on stream. This work demonstrates that isolated atoms and nanoparticles of the same metal on the same support can exhibit uniquely different catalytic selectivity in competing parallel reaction pathways and that disintegration of nanoparticles under reaction conditions can play a significant role in controlling stability. PMID:25671686

  4. Dynamic formation of single-atom catalytic active sites on ceria-supported gold nanoparticles

    PubMed Central

    Wang, Yang-Gang; Mei, Donghai; Glezakou, Vassiliki-Alexandra; Li, Jun; Rousseau, Roger

    2015-01-01

    Catalysis by gold supported on reducible oxides has been extensively studied, yet issues such as the nature of the catalytic site and the role of the reducible support remain fiercely debated topics. Here we present ab initio molecular dynamics simulations of an unprecedented dynamic single-atom catalytic mechanism for the oxidation of carbon monoxide by ceria-supported gold clusters. The reported dynamic single-atom catalytic mechanism results from the ability of the gold cation to strongly couple with the redox properties of the ceria in a synergistic manner, thereby lowering the energy of redox reactions. The gold cation can break away from the gold nanoparticle to catalyse carbon monoxide oxidation, adjacent to the metal/oxide interface and subsequently reintegrate back into the nanoparticle after the reaction is completed. Our study highlights the importance of the dynamic creation of active sites under reaction conditions and their essential role in catalysis. PMID:25735407

  5. Conformational Disorganization within the Active Site of a Recently Evolved Organophosphate Hydrolase Limits Its Catalytic Efficiency.

    PubMed

    Mabbitt, Peter D; Correy, Galen J; Meirelles, Tamara; Fraser, Nicholas J; Coote, Michelle L; Jackson, Colin J

    2016-03-01

    The evolution of new enzymatic activity is rarely observed outside of the laboratory. In the agricultural pest Lucilia cuprina, a naturally occurring mutation (Gly137Asp) in α-esterase 7 (LcαE7) results in acquisition of organophosphate hydrolase activity and confers resistance to organophosphate insecticides. Here, we present an X-ray crystal structure of LcαE7:Gly137Asp that, along with kinetic data, suggests that Asp137 acts as a general base in the new catalytic mechanism. Unexpectedly, the conformation of Asp137 observed in the crystal structure obstructs the active site and is not catalytically productive. Molecular dynamics simulations reveal that alternative, catalytically competent conformers of Asp137 are sampled on the nanosecond time scale, although these states are less populated. Thus, although the mutation introduces the new reactive group responsible for organophosphate detoxification, the catalytic efficiency appears to be limited by conformational disorganization: the frequent sampling of low-energy nonproductive states. This result is consistent with a model of molecular evolution in which initial function-changing mutations can result in enzymes that display only a fraction of their catalytic potential due to conformational disorganization. PMID:26881849

  6. Correction: Towards the rationalization of catalytic activity values by means of local hyper-softness on the catalytic site: a criticism about the use of net electric charges.

    PubMed

    Martínez-Araya, Jorge Ignacio; Grand, André; Glossman-Mitnik, Daniel

    2016-01-28

    Correction for 'Towards the rationalization of catalytic activity values by means of local hyper-softness on the catalytic site: a criticism about the use of net electric charges' by Jorge Ignacio Martínez-Araya et al., Phys. Chem. Chem. Phys., 2015, DOI: 10.1039/c5cp03822g. PMID:26524565

  7. Structural and kinetic contributions of the oxyanion binding site to the catalytic activity of acylaminoacyl peptidase.

    PubMed

    Kiss, András L; Palló, Anna; Náray-Szabó, Gábor; Harmat, Veronika; Polgár, László

    2008-05-01

    It is widely accepted that the catalytic activity of serine proteases depends primarily on the Asp-His-Ser catalytic triad and other residues within the vicinity of this motif. Some of these residues form the oxyanion binding site that stabilizes the tetrahedral intermediate by hydrogen bonding to the negatively charged oxyanion. In acylaminoacyl peptidase from the thermophile Aeropyrum pernix, the main chain NH group of Gly369 is one of the hydrogen bond donors forming the oxyanion binding site. The side chain of His367, a conserved residue in acylaminoacyl peptidases across all species, fastens the loop holding Gly369. Determination of the crystal structure of the H367A mutant revealed that this loop, including Gly369, moves away considerably, accounting for the observed three orders of magnitude decrease in the specificity rate constant. For the wild-type enzyme ln(k(cat)/K(m)) vs. 1/T deviates from linearity indicating greater rate enhancement with increasing temperature for the dissociation of the enzyme-substrate complex compared with its decomposition to product. In contrast, the H367A variant provided a linear Arrhenius plot, and its reaction was associated with unfavourable entropy of activation. These results show that a residue relatively distant from the active site can significantly affect the catalytic activity of acylaminoacyl peptidase without changing the overall structure of the enzyme. PMID:18325786

  8. Twinning in fcc lattice creates low-coordinated catalytically active sites in porous gold.

    PubMed

    Krajčí, Marian; Kameoka, Satoshi; Tsai, An-Pang

    2016-08-28

    We describe a new mechanism for creation of catalytically active sites in porous gold. Samples of porous gold prepared by de-alloying Al2Au exhibit a clear correlation between the catalytic reactivity towards CO oxidation and structural defects in the fcc lattice of Au. We have found that on the stepped {211} surfaces quite common twin boundary defects in the bulk structure of porous gold can form long close-packed rows of atoms with the coordination number CN = 6. DFT calculations confirm that on these low-coordinated Au sites dioxygen chemisorbs and CO oxidation can proceed via the Langmuir-Hinshelwood mechanism with the activation energy of 37 kJ/mol or via the CO-OO intermediate with the energy barrier of 19 kJ/mol. The existence of the twins in porous gold is stabilized by the surface energy. PMID:27586937

  9. Probing the Electrostatics of Active Site Microenvironments along the Catalytic Cycle for Escherichia coli Dihydrofolate Reductase

    PubMed Central

    2015-01-01

    Electrostatic interactions play an important role in enzyme catalysis by guiding ligand binding and facilitating chemical reactions. These electrostatic interactions are modulated by conformational changes occurring over the catalytic cycle. Herein, the changes in active site electrostatic microenvironments are examined for all enzyme complexes along the catalytic cycle of Escherichia coli dihydrofolate reductase (ecDHFR) by incorporation of thiocyanate probes at two site-specific locations in the active site. The electrostatics and degree of hydration of the microenvironments surrounding the probes are investigated with spectroscopic techniques and mixed quantum mechanical/molecular mechanical (QM/MM) calculations. Changes in the electrostatic microenvironments along the catalytic environment lead to different nitrile (CN) vibrational stretching frequencies and 13C NMR chemical shifts. These environmental changes arise from protein conformational rearrangements during catalysis. The QM/MM calculations reproduce the experimentally measured vibrational frequency shifts of the thiocyanate probes across the catalyzed hydride transfer step, which spans the closed and occluded conformations of the enzyme. Analysis of the molecular dynamics trajectories provides insight into the conformational changes occurring between these two states and the resulting changes in classical electrostatics and specific hydrogen-bonding interactions. The electric fields along the CN axes of the probes are decomposed into contributions from specific residues, ligands, and solvent molecules that make up the microenvironments around the probes. Moreover, calculation of the electric field along the hydride donor–acceptor axis, along with decomposition of this field into specific contributions, indicates that the cofactor and substrate, as well as the enzyme, impose a substantial electric field that facilitates hydride transfer. Overall, experimental and theoretical data provide evidence for

  10. Site-dependent catalytic activity of graphene oxides towards oxidative dehydrogenation of propane.

    PubMed

    Tang, Shaobin; Cao, Zexing

    2012-12-28

    Graphene oxides (GOs) may offer extraordinary potential in the design of novel catalytic systems due to the presence of various oxygen functional groups and their unique electronic and structural properties. Using first-principles calculations, we explore the plausible mechanisms for the oxidative dehydrogenation (ODH) of propane to propene by GOs and the diffusion of the surface oxygen-containing groups under an external electric field. The present results show that GOs with modified oxygen-containing groups may afford high catalytic activity for the ODH of propane to propene. The presence of hydroxyl groups around the active sites provided by epoxides can remarkably enhance the C-H bond activation of propane and the activity enhancement exhibits strong site dependence. The sites of oxygen functional groups on the GO surface can be easily tuned by the diffusion of these groups under an external electric field, which increases the reactivity of GOs towards ODH of propane. The chemically modified GOs are thus quite promising in the design of metal-free catalysis. PMID:22801590

  11. Direct Visualization of Catalytically Active Sites at the FeO-Pt(111) Interface.

    PubMed

    Kudernatsch, Wilhelmine; Peng, Guowen; Zeuthen, Helene; Bai, Yunhai; Merte, Lindsay R; Lammich, Lutz; Besenbacher, Flemming; Mavrikakis, Manos; Wendt, Stefan

    2015-08-25

    Within the area of surface science, one of the "holy grails" is to directly visualize a chemical reaction at the atomic scale. Whereas this goal has been reached by high-resolution scanning tunneling microscopy (STM) in a number of cases for reactions occurring at flat surfaces, such a direct view is often inhibited for reaction occurring at steps and interfaces. Here we have studied the CO oxidation reaction at the interface between ultrathin FeO islands and a Pt(111) support by in situ STM and density functional theory (DFT) calculations. Time-lapsed STM imaging on this inverse model catalyst in O2 and CO environments revealed catalytic activity occurring at the FeO-Pt(111) interface and directly showed that the Fe-edges host the catalytically most active sites for the CO oxidation reaction. This is an important result since previous evidence for the catalytic activity of the FeO-Pt(111) interface is essentially based on averaging techniques in conjunction with DFT calculations. The presented STM results are in accord with DFT+U calculations, in which we compare possible CO oxidation pathways on oxidized Fe-edges and O-edges. We found that the CO oxidation reaction is more favorable on the oxidized Fe-edges, both thermodynamically and kinetically. PMID:26027877

  12. Direct Visualization of Catalytically Active Sites at the FeO-Pt(111) Interface

    SciTech Connect

    Kudernatsch, Wilhelmine; Peng, Guowen; Zeuthen, Helene; Bai, Yunhai; Merte, L. R.; Lammich, Lutz; Besenbacher, Fleming; Mavrikakis, Manos; Wendt, Stefen

    2015-08-25

    Within the area of surface science, one of the “holy grails” is to directly visualize a chemical reaction at the atomic scale. Whereas this goal has been reached by high-resolution scanning tunneling microscopy (STM) in a number of cases for reactions occurring at flat surfaces, such a direct view is often inhibited for reaction occurring at steps and interfaces. Here we have studied the CO oxidation reaction at the interface between ultrathin FeO islands and a Pt(111) support by in situ STM and density functional theory (DFT) calculations. Time-lapsed STM imaging on this inverse model catalyst in O2 and CO environments revealed catalytic activity occurring at the FeO-Pt(111) interface and directly showed that the Fe-edges host the catalytically most active sites for the CO oxidation reaction. This is an important result since previous evidence for the catalytic activity of the FeO-Pt(111) interface is essentially based on averaging techniques in conjunction with DFT calculations. The presented STM results are in accord with DFTþU calculations, in which we compare possible CO oxidation pathways on oxidized Fe-edges and O-edges. We found that the CO oxidation reaction is more favorable on the oxidized Fe-edges, both thermodynamically and kinetically.

  13. Dynamic formation of single-atom catalytic active sites on ceria-supported gold nanoparticles

    DOE PAGESBeta

    Wang, Yanggang; Mei, Donghai; Glezakou, Vassiliki Alexandra; Li, Jun; Rousseau, Roger J.

    2015-03-04

    Ab initio Molecular Dynamics simulations and static Density Functional Theory calculations have been performed to investigate the reaction mechanism of CO oxidation on Au/CeO2 catalyst. It is found that under reaction condition CO adsorption significantly labializes the surface atoms of the Au cluster and leads to the formation of isolated Au+-CO species that resides on the support in the vicinity of the Au particle. In this context, we identified a dynamic single-atom catalytic mechanism at the interfacial area for CO oxidation on Au/CeO2 catalyst, which is a lower energy pathway than that of CO oxidation at the interface with themore » metal particle. This results from the ability of the single atom site to strongly couple with the redox properties of the support in a synergistic manner thereby lowering the barrier for redox reactions. We find that the single Au+ ion, which only exists under reaction conditions, breaks away from the Au cluster to catalyze CO oxidation and returns to the Au cluster after the catalytic cycle is completed. Generally, our study highlights the importance of the dynamic creation of active sites under reaction conditions and their essential role in a catalytic process.« less

  14. Dynamic formation of single-atom catalytic active sites on ceria-supported gold nanoparticles

    SciTech Connect

    Wang, Yanggang; Mei, Donghai; Glezakou, Vassiliki Alexandra; Li, Jun; Rousseau, Roger J.

    2015-03-04

    Ab initio Molecular Dynamics simulations and static Density Functional Theory calculations have been performed to investigate the reaction mechanism of CO oxidation on Au/CeO2 catalyst. It is found that under reaction condition CO adsorption significantly labializes the surface atoms of the Au cluster and leads to the formation of isolated Au+-CO species that resides on the support in the vicinity of the Au particle. In this context, we identified a dynamic single-atom catalytic mechanism at the interfacial area for CO oxidation on Au/CeO2 catalyst, which is a lower energy pathway than that of CO oxidation at the interface with the metal particle. This results from the ability of the single atom site to strongly couple with the redox properties of the support in a synergistic manner thereby lowering the barrier for redox reactions. We find that the single Au+ ion, which only exists under reaction conditions, breaks away from the Au cluster to catalyze CO oxidation and returns to the Au cluster after the catalytic cycle is completed. Generally, our study highlights the importance of the dynamic creation of active sites under reaction conditions and their essential role in a catalytic process.

  15. Dynamic formation of single-atom catalytic active sites on ceria-supported gold nanoparticles

    SciTech Connect

    Wang, Yanggang; Mei, Donghai; Glezakou, Vassiliki Alexandra; Li, Jun; Rousseau, Roger J.

    2015-03-04

    Ab initio Molecular Dynamics simulations and static Density Functional Theory calculations have been performed to investigate the reaction mechanism of CO oxidation on Au/CeO2 catalyst. It is found that under reaction condition CO adsorption significantly labializes the surface atoms of the Au cluster and leads to the formation of isolated Au+-CO species that resides on the support in the vicinity of the Au particle. In this context, we identified a dynamic single-atom catalytic mechanism at the interfacial area for CO oxidation on Au/CeO2 catalyst, which is a lower energy pathway than that of CO oxidation at the interface with the metal particle. This results from the ability of the single atom site to strongly couple with the redox properties of the support in a synergistic manner thereby lowering the barrier for redox reactions. We find that the single Au+ ion, which only exists under reaction conditions, breaks away from the Au cluster to catalyze CO oxidation and returns to the Au cluster after the catalytic cycle is completed. Generally, our study highlights the importance of the dynamic creation of active sites under reaction conditions and their essential role in a catalytic process.

  16. Structural Insights into the Catalytic Active Site and Activity of Human Nit2/ω-Amidase

    PubMed Central

    Chien, Chin-Hsiang; Gao, Quan-Ze; Cooper, Arthur J. L.; Lyu, Jyun-Hong; Sheu, Sheh-Yi

    2012-01-01

    Human nitrilase-like protein 2 (hNit2) is a putative tumor suppressor, recently identified as ω-amidase. hNit2/ω-amidase plays a crucial metabolic role by catalyzing the hydrolysis of α-ketoglutaramate (the α-keto analog of glutamine) and α-ketosuccinamate (the α-keto analog of asparagine), yielding α-ketoglutarate and oxaloacetate, respectively. Transamination between glutamine and α-keto-γ-methiolbutyrate closes the methionine salvage pathway. Thus, hNit2/ω-amidase links sulfur metabolism to the tricarboxylic acid cycle. To elucidate the catalytic specificity of hNit2/ω-amidase, we performed molecular dynamics simulations on the wild type enzyme and its mutants to investigate enzyme-substrate interactions. Binding free energies were computed to characterize factors contributing to the substrate specificity. The predictions resulting from these computations were verified by kinetic analyses and mutational studies. The activity of hNit2/ω-amidase was determined with α-ketoglutaramate and succinamate as substrates. We constructed three catalytic triad mutants (E43A, K112A, and C153A) and a mutant with a loop 116–128 deletion to validate the role of key residues and the 116–128 loop region in substrate binding and turnover. The molecular dynamics simulations successfully verified the experimental trends in the binding specificity of hNit2/ω-amidase toward various substrates. Our findings have revealed novel structural insights into the binding of substrates to hNit2/ω-amidase. A catalytic triad and the loop residues 116–128 of hNit2 play an essential role in supporting the stability of the enzyme-substrate complex, resulting in the generation of the catalytic products. These observations are predicted to be of benefit in the design of new inhibitors or activators for research involving cancer and hyperammonemic diseases. PMID:22674578

  17. Differential Assembly of Catalytic Interactions within the Conserved Active Sites of Two Ribozymes

    PubMed Central

    Herschlag, Daniel

    2016-01-01

    Molecular recognition is central to biology and a critical aspect of RNA function. Yet structured RNAs typically lack the preorganization needed for strong binding and precise positioning. A striking example is the group I ribozyme from Tetrahymena, which binds its guanosine substrate (G) orders of magnitude slower than diffusion. Binding of G is also thermodynamically coupled to binding of the oligonucleotide substrate (S) and further work has shown that the transition from E•G to E•S•G accompanies a conformational change that allows G to make the active site interactions required for catalysis. The group I ribozyme from Azoarcus has a similarly slow association rate but lacks the coupled binding observed for the Tetrahymena ribozyme. Here we test, using G analogs and metal ion rescue experiments, whether this absence of coupling arises from a higher degree of preorganization within the Azoarcus active site. Our results suggest that the Azoarcus ribozyme forms cognate catalytic metal ion interactions with G in the E•G complex, interactions that are absent in the Tetrahymena E•G complex. Thus, RNAs that share highly similar active site architectures and catalyze the same reactions can differ in the assembly of transition state interactions. More generally, an ability to readily access distinct local conformational states may have facilitated the evolutionary exploration needed to attain RNA machines that carry out complex, multi-step processes. PMID:27501145

  18. Identification of catalytically important residues in the active site of Escherichia coli transaldolase.

    PubMed

    Schörken, U; Thorell, S; Schürmann, M; Jia, J; Sprenger, G A; Schneider, G

    2001-04-01

    The roles of invariant residues at the active site of transaldolase B from Escherichia coli have been probed by site-directed mutagenesis. The mutant enzymes D17A, N35A, E96A, T156A, and S176A were purified from a talB-deficient host and analyzed with respect to their 3D structure and kinetic behavior. X-ray analysis showed that side chain replacement did not induce unanticipated structural changes in the mutant enzymes. Three mutations, N35A, E96A, and T156A resulted mainly in an effect on apparent kcat, with little changes in apparent Km values for the substrates. Residues N35 and T156 are involved in the positioning of a catalytic water molecule at the active site and the side chain of E96 participates in concert with this water molecule in proton transfer during catalysis. Substitution of Ser176 by alanine resulted in a mutant enzyme with 2.5% residual activity. The apparent Km value for the donor substrate, fructose 6-phosphate, was increased nearly fivefold while the apparent Km value for the acceptor substrate, erythrose 4-phosphate remained unchanged, consistent with a function for S176 in the binding of the C1 hydroxyl group of the donor substrate. The mutant D17A showed a 300-fold decrease in kcat, and a fivefold increase in the apparent Km value for the acceptor substrate erythrose 4-phosphate, suggesting a role of this residue in carbon-carbon bond cleavage and stabilization of the carbanion/enamine intermediate. PMID:11298760

  19. Nature of Catalytic Active Sites Present on the Surface of Advanced Bulk Tantalum Mixed Oxide Photocatalysts

    SciTech Connect

    Phivilay, Somphonh; Puretzky, Alexander A; Domen, Kazunari Domen; Wachs, Israel

    2013-01-01

    The most active photocatalyst system for water splitting under UV irradiation (270 nm) is the promoted 0.2%NiO/NaTaO3:2%La photocatalyst with optimized photonic efficiency (P.E.) of 56%, but fundamental issues about the nature of the surface catalytic active sites and their involvement in the photocatalytic process still need to be clarified. This is the first study to apply cutting edge surface spectroscopic analyses to determine the surface nature of tantalum mixed oxide photocatalysts. Surface analysis with HR-XPS (1-3nm) and HS-LEIS (0.3nm) spectroscopy indicates that the NiO and La2O3 promoters are concentrated in the surface region of the bulk NaTaO3 phase. The La2O3 is concentrated on the NaTaO3 outermost surface layers while NiO is distributed throughout the NaTaO3 surface region (1-3nm). Raman and UV-vis spectroscopy revealed that the bulk molecular and electronic structures, respectively, of NaTaO3 were not modified by the addition of the La2O3 and NiO promoters, with La2O3 resulting in a slightly more ordered structure. Photoluminescence (PL) spectroscopy reveals that the addition of La2O3 and NiO produces a greater number of electron traps resulting in the suppression of the recombination of excited electrons/holes. In contrast to earlier reports, the La2O3 is only a textural promoter (increasing the BET surface area ~7x by stabilizing smaller NaTaO3 particles), but causes a ~3x decrease in the specific photocatalytic TORs ( mol H2/m2/h) rate because surface La2O3 blocks exposed catalytic active NaTaO3 sites. The NiO promoter was found to be a potent electronic promoter that enhances the NaTaO3 surface normalized TORs by a factor of ~10-50 and TOF by a factor of ~10. The level of NiO promotion is the same in the absence and presence of La2O3 demonstrating that there is no promotional synergistic interaction between the NiO and La2O3 promoters. This study demonstrates the important contributions of the photocatalyst surface properties to the fundamental

  20. The active site loop of S-adenosylmethionine synthetase modulates catalytic efficiency.

    PubMed

    Taylor, John C; Takusagawa, Fusao; Markham, George D

    2002-07-30

    Crystallographic studies of Escherichia coli S-adenosylmethionine synthetase (ATP:L-methionine S-adenosyltransferase, MAT) have defined a flexible polypeptide loop that can gate access to the active site without contacting the substrates. The influence of the length and sequence of this active site loop on catalytic efficiency has been characterized in a mutant in which the E. coli MAT sequence (DRADPLEQ) has been replaced with the distinct sequence of the corresponding region of the otherwise highly homologous rat liver enzyme (HDLRNEEDV). Four additional mutants in which the entire DRADPLEQ sequence was replaced by five, six, seven, or eight glycines have been studied to unveil the effects of loop length and the influence of side chains. In all of the mutants, the maximal rate of S-adenosylmethionine formation (k(cat)) is diminished by more than 200-fold whereas the rate of hydrolysis of the tripolyphosphate intermediate is decreased by less than 3-fold. Thus, the function of the loop is localized to the first step in the overall reaction. The K(m) for methionine increases in all of the oligoglycine mutants, whereas the K(m) values for ATP are not substantially different. The k(cat) for the wild-type enzyme is decreased by increases in solution microviscosity with 55% of the maximal dependence. Thus, a diffusional event is coupled to the chemical step of AdoMet formation, which is known to be rate-limiting. The results indicate that a conformational change, possibly loop closure, is associated with AdoMet synthesis. The data integrate a previously discovered conformational change associated with PPP(i) binding to the E x AdoMet complex into the reaction sequence, reflecting a difference in protein conformation in the E x AdoMet x PPP(i) complex whether it is formed from the E x ATP x methionine complex or from binding of exogenous PPP(i). The temperature dependence of the k(cat) for S-adenosylmethionine formation shows that the removal of the side chains in the

  1. A single active catalytic site is sufficient to promote transport in P-glycoprotein

    PubMed Central

    Bársony, Orsolya; Szalóki, Gábor; Türk, Dóra; Tarapcsák, Szabolcs; Gutay-Tóth, Zsuzsanna; Bacsó, Zsolt; Holb, Imre J.; Székvölgyi, Lóránt; Szabó, Gábor; Csanády, László; Szakács, Gergely; Goda, Katalin

    2016-01-01

    P-glycoprotein (Pgp) is an ABC transporter responsible for the ATP-dependent efflux of chemotherapeutic compounds from multidrug resistant cancer cells. Better understanding of the molecular mechanism of Pgp-mediated transport could promote rational drug design to circumvent multidrug resistance. By measuring drug binding affinity and reactivity to a conformation-sensitive antibody we show here that nucleotide binding drives Pgp from a high to a low substrate-affinity state and this switch coincides with the flip from the inward- to the outward-facing conformation. Furthermore, the outward-facing conformation survives ATP hydrolysis: the post-hydrolytic complex is stabilized by vanadate, and the slow recovery from this state requires two functional catalytic sites. The catalytically inactive double Walker A mutant is stabilized in a high substrate affinity inward-open conformation, but mutants with one intact catalytic center preserve their ability to hydrolyze ATP and to promote drug transport, suggesting that the two catalytic sites are randomly recruited for ATP hydrolysis. PMID:27117502

  2. A single active catalytic site is sufficient to promote transport in P-glycoprotein.

    PubMed

    Bársony, Orsolya; Szalóki, Gábor; Türk, Dóra; Tarapcsák, Szabolcs; Gutay-Tóth, Zsuzsanna; Bacsó, Zsolt; Holb, Imre J; Székvölgyi, Lóránt; Szabó, Gábor; Csanády, László; Szakács, Gergely; Goda, Katalin

    2016-01-01

    P-glycoprotein (Pgp) is an ABC transporter responsible for the ATP-dependent efflux of chemotherapeutic compounds from multidrug resistant cancer cells. Better understanding of the molecular mechanism of Pgp-mediated transport could promote rational drug design to circumvent multidrug resistance. By measuring drug binding affinity and reactivity to a conformation-sensitive antibody we show here that nucleotide binding drives Pgp from a high to a low substrate-affinity state and this switch coincides with the flip from the inward- to the outward-facing conformation. Furthermore, the outward-facing conformation survives ATP hydrolysis: the post-hydrolytic complex is stabilized by vanadate, and the slow recovery from this state requires two functional catalytic sites. The catalytically inactive double Walker A mutant is stabilized in a high substrate affinity inward-open conformation, but mutants with one intact catalytic center preserve their ability to hydrolyze ATP and to promote drug transport, suggesting that the two catalytic sites are randomly recruited for ATP hydrolysis. PMID:27117502

  3. Highly Ordered Mesoporous Cobalt-Containing Oxides: Structure, Catalytic Properties, and Active Sites in Oxidation of Carbon Monoxide.

    PubMed

    Gu, Dong; Jia, Chun-Jiang; Weidenthaler, Claudia; Bongard, Hans-Josef; Spliethoff, Bernd; Schmidt, Wolfgang; Schüth, Ferdi

    2015-09-01

    Co3O4 with a spinel structure is a very active oxide catalyst for the oxidation of CO. In such catalysts, octahedrally coordinated Co(3+) is considered to be the active site, while tetrahedrally coordinated Co(2+) is assumed to be basically inactive. In this study, a highly ordered mesoporous CoO has been prepared by H2 reduction of nanocast Co3O4 at low temperature (250 °C). The as-prepared CoO material, which has a rock-salt structure with a single Co(2+) octahedrally coordinated by lattice oxygen in Fm3̅m symmetry, exhibited unexpectedly high activity for CO oxidation. Careful investigation of the catalytic behavior of mesoporous CoO catalyst led to the conclusion that the oxidation of surface Co(2+) to Co(3+) causes the high activity. Other mesoporous spinels (CuCo2O4, CoCr2O4, and CoFe2O4) with different Co species substituted with non/low-active metal ions were also synthesized to investigate the catalytically active site of cobalt-based catalysts. The results show that not only is the octahedrally coordinated Co(3+) highly active but also the octahedrally coordinated Co(2+) species in CoFe2O4 with an inverse spinel structure shows some activity. These results suggest that the octahedrally coordinated Co(2+) species is easily oxidized and shows high catalytic activity for CO oxidation. PMID:26301797

  4. Experimental Active-Site Mapping by Fragments: Hot Spots Remote from the Catalytic Center of Endothiapepsin.

    PubMed

    Radeva, Nedyalka; Krimmer, Stefan G; Stieler, Martin; Fu, Kan; Wang, Xiaojie; Ehrmann, Frederik R; Metz, Alexander; Huschmann, Franziska U; Weiss, Manfred S; Mueller, Uwe; Schiebel, Johannes; Heine, Andreas; Klebe, Gerhard

    2016-08-25

    Successful optimization of a given lead scaffold requires thorough binding-site mapping of the target protein particular in regions remote from the catalytic center where high conservation across protein families is given. We screened a 361-entry fragment library for binding to the aspartic protease endothiapepsin by crystallography. This enzyme is frequently used as a surrogate for the design of renin and β-secretase inhibitors. A hit rate of 20% was achieved, providing 71 crystal structures. Here, we discuss 45 binding poses of fragments accommodated in pockets remote from the catalytic dyad. Three major hot spots are discovered in remote binding areas: Asp81, Asp119, and Phe291. Compared to the dyad binders, bulkier fragments occupy these regions. Many of the discovered fragments suggest an optimization concept on how to grow them into larger ligands occupying adjacent binding pockets that will possibly endow them with the desired selectivity for one given member of a protein family. PMID:27463859

  5. Simultaneous pore enlargement and introduction of highly dispersed Fe active sites in MSNs for enhanced catalytic activity

    SciTech Connect

    Gu Jinlou; Dong Xu; Elangovan, S.P.; Li Yongsheng; Zhao Wenru; Iijima, Toshio; Yamazaki, Yasuo; Shi Jianlin

    2012-02-15

    An effective post-hydrothermal treatment strategy has been developed to dope highly dispersed iron catalytical centers into the framework of mesoporous silica, to keep the particle size in nanometric scale, and in the meanwhile, to expand the pore size of the synthesized mesoporous silica nanoparticles (MSNs). Characterization techniques such as XRD, BET, SEM and TEM support that the synthesized samples are long period ordered with particles size about 100 nm and a relatively large pore size of ca. 3.5 nm. UV-vis, XPS and EPR measurements demonstrate that the introduced iron active centers are highly dispersed in a coordinatively unsaturated status. NH{sub 3}-TPD verifies that the acid amount of iron-doped MSNs is quite high. The synthesized nanocatalysts show an excellent catalytic performance for benzylation of benzene by benzyl chloride, and they present relatively higher yield and selectivity to diphenylmethane with a lower iron content and much shorter reaction time. - Graphical abstract: Uniform MSNs with iron active centers and large pore size have been prepared by a newly developed strategy, which demonstrates enhanced catalytic performance for benzylation of benzene by benzyl chloride. Highlights: Black-Right-Pointing-Pointer Iron species were introduced into the framework of mesoporous silica nanoparticles with uniform dispersion. Black-Right-Pointing-Pointer The pore sizes of the synthesized nanocatalysts were expanded. Black-Right-Pointing-Pointer The acidic site quantities were quite high and the acidic centers were accessible. Black-Right-Pointing-Pointer The nanocatalysts presented higher yield and selectivity to diphenylmethane with significantly lower Fe content.

  6. Dimer-dimer interaction of the bacterial selenocysteine synthase SelA promotes functional active site formation and catalytic specificity

    PubMed Central

    Itoh, Yuzuru; Bröcker, Markus J.; Sekine, Shun-ichi; Söll, Dieter; Yokoyama, Shigeyuki

    2015-01-01

    The 21st amino acid, selenocysteine (Sec), is incorporated translationally into proteins, and is synthesized on its specific tRNA (tRNASec). In Bacteria, the selenocysteine synthase SelA converts Ser-tRNASec, formed by seryl-tRNA synthetase, to Sec-tRNASec. SelA, a member of the fold-type-I pyridoxal 5′-phosphate (PLP)-dependent enzyme superfamily, has an exceptional homodecameric quaternary structure with a molecular mass of about 500 kDa. Our previously determined crystal structures of Aquifex aeolicus SelA complexed with tRNASec revealed that the ring-shaped decamer is composed of pentamerized SelA dimers, with two SelA dimers arranged to collaboratively interact with one Ser-tRNASec. The SelA catalytic site is close to the dimer-dimer interface, but the significance of the dimer-pentamerization in the catalytic site formation remained elusive. In the present study, we examined the quaternary interactions, and demonstrated their importance for SelA activity by systematic mutagenesis. Furthermore, we determined the crystal structures of “depentamerized” SelA variants with mutations at the dimer-dimer interface that prevent pentamerization. These dimeric SelA variants formed a distorted and inactivated catalytic site, and confirmed that the pentamer interactions are essential for productive catalytic site formation. Intriguingly, the conformation of the non-functional active site of dimeric SelA shares structural features with other fold-type-I PLP-dependent enzymes with native dimer or tetramer (dimer-of-dimers) quaternary structures. PMID:24456689

  7. Efficient Catalytic Ozonation over Reduced Graphene Oxide for p-Hydroxylbenzoic Acid (PHBA) Destruction: Active Site and Mechanism.

    PubMed

    Wang, Yuxian; Xie, Yongbing; Sun, Hongqi; Xiao, Jiadong; Cao, Hongbin; Wang, Shaobin

    2016-04-20

    Nanocarbons have been demonstrated as promising environmentally benign catalysts for advanced oxidation processes (AOPs) upgrading metal-based materials. In this study, reduced graphene oxide (rGO) with a low level of structural defects was synthesized via a scalable method for catalytic ozonation of p-hydroxylbenzoic acid (PHBA). Metal-free rGO materials were found to exhibit a superior activity in activating ozone for catalytic oxidation of organic phenolics. The electron-rich carbonyl groups were identified as the active sites for the catalytic reaction. Electron spin resonance (ESR) and radical competition tests revealed that superoxide radical ((•)O2(-)) and singlet oxygen ((1)O2) were the reactive oxygen species (ROS) for PHBA degradation. The intermediates and the degradation pathways were illustrated from mass spectroscopy. It was interesting to observe that addition of NaCl could enhance both ozonation and catalytic ozonation efficiencies and make ·O2(-) as the dominant ROS. Stability of the catalysts was also evaluated by the successive tests. Loss of specific surface area and changes in the surface chemistry were suggested to be responsible for catalyst deactivation. PMID:27007603

  8. Examination of an active-site electrostatic node in the cAMP-dependent protein kinase catalytic subunit.

    PubMed Central

    Grant, B. D.; Tsigelny, I.; Adams, J. A.; Taylor, S. S.

    1996-01-01

    The active site of the cAMP-dependent protein kinase catalytic subunit harbors a cluster of acidic residues-Asp 127, Glu 170, Glu 203, Glu 230, and Asp 241-that are not conserved throughout the protein kinase family. Based on crystal structures of the catalytic subunit, these amino acids are removed from the site of phosphoryl transfer and are implicated in substrate recognition. Glu 230, the most buried of these acidic residues, was mutated to Ala (rC[E230A]) and Gln (rC[E230Q]) and overexpressed in Escherichia coli. In contrast to the mostly insoluble and destabilized rC[E230A], rC[E230Q] is largely soluble, purifies like wild-type enzyme, and displays wild-type-like thermal stability. The mutation in rC[E230Q] causes an order of magnitude decrease in the affinity for a heptapeptide substrate, Kemptide. In addition, two independent kinetic techniques were used to dissect phosphoryl transfer and product release steps in the reaction pathway. Viscosometric and pre-steady-state quench-flow analyses revealed that the phosphoryl transfer rate constant decreases by an order of magnitude, whereas the product release rate constant remains unperturbed. Electrostatic alterations in the rC[E230Q] active site were assessed using modeling techniques that provide molecular interpretations for the substrate affinity and phosphoryl transfer rate decreases observed experimentally. These observations indicate that subsite recognition elements in the catalytic subunit make electrostatic contributions that are important not only for peptide affinity, but also for catalysis. Protein kinases may, therefore, discriminate substrates by not only binding them tightly, but also by only turning over ones that complement the electrostatic character of the active site. PMID:8819164

  9. Effect of chromium oxide as active site over TiO2-PILC for selective catalytic oxidation of NO.

    PubMed

    Zhang, Jingxin; Zhang, Shule; Cai, Wei; Zhong, Qin

    2013-12-01

    This study introduced TiO2-pillared clays (TiO2-PILC) as a support for the catalytic oxidation of NO and analyzed the performance of chromium oxides as the active site of the oxidation process. Cr-based catalysts were prepared by a wet impregnation method. It was found that the 10 wt.% chromium doping on the support achieved the best catalytic activity. At 350 degrees C, the NO conversion was 61% under conditions of GHSV = 23600 hr(-1). The BET data showed that the support particles had a mesoporous structure. H2-TPR showed that Cr(10)TiP (10 wt.% Cr doping on TiO2-PILC) clearly exhibited a smooth single peak. EPR and XPS were used to elucidate the oxidation process. During the NO + O2 adsorption, the intensity of evolution of superoxide ions (O2(-)) increased. The content of Cr3+ on the surface of the used catalyst was 40.37%, but when the used catalyst continued adsorbing NO, the Cr3+ increased to 50.28%. Additionally, O(alpha)/O(beta) increased markedly through the oxidation process. The NO conversion decreased when SO2 was added into the system, but when the SO2 was removed, the catalytic activity recovered almost up to the initial level. FT-IR spectra did not show a distinct characteristic peak of SO4(2-). PMID:24649682

  10. Active-site motions and polarity enhance catalytic turnover of hydrated subtilisin dissolved in organic solvents.

    PubMed

    Hudson, Elton P; Eppler, Ross K; Beaudoin, Julianne M; Dordick, Jonathan S; Reimer, Jeffrey A; Clark, Douglas S

    2009-04-01

    The enzyme subtilisin Carlsberg was surfactant-solubilized into two organic solvents, isooctane and tetrahydrofuran, and hydrated through stepwise changes in the thermodynamic water activity, a(w). The apparent turnover number k(cat)(app) in these systems ranged from 0.2 to 80 s(-1) and increased 11-fold in isooctane and up to 50-fold in tetrahydrofuran with increasing a(w). (19)F NMR relaxation experiments employing an active-site inhibitor were used to assess the dependence of active-site motions on a(w). The rates of NMR-derived fast (k > 10(7) s(-1)) and slow (k < 10(4) s(-1)) active-site motions increased in both solvents upon hydration, but only the slow motions correlated with k(cat). The (19)F chemical shift was a sensitive probe of the local electronic environment and provided an empirical measure of the active-site dielectric constant epsilon(as), which increased with hydration to epsilon(as) approximately 13 in each solvent. In both solvents, the transition state free energy data and epsilon(as) followed Kirkwood's model for the continuum solvation of a dipole, indicating that water also enhanced catalysis by altering the active-site's electronic environment and increasing its polarity to better stabilize the transition state. These results reveal that favorable dynamic and electrostatic effects both contribute to accelerated catalysis by solubilized subtilisin Carlsberg upon hydration in organic solvents. PMID:19317505

  11. Understanding the effect of magnesium ion concentration on the catalytic activity of ribonuclease H through computation: Does a third metal binding site modulate endonuclease activity?

    PubMed Central

    Ho, Ming-Hsun; De Vivo, Marco; Peraro, Matteo Dal; Klein, Michael L.

    2010-01-01

    Ribonuclease H (RNase H) belongs to the nucleotidyl-transferase (NT) superfamily and hydrolyzes the phosphodiester linkage on the RNA strand of a DNA/RNA hybrid duplex. Due to its activity in HIV reverse transcription, it represents a promising target for anti-HIV drug design. While crystallographic data have located two ions in the catalytic site, there is ongoing debate concerning just how many metal ions bound at the active site are optimal for catalysis. Indeed, experiments have shown a dependency of the catalytic activity on the Mg2+ concentration. Moreover, in RNase H the glutamate residue E188 has been shown to be essential for full enzymatic activation regardless of the Mg2+ concentration. The catalytic center is known to contain two Mg2+ ions (Nowotny et al.) and E188 is not one of the primary metal ligands. Herein, classical molecular dynamics (MD) simulations are employed to study the metal-ligand coordination in RNase H at different concentration of Mg2+. Importantly, the presence of a third Mg2+ ion, bound to the second-shell ligand E188, is persistent feature of the MD simulations. Free energy calculations have identified two distinct conformations depending on the concentration of Mg2+. At standard concentration, a third Mg2+ is found in the catalytic pocket but it does not perturb the optimal RNase H active conformation. However, at higher concentration, the third Mg2+ ion heavily perturbs the nucleophilic water and thereby influences the catalytic efficiency of RNase H. In addition, the E188A mutant shows no ability to engage additional Mg2+ ions nearby the catalytic pocket. This finding likely explains the decrease in catalytic activity of E188A, and also supports the key role of E188 in localizing the third Mg2+ ion at the active site. Glutamate residues are commonly found surrounding the metal center in the endonuclease family, which suggests that this structural motif may be an important feature to enhance catalytic activity. The present MD

  12. Analyzing the catalytic role of active site residues in the Fe-type nitrile hydratase from Comamonas testosteroni Ni1.

    PubMed

    Martinez, Salette; Wu, Rui; Krzywda, Karoline; Opalka, Veronika; Chan, Hei; Liu, Dali; Holz, Richard C

    2015-07-01

    A strictly conserved active site arginine residue (αR157) and two histidine residues (αH80 and αH81) located near the active site of the Fe-type nitrile hydratase from Comamonas testosteroni Ni1 (CtNHase), were mutated. These mutant enzymes were examined for their ability to bind iron and hydrate acrylonitrile. For the αR157A mutant, the residual activity (k cat = 10 ± 2 s(-1)) accounts for less than 1% of the wild-type activity (k cat = 1100 ± 30 s(-1)) while the K m value is nearly unchanged at 205 ± 10 mM. On the other hand, mutation of the active site pocket αH80 and αH81 residues to alanine resulted in enzymes with k cat values of 220 ± 40 and 77 ± 13 s(-1), respectively, and K m values of 187 ± 11 and 179 ± 18 mM. The double mutant (αH80A/αH81A) was also prepared and provided an enzyme with a k cat value of 132 ± 3 s(-1) and a K m value of 213 ± 61 mM. These data indicate that all three residues are catalytically important, but not essential. X-ray crystal structures of the αH80A/αH81A, αH80W/αH81W, and αR157A mutant CtNHase enzymes were solved to 2.0, 2.8, and 2.5 Å resolutions, respectively. In each mutant enzyme, hydrogen-bonding interactions crucial for the catalytic function of the αCys(104)-SOH ligand are disrupted. Disruption of these hydrogen bonding interactions likely alters the nucleophilicity of the sulfenic acid oxygen and the Lewis acidity of the active site Fe(III) ion. PMID:26077812

  13. Active-site motions and polarity enhance catalytic turnover of hydrated subtilisin dissolved in organic solvents

    PubMed Central

    Hudson, Elton P; Eppler, Ross K; Beaudoin, Julianne M; Dordick, Jonathan S; Reimer, Jeffrey A; Clark, Douglas S

    2009-01-01

    The enzyme subtilisin Carlsberg was surfactant-solubilized into two organic solvents, isooctane and tetrahydrofuran, and hydrated through stepwise changes in the thermodynamic water activity, aw. The apparent turnover number kcatapp in these systems ranged from 0.2 to 80 s−1 and increased 11-fold in isooctane and up to 50-fold in tetrahydrofuran with increasing aw. 19F-NMR relaxation experiments employing an active-site inhibitor were used to assess the dependence of active-site motions on aw. The rates of NMR-derived fast (k > 107 s−1) and slow (k < 104 s−1) active-site motions increased in both solvents upon hydration, but only the slow motions correlated with kcat. The 19F chemical shift was a sensitive probe of the local electronic environment and provided an empirical measure of the active-site dielectric constant εas, which increased with hydration to εas ≈ 13 in each solvent. In both solvents the transition state free energy data and εas followed Kirkwood’s model for the continuum solvation of a dipole, indicating that water also enhanced catalysis by altering the active-site’s electronic environment and increasing its polarity to better stabilize the transition state. These results reveal that favorable dynamic and electrostatic effects both contribute to accelerated catalysis by solubilized subtilisin Carlsberg upon hydration in organic solvents. PMID:19317505

  14. An active site rearrangement within the Tetrahymena group I ribozyme releases nonproductive interactions and allows formation of catalytic interactions.

    PubMed

    Sengupta, Raghuvir N; Van Schie, Sabine N S; Giambaşu, George; Dai, Qing; Yesselman, Joseph D; York, Darrin; Piccirilli, Joseph A; Herschlag, Daniel

    2016-01-01

    Biological catalysis hinges on the precise structural integrity of an active site that binds and transforms its substrates and meeting this requirement presents a unique challenge for RNA enzymes. Functional RNAs, including ribozymes, fold into their active conformations within rugged energy landscapes that often contain misfolded conformers. Here we uncover and characterize one such "off-pathway" species within an active site after overall folding of the ribozyme is complete. The Tetrahymena group I ribozyme (E) catalyzes cleavage of an oligonucleotide substrate (S) by an exogenous guanosine (G) cofactor. We tested whether specific catalytic interactions with G are present in the preceding E•S•G and E•G ground-state complexes. We monitored interactions with G via the effects of 2'- and 3'-deoxy (-H) and -amino (-NH(2)) substitutions on G binding. These and prior results reveal that G is bound in an inactive configuration within E•G, with the nucleophilic 3'-OH making a nonproductive interaction with an active site metal ion termed MA and with the adjacent 2'-OH making no interaction. Upon S binding, a rearrangement occurs that allows both -OH groups to contact a different active site metal ion, termed M(C), to make what are likely to be their catalytic interactions. The reactive phosphoryl group on S promotes this change, presumably by repositioning the metal ions with respect to G. This conformational transition demonstrates local rearrangements within an otherwise folded RNA, underscoring RNA's difficulty in specifying a unique conformation and highlighting Nature's potential to use local transitions of RNA in complex function. PMID:26567314

  15. Catalytic roles of flexible regions at the active site of ribulose-bisphosphate carboxylase/oxygenase (Rubisco)

    SciTech Connect

    Hartman, F.C.; Harpel, M.R.; Chen, Yuh-Ru; Larson, E.M.; Larimer, F.W.

    1995-12-31

    Chemical and mutagenesis studies of Rubisco have identified Lys329 and Glu48 as active-site residues that are located in distinct, interacting domains from adjacent subunits. Crystallographic analyses have shown that Lys329 is the apical residue in a 12-residue flexible loop (loop 6) of the {Beta},{alpha}-barrel domain of the active site and that Glu48 resides at the end of helix B of the N-terminal domain of the active site. When phosphorylated ligands are bound by the enzyme, loop 6 adopts a closed conformation and, in concert with repositioning of helix B, thereby occludes the active site from the external environment. In this closed conformation, the {gamma}-carboxylate of Glu48 and the {epsilon}-amino group of Lys329 engage in intersubunit electrostatic interaction. By use of appropriate site-directed mutants of Rhodospirillum rubrum Rubisco, we are addressing several issues: the catalytic roles of Lys329 and Glu48, the functional significance of the intersubunit salt bridge comprised of these two residues, and the roles of loop 6 and helix B in stabilizing labile reaction intermediates. Characterization of novel products derived from misprocessing of D-ribulose-1,5-bisphosphate (RuBP) by the mutant proteins have illuminated the structure of the key intermediate in the normal oxygenase pathway.

  16. Substrate conformational transitions in the active site of chorismate mutase: Their role in the catalytic mechanism

    PubMed Central

    Guo, Hong; Cui, Qiang; Lipscomb, William N.; Karplus, Martin

    2001-01-01

    Chorismate mutase acts at the first branch-point of aromatic amino acid biosynthesis and catalyzes the conversion of chorismate to prephenate. The results of molecular dynamics simulations of the substrate in solution and in the active site of chorismate mutase are reported. Two nonreactive conformers of chorismate are found to be more stable than the reactive pseudodiaxial chair conformer in solution. It is shown by QM/MM molecular dynamics simulations, which take into account the motions of the enzyme, that when these inactive conformers are bound to the active site, they are rapidly converted to the reactive chair conformer. This result suggests that one contribution of the enzyme is to bind the more prevalent nonreactive conformers and transform them into the active form in a step before the chemical reaction. The motion of the reactive chair conformer in the active site calculated by using the QM/MM potential generates transient structures that are closer to the transition state than is the stable CHAIR conformer. PMID:11481470

  17. Catalytic site interactions in yeast OMP synthase.

    PubMed

    Hansen, Michael Riis; Barr, Eric W; Jensen, Kaj Frank; Willemoës, Martin; Grubmeyer, Charles; Winther, Jakob R

    2014-01-15

    The enigmatic kinetics, half-of-the-sites binding, and structural asymmetry of the homodimeric microbial OMP synthases (orotate phosphoribosyltransferase, EC 2.4.2.10) have been proposed to result from an alternating site mechanism in these domain-swapped enzymes [R.W. McClard et al., Biochemistry 45 (2006) 5330-5342]. This behavior was investigated in the yeast enzyme by mutations in the conserved catalytic loop and 5-phosphoribosyl-1-diphosphate (PRPP) binding motif. Although the reaction is mechanistically sequential, the wild-type (WT) enzyme shows parallel lines in double reciprocal initial velocity plots. Replacement of Lys106, the postulated intersubunit communication device, produced intersecting lines in kinetic plots with a 2-fold reduction of kcat. Loop (R105G K109S H111G) and PRPP-binding motif (D131N D132N) mutant proteins, each without detectable enzymatic activity and ablated ability to bind PRPP, complemented to produce a heterodimer with a single fully functional active site showing intersecting initial velocity plots. Equilibrium binding of PRPP and orotidine 5'-monophosphate showed a single class of two binding sites per dimer in WT and K106S enzymes. Evidence here shows that the enzyme does not follow half-of-the-sites cooperativity; that interplay between catalytic sites is not an essential feature of the catalytic mechanism; and that parallel lines in steady-state kinetics probably arise from tight substrate binding. PMID:24262852

  18. In silico Investigation of the PglB Active Site Reveals Transient Catalytic States and Octahedral Metal Ion Coordination.

    PubMed

    Pedebos, Conrado; Arantes, Pablo Ricardo; Giesel, Guilherme Menegon; Verli, Hugo

    2015-11-01

    The last step of the bacterial N-glycosylation pathway involves PglB, an oligosaccharyltransferase, which is responsible for the en bloc transfer of a fully assembled oligosaccharide chain to a protein possessing the extended motif D/E-X-N-X-S/T. Recently, this molecule had its full structure elucidated, enabling the description of its domains and the proposition of a catalytic mechanism. By employing molecular dynamics simulations, we were able to evaluate structural aspects of PglB, suggesting prevalent motions that may bring insights into the mechanism of the glycosylated peptide detachment. Additionally, we identified transient states at the catalytic site, in which the previously described carboxamide twisting mechanism was observed. Aided by quantum mechanics calculations for each different conformational states of the catalytic site, we determined the presence of an octahedral metal coordination, along with the presence of one water molecule at the catalytic site. PMID:26220543

  19. Structural Mutations that Probe the Interactions between the Catalytic and Dianion Activation Sites at Triosephosphate Isomerase‡

    PubMed Central

    Zhai, Xiang; Amyes, Tina L.; Wierenga, Rik K.; Loria, J. Patrick; Richard, John P.

    2013-01-01

    Triosephosphate isomerase (TIM) catalyzes the isomerization of dihydroxyacetone phosphate to form D-glyceraldehyde 3-phosphate. The effects of two structural mutations at TIM on the kinetic parameters for catalysis of the reaction of the truncated substrate glycolaldehyde (GA) and the activation of this reaction by phosphite dianion are reported. The P168A mutation results in similar 50-fold and 80-fold decreases, respectively, in (kcat/Km)E and (kcat/Km)E•HPi for deprotonation of GA catalyzed by free TIM and by the TIM•HPO32− complex. The mutation has little effect on the observed and intrinsic phosphite dianion binding energy, or on the magnitude of phosphite dianion activation of TIM for catalysis of deprotonation of GA. A loop 7 replacement mutant (L7RM) of TIM from chicken muscle was prepared by substitution of the archaeal sequence 208-TGAG for 208-YGGS. The L7RM exhibits a 25-fold decrease in (kcat/Km)E and a larger 170-fold decrease in (kcat/Km)E•HPi for reactions of GA. The mutation has little effect on the observed and intrinsic phosphodianion binding energy, and only a modest effect on phosphite dianion activation of TIM. The observation that both the P168A and loop 7 replacement mutations affect mainly the kinetic parameters for TIM-catalyzed deprotonation, but result in much smaller changes in the parameters for enzyme activation by phosphite dianion provide support for the conclusion that catalysis of proton transfer and dianion activation of TIM take place at separate, weakly interacting, sites in the protein catalyst. PMID:23909928

  20. Structural definition of the active site and catalytic mechanism of 3,4-dihydroxy-2-butanone-4-phosphate synthase.

    PubMed

    Liao, Der-Ing; Zheng, Ya-Jun; Viitanen, Paul V; Jordan, Douglas B

    2002-02-12

    X-ray crystal structures of L-3,4-dihydroxy-2-butanone-4-phosphate synthase from Magnaporthe grisea are reported for the E-SO(4)(2-), E-SO(4)(2-)-Mg(2+), E-SO(4)(2)(-)-Mn(2+), E-SO(4)(2)(-)-Mn(2+)-glycerol, and E-SO(4)(2)(-)-Zn(2+) complexes with resolutions that extend to 1.55, 0.98, 1.60, 1.16, and 1.00 A, respectively. Active-site residues of the homodimer are fully defined. The structures were used to model the substrate ribulose 5-phosphate in the active site with the phosphate group anchored at the sulfate site and the placement of the ribulose group guided by the glycerol site. The model includes two Mg(2+) cations that bind to the oxygen substituents of the C2, C3, C4, and phosphate groups of the substrate, the side chains of Glu37 and His153, and water molecules. The position of the metal cofactors and the substrate's phosphate group are further stabilized by an extensive hydrogen-bond and salt-bridge network. On the basis of their proximity to the substrate's reaction participants, the imidazole of an Asp99-His136 dyad from one subunit, the side chains of the Asp41, Cys66, and Glu174 residues from the other subunit, and Mg(2+)-activated water molecules are proposed to serve specific roles in the catalytic cycle as general acid-base functionalities. The model suggests that during the 1,2-shift step of the reaction, the substrate's C3 and C4 hydroxyl groups are cis to each other. A cis transition state is calculated to have an activation barrier that is 2 kcal/mol greater than that of the trans transition state in the absence of the enzyme. PMID:11827524

  1. Structural definition of the active site and catalytic mechanism of 3,4-dihydroxy-2-butanone 4-phosphate synthase

    SciTech Connect

    Liao, D.-I.; Zheng, Y.-J.; Viitanen, P.V.; Jordan, D.B.

    2010-03-08

    X-ray crystal structures of L-3,4-dihydroxy-2-butanone-4-phosphate synthase from Magnaporthe grisea are reported for the E-SO{sub 4}{sup 2-}, E-{sub 4}{sup 2-}-Mg{sup 2+}, E-SO{sub 4}{sup 2-}-Mn{sup 2+}, E-SO{sub 4}{sup 2-}-Mn{sup 2+}-glycerol, and E-SO{sub 4}{sup 2-}-Zn{sup 2+} complexes with resolutions that extend to 1.55, 0.98, 1.60, 1.16, and 1.00 {angstrom}, respectively. Active-site residues of the homodimer are fully defined. The structures were used to model the substrate ribulose 5-phosphate in the active site with the phosphate group anchored at the sulfate site and the placement of the ribulose group guided by the glycerol site. The model includes two Mg{sup 2+} cations that bind to the oxygen substituents of the C2, C3, C4, and phosphate groups of the substrate, the side chains of Glu37 and His153, and water molecules. The position of the metal cofactors and the substrate's phosphate group are further stabilized by an extensive hydrogen-bond and salt-bridge network. On the basis of their proximity to the substrate's reaction participants, the imidazole of an Asp99-His136 dyad from one subunit, the side chains of the Asp41, Cys66, and Glu174 residues from the other subunit, and Mg{sup 2+}-activated water molecules are proposed to serve specific roles in the catalytic cycle as general acid-base functionalities. The model suggests that during the 1,2-shift step of the reaction, the substrate's C3 and C4 hydroxyl groups are cis to each other. A cis transition state is calculated to have an activation barrier that is 2 kcal/mol greater than that of the trans transition state in the absence of the enzyme.

  2. The C-terminal tail inhibitory phosphorylation sites of PTEN regulate its intrinsic catalytic activity and the kinetics of its binding to phosphatidylinositol-4,5-bisphosphate.

    PubMed

    Chia, Yeong-Chit Joel; Catimel, Bruno; Lio, Daisy Sio Seng; Ang, Ching-Seng; Peng, Benjamin; Wu, Hong; Zhu, Hong-Jian; Cheng, Heung-Chin

    2015-12-01

    Dephosphorylation of four major C-terminal tail sites and occupancy of the phosphatidylinositol-4,5-bisphosphate [PI(4,5)P2]-binding site of PTEN cooperate to activate its phospholipid phosphatase activity and facilitate its recruitment to plasma membrane. Our investigation of the mechanism by which phosphorylation of these C-terminal sites controls the PI(4,5)P2-binding affinity and catalytic activity of PTEN resulted in the following findings. First, dephosphorylation of all four sites leads to full activation; and phosphorylation of any one site significantly reduces the intrinsic catalytic activity of PTEN. These findings suggest that coordinated inhibition of the upstream protein kinases and activation of the protein phosphatases targeting the four sites are needed to fully activate PTEN phosphatase activity. Second, PI(4,5)P2 cannot activate the phosphopeptide phosphatase activity of PTEN, suggesting that PI(4,5)P2 can only activate the phospholipid phosphatase activity but not the phosphoprotein phosphatase activity of PTEN. Third, dephosphorylation of all four sites significantly decreases the affinity of PTEN for PI(4,5)P2. Since PI(4,5)P2 is a major phospholipid co-localizing with the phospholipid- and phosphoprotein-substrates in plasma membrane, we hypothesise that the reduced affinity facilitates PTEN to "hop" on the plasma membrane to dephosphorylate these substrates. PMID:26471078

  3. The crystal structure of Escherichia coli heat shock protein YedU reveals three potential catalytic active sites

    PubMed Central

    Zhao, Yonghong; Liu, Deqian; Kaluarachchi, Warna D.; Bellamy, Henry D.; White, Mark A.; Fox, Robert O.

    2003-01-01

    The mRNA of Escherichia coli yedU gene is induced 31-fold upon heat shock. The 31-kD YedU protein, also calls Hsp31, is highly conserved in several human pathogens and has chaperone activity. We solved the crystal structure of YedU at 2.2 Å resolution. YedU monomer has an α/β/α sandwich domain and a small α/β domain. YedU is a dimer in solution, and its crystal structure indicates that a significant amount of surface area is buried upon dimerization. There is an extended hydrophobic patch that crosses the dimer interface on the surface of the protein. This hydrophobic patch is likely the substrate-binding site responsible for the chaperone activity. The structure also reveals a potential protease-like catalytic triad composed of Cys184, His185, and Asp213, although no enzymatic activity could be identified. YedU coordinates a metal ion using His85, His122, and Glu90. This 2-His-1-carboxylate motif is present in carboxypeptidase A (a zinc enzyme), and a number of dioxygenases and hydroxylases that utilize iron as a cofactor, suggesting another potential function for YedU. PMID:14500888

  4. Active site mutants of Escherichia coli dethiobiotin synthetase: effects of mutations on enzyme catalytic and structural properties.

    PubMed

    Yang, G; Sandalova, T; Lohman, K; Lindqvist, Y; Rendina, A R

    1997-04-22

    Five active site residues, Thr11, Glu12, Lys15, Lys37, and Ser41, implicated by the protein crystal structure studies of Escherichia coli DTBS, were mutated to determine their function in catalysis and substrate binding. Nine mutant enzymes, T11V, E12A, E12D, K15Q, K37L, K37Q, K37R, S41A, and S41C, were overproduced in an E. coli strain lacking a functional endogenous DTBS gene and purified to homogeneity. Replacement of Thr11 with valine resulted in a 24,000-fold increase in the Km(ATP) with little or no change in the Kd(ATP), KM(DAPA) and DTBS k(cat), suggesting an essential role for this residue in the steady-state affinity for ATP. The two Glu12 mutants showed essentially wild-type DTBS activity (slightly elevated k(cat)'s). Unlike wild-type DTBS, E12A had the same apparent KM(DAPA) at subsaturating and saturating ATP concentrations, indicating a possible role for Glu12 in the binding synergy between DAPA and ATP. The mutations in Lys15 and Lys37 resulted in loss of catalytic activity (0.01% and <0.9% of wild-type DTBS k(cat) for K15Q and the Lys37 mutant enzymes, respectively) and higher KM's for both DAPA (40-fold and >100-fold higher than wild-type for the K15Q and Lys37 mutant enzymes, respectively) and ATP (1800-fold and >10-fold higher than wild-type for K15Q and the K37 mutant enzymes, respectively). These results strongly suggest that Lys15 and Lys37 are crucial to both catalysis and substrate binding. S41A and S41C had essentially the same k(cat) as wild-type and had moderate increases in the DAPA and ATP KM and Kd (ATP) values. Replacement of Ser41 with cysteine resulted in larger effects than replacement with alanine. These data suggest that the H-bond between N7 of DAPA and the Ser41 side chain is not very important for catalysis. The catalytic behavior of these mutant enzymes was also studied by pulse-chase experiments which produced results consistent with the steady-state kinetic analyses. X-ray crystallographic studies of four mutant enzymes, S

  5. Comparative Enzymology in the Alkaline Phosphatase Superfamily to Determine the Catalytic Role of an Active Site Metal Ion

    PubMed Central

    Zalatan, Jesse G.; Fenn, Timothy D.; Herschlag, Daniel

    2009-01-01

    Mechanistic models for biochemical systems are frequently proposed from structural data. Site-directed mutagenesis can be used to test the importance of proposed functional sites, but these data do not necessarily indicate how these sites contribute to function. Herein we apply an alternative approach to the catalytic mechanism of alkaline phosphatase (AP), a widely-studied, prototypical bimetallo enzyme. A third metal ion site in AP has been suggested to provide general base catalysis, but comparison with an evolutionarily-related enzyme casts doubt on this model. Removal of this metal site from AP has large differential effects on reactions of cognate and promiscuous substrates, and the results are inconsistent with general base catalysis. Instead, these and additional results suggest that the third metal ion stabilizes the transferred phosphoryl group in the transition state. These results establish a new mechanistic model for this prototypical bimetallo enzyme and demonstrate the power of a comparative approach for probing biochemical function. PMID:18851975

  6. On the mechanism of sulfite activation of chloroplast thylakoid ATPase and the relation of ADP tightly bound at a catalytic site to the binding change mechanism

    SciTech Connect

    Du, Z.; Boyer, P.D. )

    1990-01-16

    Washed chloroplast thylakoid membranes upon exposure to ({sup 3}H)ADP retain in tightly bound ({sup 3}H)ADP on a catalytic site of the ATP synthase. The presence of sufficient endogenous or added Mg{sup 2+} results in an enzyme with essentially no ATPase activity. Sulfite activates the ATPase, and many molecules of ATP per synthase can be hydrolyzed before most of the bound ({sup 3}H)ADP is released, a result interpreted as indicating that the ADP is not bound at a site participating in catalysis by the sulfite-activated enzyme. The authors present evidence that this is not the case. The Mg{sup 2+}- and ADP-inhibited enzyme when exposed to MgATP and 20-100 mM sulfite shows a lag of about 1 min at 22{degree}C and of about 15 s at 37{degree}C before reaching the same steady-state rate as attained with light-activated ATPase that has not been inhibited by Mg{sup 2+} and ADP. The lag is not eliminated if the enzyme is exposed to sulfite prior to MgATP addition, indicating that ATPase turnover is necessary for the activation. The release of most of the bound ({sup 3}H)ADP parallels the onset of ATPase activity, although some ({sup 3}H)ADP is not released even with prolonged catalytic turnover and may be on poorly active or inactive enzyme or at noncatalytic sites. The results are consistent with most of the tightly bound ({sup 3}H)ADP being at a catalytic site and being replaced as this Mg{sup 2+}- and ADP-inhibited site regains equivalent participation with other catalytic sites on the activated enzyme. The sulfite activation can be explained by sulfite combination at a P{sub i} binding site of the enzyme-ADP-Mg{sup 2+} complex to give a form more readily activated by ATP binding at an alternative site.

  7. Identification of two catalytic residues in RAG1 that define a single active site within the RAG1/RAG2 protein complex.

    PubMed

    Fugmann, S D; Villey, I J; Ptaszek, L M; Schatz, D G

    2000-01-01

    During V(D)J recombination, the RAG1 and RAG2 proteins cooperate to catalyze a series of DNA bond breakage and strand transfer reactions. The structure, location, and number of active sites involved in RAG-mediated catalysis have as yet not been determined. Using protein secondary structure prediction algorithms, we have identified a region of RAG1 with possible structural similarities to the active site regions of transposases and retroviral integrases. Based on this information, we have identified two aspartic acid residues in RAG1 (D600 and D708) that function specifically in catalysis. The results support a model in which RAG1 contains a single, divalent metal ion binding active site structurally related to the active sites of transposases/integrases and responsible for all catalytic functions of the RAG protein complex. PMID:10678172

  8. Dimer-dimer interaction of the bacterial selenocysteine synthase SelA promotes functional active-site formation and catalytic specificity.

    PubMed

    Itoh, Yuzuru; Bröcker, Markus J; Sekine, Shun-ichi; Söll, Dieter; Yokoyama, Shigeyuki

    2014-04-17

    The 21st amino acid, selenocysteine (Sec), is incorporated translationally into proteins and is synthesized on its specific tRNA (tRNA(Sec)). In Bacteria, the selenocysteine synthase SelA converts Ser-tRNA(Sec), formed by seryl-tRNA synthetase, to Sec-tRNA(Sec). SelA, a member of the fold-type-I pyridoxal 5'-phosphate-dependent enzyme superfamily, has an exceptional homodecameric quaternary structure with a molecular mass of about 500kDa. Our previously determined crystal structures of Aquifex aeolicus SelA complexed with tRNA(Sec) revealed that the ring-shaped decamer is composed of pentamerized SelA dimers, with two SelA dimers arranged to collaboratively interact with one Ser-tRNA(Sec). The SelA catalytic site is close to the dimer-dimer interface, but the significance of the dimer pentamerization in the catalytic site formation remained elusive. In the present study, we examined the quaternary interactions and demonstrated their importance for SelA activity by systematic mutagenesis. Furthermore, we determined the crystal structures of "depentamerized" SelA variants with mutations at the dimer-dimer interface that prevent pentamerization. These dimeric SelA variants formed a distorted and inactivated catalytic site and confirmed that the pentamer interactions are essential for productive catalytic site formation. Intriguingly, the conformation of the non-functional active site of dimeric SelA shares structural features with other fold-type-I pyridoxal 5'-phosphate-dependent enzymes with native dimer or tetramer (dimer-of-dimers) quaternary structures. PMID:24456689

  9. Mutagenesis and crystallographic studies of the catalytic residues of the papain family protease bleomycin hydrolase: new insights into active-site structure

    PubMed Central

    O'Farrell, Paul A.; Joshua-Tor, Leemor

    2006-01-01

    Bleomycin hydrolase (BH) is a hexameric papain family cysteine protease which is involved in preparing peptides for antigen presentation and has been implicated in tumour cell resistance to bleomycin chemotherapy. Structures of active-site mutants of yeast BH yielded unexpected results. Replacement of the active-site asparagine with alanine, valine or leucine results in the destabilization of the histidine side chain, demonstrating unambiguously the role of the asparagine residue in correctly positioning the histidine for catalysis. Replacement of the histidine with alanine or leucine destabilizes the asparagine position, indicating a delicate arrangement of the active-site residues. In all of the mutants, the C-terminus of the protein, which lies in the active site, protrudes further into the active site. All mutants were compromised in their catalytic activity. The structures also revealed the importance of a tightly bound water molecule which stabilizes a loop near the active site and which is conserved throughout the papain family. It is displaced in a number of the mutants, causing destabilization of this loop and a nearby loop, resulting in a large movement of the active-site cysteine. The results imply that this water molecule plays a key structural role in this family of enzymes. PMID:17007609

  10. Processing of the yellow fever virus nonstructural polyprotein: a catalytically active NS3 proteinase domain and NS2B are required for cleavages at dibasic sites.

    PubMed Central

    Chambers, T J; Grakoui, A; Rice, C M

    1991-01-01

    The vaccinia virus-T7 transient expression system was used to further examine the role of the NS3 proteinase in processing of the yellow fever (YF) virus nonstructural polyprotein in BHK cells. YF virus-specific polyproteins and cleavage products were identified by immunoprecipitation with region-specific antisera, by size, and by comparison with authentic YF virus polypeptides. A YF virus polyprotein initiating with a signal sequence derived from the E protein fused to the N terminus of NS2A and extending through the N-terminal 356 amino acids of NS5 exhibited processing at the 2A-2B, 2B-3, 3-4A, 4A-4B, and 4B-5 cleavage sites. Similar results were obtained with polyproteins whose N termini began within NS2A (position 110) or with NS2B. When the NS3 proteinase domain was inactivated by replacing the proposed catalytic Ser-138 with Ala, processing at all sites was abolished. The results suggest that an active NS3 proteinase domain is necessary for cleavage at the diabasic nonstructural cleavage sites and that cleavage at the proposed 4A-4B signalase site requires prior cleavage at the 4B-5 site. Cleavages were not observed with a polyprotein whose N terminus began with NS3, but cleavage at the 4B-5 site could be restored by supplying the the NS2B protein in trans. Several experimental results suggested that trans cleavage at the 4B-5 site requires association of NS2B and the NS3 proteinase domain. Coexpression of different proteinases and catalytically inactive polyprotein substrates revealed that trans cleavage at the 2B-3 and 4B-5 sites was relatively efficient when compared with trans cleavage at the 2A-2B and 3-4A sites. Images PMID:1833562

  11. Enhancement of the catalytic activity of ferulic acid decarboxylase from Enterobacter sp. Px6-4 through random and site-directed mutagenesis.

    PubMed

    Lee, Hyunji; Park, Jiyoung; Jung, Chaewon; Han, Dongfei; Seo, Jiyoung; Ahn, Joong-Hoon; Chong, Youhoon; Hur, Hor-Gil

    2015-11-01

    The enzyme ferulic acid decarboxylase (FADase) from Enterobacter sp. Px6-4 catalyzes the decarboxylation reaction of lignin monomers and phenolic compounds such as p-coumaric acid, caffeic acid, and ferulic acid into their corresponding 4-vinyl derivatives, that is, 4-vinylphenol, 4-vinylcatechol, and 4-vinylguaiacol, respectively. Among various ferulic acid decarboxylase enzymes, we chose the FADase from Enterobacter sp. Px6-4, whose crystal structure is known, and produced mutants to enhance its catalytic activity by random and site-directed mutagenesis. After three rounds of sequential mutations, FADase(F95L/D112N/V151I) showed approximately 34-fold higher catalytic activity than wild-type for the production of 4-vinylguaiacol from ferulic acid. Docking analyses suggested that the increased activity of FADase(F95L/D112N/V151I) could be due to formation of compact active site compared with that of the wild-type FADase. Considering the amount of phenolic compounds such as lignin monomers in the biomass components, successfully bioengineered FADase(F95L/D112N/V151I) from Enterobacter sp. Px6-4 could provide an ecofriendly biocatalytic tool for producing diverse styrene derivatives from biomass. PMID:26059194

  12. The role of lattice anion vacancies in the activation of CO and as the catalytic site for methanol synthesis over zirconium dioxide and yttria-doped zirconium dioxide

    SciTech Connect

    Silver, R.G.; Hou, C.J.; Ekerdt, J.G. )

    1989-08-01

    The role of lattice oxygen anion vacancy sites in the activation of CO and in the synthesis of methanol was investigated over ZrO{sub 2}. The study involved a comparison of the amounts of CO and SO{sub 3} which adsorbed, the amount of methoxide which could be titrated from zirconia, and the rate of catalytic synthesis of methane and methanol as a function of crystalline phase, calcination conditions, and Y{sub 2}O{sub 3} levels in yttria-doped ZrO{sub 2}. Infrared and temperature-programmed desorption results established that CO adsorbed as formate and that SO{sub 3} adsorbed as the sulfate (ZrO){sub 3}S{double bond}O. Uptake studies over yttria-doped ZrO{sub 2} demonstrate that SO{sub 3} interacts with anion vacancy sites to form the sulfate. A maximum in SO{sub 3} and CO adsorption and methanol titration occurred at yttria dopant levels where ionic conductivity is highest for yttria-doped ZrO{sub 2}. The correspondence between the amount of formate or sulfate adsorbed and the amount of methanol produced from the basis for concluding that surface oxygen anion vacancies are the catalytic sites for CO activation and methanol synthesis.

  13. A catalytic diad involved in substrate-assisted catalysis: NMR study of hydrogen bonding and dynamics at the active site of phosphatidylinositol-specific phospholipase C.

    PubMed

    Ryan, M; Liu, T; Dahlquist, F W; Griffith, O H

    2001-08-14

    Phosphatidylinositol-specific phospholipase Cs (PI-PLCs, EC 3.1.4.10) are ubiquitous enzymes that cleave phosphatidylinositol or phosphorylated derivatives, generating second messengers in eukaryotic cells. A catalytic diad at the active site of Bacillus cereus PI-PLC composed of aspartate-274 and histidine-32 was postulated from the crystal structure to form a catalytic triad with the 2-OH group of the substrate [Heinz, D. W., et al. (1995) EMBO J. 14, 3855-3863]. This catalytic diad has been observed directly by proton NMR. The single low-field line in the 1H NMR spectrum is assigned by site-directed mutagenesis: The peak is present in the wild type but absent in the mutants H32A and D274A, and arises from the histidine Hdelta1 forming the Asp274-His32 hydrogen bond. This hydrogen is solvent-accessible, and exchanges slowly with H2O on the NMR time scale. The position of the low-field peak shifts from 16.3 to 13.8 ppm as the pH is varied from 4 to 9, reflecting a pKa of 8.0 at 6 degrees C, which is identified with the pKa of His32. The Hdelta1 signal is modulated by rapid exchange of the Hepsilon2 with the solvent. Estimates of the exchange rate as a function of pH and protection factors are derived from a line shape analysis. The NMR behavior is remarkably similar to that of the serine proteases. The postulated function of the Asp274-His32 diad is to hydrogen-bond with the 2-OH of phosphatidylinositol (PI) substrate to form a catalytic triad analogous to Asp-His-Ser of serine proteases. This is an example of substrate-assisted catalysis where the substrate provides the catalytic nucleophile of the triad. This hydrogen bond becomes shorter as the imidazole is protonated, suggesting it is stronger in the transition state, contributing further to the catalytic efficiency. The hydrogen bond fits the NMR criteria for a short, strong hydrogen bond, i.e., a highly deshielded proton resonance, bond length of 2.64 +/- 0.04 A at pH 6 measured by NMR, a D/H fractionation

  14. Two distinct modes of metal ion binding in the nuclease active site of a viral DNA-packaging terminase: insight into the two-metal-ion catalytic mechanism

    PubMed Central

    Zhao, Haiyan; Lin, Zihan; Lynn, Anna Y.; Varnado, Brittany; Beutler, John A.; Murelli, Ryan P.; Le Grice, Stuart F. J.; Tang, Liang

    2015-01-01

    Many dsDNA viruses encode DNA-packaging terminases, each containing a nuclease domain that resolves concatemeric DNA into genome-length units. Terminase nucleases resemble the RNase H-superfamily nucleotidyltransferases in folds, and share a two-metal-ion catalytic mechanism. Here we show that residue K428 of a bacteriophage terminase gp2 nuclease domain mediates binding of the metal cofactor Mg2+. A K428A mutation allows visualization, at high resolution, of a metal ion binding mode with a coupled-octahedral configuration at the active site, exhibiting an unusually short metal-metal distance of 2.42 Å. Such proximity of the two metal ions may play an essential role in catalysis by generating a highly positive electrostatic niche to enable formation of the negatively charged pentacovalent phosphate transition state, and provides the structural basis for distinguishing Mg2+ from Ca2+. Using a metal ion chelator β-thujaplicinol as a molecular probe, we observed a second mode of metal ion binding at the active site, mimicking the DNA binding state. Arrangement of the active site residues differs drastically from those in RNase H-like nucleases, suggesting a drifting of the active site configuration during evolution. The two distinct metal ion binding modes unveiled mechanistic details of the two-metal-ion catalysis at atomic resolution. PMID:26450964

  15. SET7/9 Catalytic Mutants Reveal the Role of Active Site Water Molecules in Lysine Multiple Methylation

    SciTech Connect

    Del Rizzo, Paul A.; Couture, Jean-François; Dirk, Lynnette M.A.; Strunk, Bethany S.; Roiko, Marijo S.; Brunzelle, Joseph S.; Houtz, Robert L.; Trievel, Raymond C.

    2010-11-15

    SET domain lysine methyltransferases (KMTs) methylate specific lysine residues in histone and non-histone substrates. These enzymes also display product specificity by catalyzing distinct degrees of methylation of the lysine {epsilon}-amino group. To elucidate the molecular mechanism underlying this specificity, we have characterized the Y245A and Y305F mutants of the human KMT SET7/9 (also known as KMT7) that alter its product specificity from a monomethyltransferase to a di- and a trimethyltransferase, respectively. Crystal structures of these mutants in complex with peptides bearing unmodified, mono-, di-, and trimethylated lysines illustrate the roles of active site water molecules in aligning the lysine {epsilon}-amino group for methyl transfer with S-adenosylmethionine. Displacement or dissociation of these solvent molecules enlarges the diameter of the active site, accommodating the increasing size of the methylated {epsilon}-amino group during successive methyl transfer reactions. Together, these results furnish new insights into the roles of active site water molecules in modulating lysine multiple methylation by SET domain KMTs and provide the first molecular snapshots of the mono-, di-, and trimethyl transfer reactions catalyzed by these enzymes.

  16. Effects of vaccinia virus uracil DNA glycosylase catalytic site and deoxyuridine triphosphatase deletion mutations individually and together on replication in active and quiescent cells and pathogenesis in mice

    PubMed Central

    De Silva, Frank S; Moss, Bernard

    2008-01-01

    Background Low levels of uracil in DNA result from misincorporation of dUMP or cytosine deamination. Vaccinia virus (VACV), the prototype poxvirus, encodes two enzymes that can potentially reduce the amount of uracil in DNA. Deoxyuridine triphosphatase (dUTPase) hydrolyzes dUTP, generating dUMP for biosynthesis of thymidine nucleotides while decreasing the availability of dUTP for misincorporation; uracil DNA glycosylase (UNG) cleaves uracil N-glycosylic bonds in DNA initiating base excision repair. Studies with actively dividing cells showed that the VACV UNG protein is required for DNA replication but the UNG catalytic site is not, whereas the dUTPase gene can be deleted without impairing virus replication. Recombinant VACV with an UNG catalytic site mutation was attenuated in vivo, while a dUTPase deletion mutant was not. However, the importance of the two enzymes for replication in quiescent cells, their possible synergy and roles in virulence have not been fully assessed. Results VACV mutants lacking the gene encoding dUTPase or with catalytic site mutations in UNG and double UNG/dUTPase mutants were constructed. Replication of UNG and UNG/dUTPase mutants were slightly reduced compared to wild type or the dUTPase mutant in actively dividing cells. Viral DNA replication was reduced about one-third under these conditions. After high multiplicity infection of quiescent fibroblasts, yields of wild type and mutant viruses were decreased by 2-logs with relative differences similar to those observed in active fibroblasts. However, under low multiplicity multi-step growth conditions in quiescent fibroblasts, replication of the dUTPase/UNG mutant was delayed and 5-fold lower than that of either single mutant or parental virus. This difference was exacerbated by 1-day serial passages on quiescent fibroblasts, resulting in 2- to 3-logs lower titer of the double mutant compared to the parental and single mutant viruses. Each mutant was more attenuated than a revertant

  17. Predictions of Cleavability of Calpain Proteolysis by Quantitative Structure-Activity Relationship Analysis Using Newly Determined Cleavage Sites and Catalytic Efficiencies of an Oligopeptide Array*

    PubMed Central

    Shinkai-Ouchi, Fumiko; Koyama, Suguru; Ono, Yasuko; Hata, Shoji; Ojima, Koichi; Shindo, Mayumi; duVerle, David; Ueno, Mika; Kitamura, Fujiko; Doi, Naoko; Takigawa, Ichigaku; Mamitsuka, Hiroshi; Sorimachi, Hiroyuki

    2016-01-01

    Calpains are intracellular Ca2+-regulated cysteine proteases that are essential for various cellular functions. Mammalian conventional calpains (calpain-1 and calpain-2) modulate the structure and function of their substrates by limited proteolysis. Thus, it is critically important to determine the site(s) in proteins at which calpains cleave. However, the calpains' substrate specificity remains unclear, because the amino acid (aa) sequences around their cleavage sites are very diverse. To clarify calpains' substrate specificities, 84 20-mer oligopeptides, corresponding to P10-P10′ of reported cleavage site sequences, were proteolyzed by calpains, and the catalytic efficiencies (kcat/Km) were globally determined by LC/MS. This analysis revealed 483 cleavage site sequences, including 360 novel ones. The kcat/Kms for 119 sites ranged from 12.5–1,710 M−1s−1. Although most sites were cleaved by both calpain-1 and −2 with a similar kcat/Km, sequence comparisons revealed distinct aa preferences at P9-P7/P2/P5′. The aa compositions of the novel sites were not statistically different from those of previously reported sites as a whole, suggesting calpains have a strict implicit rule for sequence specificity, and that the limited proteolysis of intact substrates is because of substrates' higher-order structures. Cleavage position frequencies indicated that longer sequences N-terminal to the cleavage site (P-sites) were preferred for proteolysis over C-terminal (P′-sites). Quantitative structure-activity relationship (QSAR) analyses using partial least-squares regression and >1,300 aa descriptors achieved kcat/Km prediction with r = 0.834, and binary-QSAR modeling attained an 87.5% positive prediction value for 132 reported calpain cleavage sites independent of our model construction. These results outperformed previous calpain cleavage predictors, and revealed the importance of the P2, P3′, and P4′ sites, and P1-P2 cooperativity. Furthermore, using our

  18. Predictions of Cleavability of Calpain Proteolysis by Quantitative Structure-Activity Relationship Analysis Using Newly Determined Cleavage Sites and Catalytic Efficiencies of an Oligopeptide Array.

    PubMed

    Shinkai-Ouchi, Fumiko; Koyama, Suguru; Ono, Yasuko; Hata, Shoji; Ojima, Koichi; Shindo, Mayumi; duVerle, David; Ueno, Mika; Kitamura, Fujiko; Doi, Naoko; Takigawa, Ichigaku; Mamitsuka, Hiroshi; Sorimachi, Hiroyuki

    2016-04-01

    Calpains are intracellular Ca(2+)-regulated cysteine proteases that are essential for various cellular functions. Mammalian conventional calpains (calpain-1 and calpain-2) modulate the structure and function of their substrates by limited proteolysis. Thus, it is critically important to determine the site(s) in proteins at which calpains cleave. However, the calpains' substrate specificity remains unclear, because the amino acid (aa) sequences around their cleavage sites are very diverse. To clarify calpains' substrate specificities, 84 20-mer oligopeptides, corresponding to P10-P10' of reported cleavage site sequences, were proteolyzed by calpains, and the catalytic efficiencies (kcat/Km) were globally determined by LC/MS. This analysis revealed 483 cleavage site sequences, including 360 novel ones. Thekcat/Kms for 119 sites ranged from 12.5-1,710 M(-1)s(-1) Although most sites were cleaved by both calpain-1 and -2 with a similarkcat/Km, sequence comparisons revealed distinct aa preferences at P9-P7/P2/P5'. The aa compositions of the novel sites were not statistically different from those of previously reported sites as a whole, suggesting calpains have a strict implicit rule for sequence specificity, and that the limited proteolysis of intact substrates is because of substrates' higher-order structures. Cleavage position frequencies indicated that longer sequences N-terminal to the cleavage site (P-sites) were preferred for proteolysis over C-terminal (P'-sites). Quantitative structure-activity relationship (QSAR) analyses using partial least-squares regression and >1,300 aa descriptors achievedkcat/Kmprediction withr= 0.834, and binary-QSAR modeling attained an 87.5% positive prediction value for 132 reported calpain cleavage sites independent of our model construction. These results outperformed previous calpain cleavage predictors, and revealed the importance of the P2, P3', and P4' sites, and P1-P2 cooperativity. Furthermore, using our binary-QSAR model

  19. Unveiling hidden catalytic contributions of the conserved His/Trp-III in tyrosine recombinases: assembly of a novel active site in Flp recombinase harboring alanine at this position

    PubMed Central

    Ma, Chien-Hui; Kwiatek, Agnieszka; Bolusani, Swetha; Voziyanov, Yuri; Jayaram, Makkuni

    2007-01-01

    Summary The catalytic pentad of tyrosine recombinases, that assists the tyrosine nucleophile, includes a conserved histidine/tryptophan (His/Trp-III). Flp and Cre harbor tryptophan at this position; most of their kin recombinases display histidine. Contrary to the conservation rule, Flp(W330F) is a much stronger recombinase than Flp(W330H). The hydrophobicity of Trp-330 or Phe-330 is utilized in correctly positioning Tyr-343 during the strand cleavage step of recombination. Why then is phenylalanine almost never encountered in the recombinase family at this conserved position? Using exogenous nucleophiles and synthetic methylphosphonate or 5'-thiolate substrates, we decipher that Trp-330 also assists in the activation of the scissile phosphate and the departure of the 5'-hydroxyl leaving group. These two functions are consistent with the hydrogen bonding property of Trp-330 as well as its location in structures of the Flp recombination complexes. However, van der Waals contact between Trp-330 and Arg-308 may also be important for the phosphate activation step. A structure based suppression strategy permits the inactive variant Flp(W330A) to be rescued by a second site mutation A339M. Modeling alanine and methionine at positions 330 and 339, respectively, in the Flp crystal structure suggests a plausible mechanism for active site restoration. Successful suppression suggests the possibility of evolving, by design, new active site configurations for tyrosine recombination. PMID:17367810

  20. Active sites, deactivation and stabilization of Fe-ZSM-5 for the selective catalytic reduction (SCR) of NO with NH(3).

    PubMed

    Kröcher, Oliver; Brandenberger, Sandro

    2012-01-01

    Fe-ZSM-5 has been systematically investigated as catalyst for the selective catalytic reduction (SCR) of NO with NH(3), concentrating on the active sites, the deactivation mechanism during hydrothermal aging and the chemical possibilities to stabilize this type of SCR catalyst. Regarding the active SCR sites, it could be shown that monomeric species start to become active at the lowest temperatures (E(a,app) ≈ 36.3 ± 0.2 kJ/mol), followed by dimeric species at intermediate temperatures (E(a,app) ≈ 77 ± 16 kJ/mol) and oligomeric species at high temperatures. Experiments with Fe-ZSM-5 samples, in which the Brønsted acidity was specifically removed, proved that Brønsted acidity is not required for high SCR activity and that NH(3) can also be adsorbed on other acidic sites on the zeolite surface. The hydrothermal deactivation of Fe-ZSM-5 could be explained by the migration of active iron ions from the exchange sites. Parallel to the iron migration dealumination of the zeolite framework occurs, which has to be regarded as an independent process. The migration of iron can be reduced by the targeted reaction of the aluminum hydroxide groups in the lattice with trimethylaluminium followed by calcination. With respect to the application of iron zeolites in the SCR process in diesel vehicles, the most efficient stabilization method would be to switch from the ZSM-5 to the BEA structure type. The addition of NO(2) to the feed gas is another effective measure to increase the activity of even strongly deactivated iron zeolites tremendously. PMID:23211727

  1. Cutoff lensing: predicting catalytic sites in enzymes

    PubMed Central

    Aubailly, Simon; Piazza, Francesco

    2015-01-01

    Predicting function-related amino acids in proteins with unknown function or unknown allosteric binding sites in drug-targeted proteins is a task of paramount importance in molecular biomedicine. In this paper we introduce a simple, light and computationally inexpensive structure-based method to identify catalytic sites in enzymes. Our method, termed cutoff lensing, is a general procedure consisting in letting the cutoff used to build an elastic network model increase to large values. A validation of our method against a large database of annotated enzymes shows that optimal values of the cutoff exist such that three different structure-based indicators allow one to recover a maximum of the known catalytic sites. Interestingly, we find that the larger the structures the greater the predictive power afforded by our method. Possible ways to combine the three indicators into a single figure of merit and into a specific sequential analysis are suggested and discussed with reference to the classic case of HIV-protease. Our method could be used as a complement to other sequence- and/or structure-based methods to narrow the results of large-scale screenings. PMID:26445900

  2. Cutoff lensing: predicting catalytic sites in enzymes

    NASA Astrophysics Data System (ADS)

    Aubailly, Simon; Piazza, Francesco

    2015-10-01

    Predicting function-related amino acids in proteins with unknown function or unknown allosteric binding sites in drug-targeted proteins is a task of paramount importance in molecular biomedicine. In this paper we introduce a simple, light and computationally inexpensive structure-based method to identify catalytic sites in enzymes. Our method, termed cutoff lensing, is a general procedure consisting in letting the cutoff used to build an elastic network model increase to large values. A validation of our method against a large database of annotated enzymes shows that optimal values of the cutoff exist such that three different structure-based indicators allow one to recover a maximum of the known catalytic sites. Interestingly, we find that the larger the structures the greater the predictive power afforded by our method. Possible ways to combine the three indicators into a single figure of merit and into a specific sequential analysis are suggested and discussed with reference to the classic case of HIV-protease. Our method could be used as a complement to other sequence- and/or structure-based methods to narrow the results of large-scale screenings.

  3. Residues Distal to the Active Site Contribute to Enhanced Catalytic Activity of Variant and Hybrid β-Lactamases Derived from CTX-M-14 and CTX-M-15

    PubMed Central

    He, Dandan; Chiou, Jiachi; Zeng, Zhenling; Liu, Lanping; Chen, Xiaojie; Zeng, Li; Chan, Edward Wai Chi

    2015-01-01

    A variety of CTX-M-type extended-spectrum β-lactamases (ESBLs), including hybrid ones, have been reported in China that are uncommon elsewhere. To better characterize the substrate profiles and enzymatic mechanisms of these enzymes, we performed comparative kinetic analyses of both parental and hybrid CTX-M enzymes, including CTX-M-15, -132, -123, -64, -14 and -55, that are known to confer variable levels of β-lactam resistance in the host strains. All tested enzymes were susceptible to serine β-lactamase inhibitors, with sulbactam exhibiting the weakest inhibitory effects. CTX-M-55, which differs from CTX-M-15 by one substitution, A77V, displayed enhanced catalytic activity (kcat/Km) against expanded-spectrum cephalosporins (ESCs). CTX-M-55 exhibits higher structure stability, most likely by forming hydrophobic interactions between A77V and various key residues in different helices, thereby stabilizing the core architecture of the helix cluster, and indirectly contributes to a more stable active site conformation, which in turn shows higher catalytic efficiency and is more tolerant to temperature change. Analyses of the hybrids and their parental prototypes showed that evolution from CTX-M-15 to CTX-M-132, CTX-M-123, and CTX-M-64, characterized by gradual enhancement of catalytic activity to ESCs, was attributed to introduction of different substitutions to amino acids distal to the active site of CTX-M-15. Similarly, the increased hydrolytic activities against cephalosporins and sensitivity to β-lactamase inhibitors, clavulanic acid and sulbactam, of CTX-M-64 were partly due to the amino acids that were different from CTX-M-14 and located at both the C and N termini of CTX-M-64. These data indicate that residues distal to the active site of CTX-Ms contributed to their enhanced catalytic activities to ESCs. PMID:26169409

  4. Conformational Flexibility of a Short Loop near the Active Site of the SARS-3CLpro is Essential to Maintain Catalytic Activity

    NASA Astrophysics Data System (ADS)

    Li, Chunmei; Teng, Xin; Qi, Yifei; Tang, Bo; Shi, Hailing; Ma, Xiaomin; Lai, Luhua

    2016-02-01

    The SARS 3C-like proteinase (SARS-3CLpro), which is the main proteinase of the SARS coronavirus, is essential to the virus life cycle. This enzyme has been shown to be active as a dimer in which only one protomer is active. However, it remains unknown how the dimer structure maintains an active monomer conformation. It has been observed that the Ser139-Leu141 loop forms a short 310-helix that disrupts the catalytic machinery in the inactive monomer structure. We have tried to disrupt this helical conformation by mutating L141 to T in the stable inactive monomer G11A/R298A/Q299A. The resulting tetra-mutant G11A/L141T/R298A/Q299A is indeed enzymatically active as a monomer. Molecular dynamics simulations revealed that the L141T mutation disrupts the 310-helix and helps to stabilize the active conformation. The coil-310-helix conformational transition of the Ser139-Leu141 loop serves as an enzyme activity switch. Our study therefore indicates that the dimer structure can stabilize the active conformation but is not a required structure in the evolution of the active enzyme, which can also arise through simple mutations.

  5. Active-Site Models for the Nickel-Iron Hydrogenases: Effects of Ligands on Reactivity and Catalytic Properties

    PubMed Central

    Carroll, Maria E.; Barton, Bryan E.; Gray, Danielle L.; Mack, Amanda E.; Rauchfuss, Thomas B.

    2011-01-01

    Described are new derivatives of the type [HNiFe(SR)2(diphosphine)(CO)3]+, which feature a Ni(diphosphine) group linked to a Fe(CO)3 group via two bridging thiolate ligands. Previous work had described [HNiFe(pdt)(dppe)(CO)3]+ ([1H]+) and its activity as a catalyst for the reduction of protons. Work described in this paper focused on the effects of the diphosphine attached to nickel as well as the dithiolate bridge, 1,3-propanedithiolate (pdt) vs 1,2-ethanedithiolate (edt). A new synthetic route to these Ni-Fe dithiolates is described, involving reaction of Ni(SR)2(diphosphine) with FeI2(CO)4 followed by in situ reduction with cobaltocene. Evidence is presented that this route proceeds via metastable μ-iodo derivatives. Attempted isolation of such species led to the crystallization of NiFe(Me2pdt)(dppe)I2, which features tetrahedral Fe(II) and square planar Ni(II) centers (Me2pdt = 2,2-dimethylpropanedithiol). The new tricarbonyls prepared in this work are NiFe(pdt)(dcpe)(CO)3 (2, dcpe = 1,2-bis(dicyclohexylphosphino)ethane), NiFe(edt)(dppe)(CO)3 (3), and NiFe(edt)(dcpe)(CO)3 (4). Attempted preparation of a phenylthiolate-bridged complex via the FeI2(CO)4 + Ni(SPh)2(dppe) route gave the tetrametallic species [(CO)2Fe(SPh)2Ni(CO)]2(μ-dppe)2. Crystallographic analysis of the edt-dcpe compund [2H]BF4 and the edt-dppe compound [3H]BF4 verified their close resemblance. Each features pseudo-octahedral Fe and square pyramidal Ni centers. Starting from [4H]BF4 we prepared the PPh3 derivative [HNiFe(edt)(dppe)(PPh3)(CO)2]BF4 ([5H]BF4), which was obtained as a ~2:1 mixture of unsymmetrical and symmetrical isomers. Acid-base measurements indicate that changing from Ni(dppe) to Ni(dcpe) decreases the acidity of the cationic hydride complexes by 2.5 pKaMeCN units, from ~11 to ~13.5 (previous work showed that substitution at Fe leads to more dramatic effects). The redox potentials are more strongly affected by the change from dppe to dcpe, for example the [2]0/+ couple occurs

  6. Study of Single Catalytic Events at Copper-in-Charcoal: Localization of Click Activity Through Subdiffraction Observation of Single Catalytic Events.

    PubMed

    Decan, Matthew R; Scaiano, Juan C

    2015-10-15

    Single molecule fluorescence microscopy reveals that copper-in-charcoal--a high performance click catalyst- has remarkably few catalytic sites, with 90% of the charcoal particles being inactive, and for the catalytic ones the active sites represent a minute fraction (∼0.003%) of the surface. The intermittent nature of the catalytic events enables subdiffraction resolution and mapping of the catalytic sites. PMID:26722775

  7. Thioredoxin binding site of phosphoribulokinase overlaps the catalytic site. [R

    SciTech Connect

    Porter, M.A.; Hartman, F.C.

    1986-01-01

    The ATP-regulatory binding site of phosphoribulokinase was studied using bromoacetylethanolamine phosphate (BrAcNHEtOP). BrAcNHEtOP binds to the active-regulatory binding site of the protein. Following trypsin degradation of the labeled protein, fragments were separated by HPLC and sequenced. (DT)

  8. Structure of the catalytic chain of Methanococcus jannaschii aspartate transcarbamoylase in a hexagonal crystal form: Insights into the path of carbamoyl phosphate to the active site of the enzyme

    SciTech Connect

    Vitali J.; Soares A.; Singh, A. K.; Colaneri, M. J.

    2012-05-01

    Crystals of the catalytic chain of Methanococcus jannaschii aspartate transcarbamoylase (ATCase) grew in the presence of the regulatory chain in the hexagonal space group P6{sub 3}22, with one monomer per asymmetric unit. This is the first time that crystals with only one monomer in the asymmetric unit have been obtained; all known structures of the catalytic subunit contain several crystallographically independent monomers. The symmetry-related chains form the staggered dimer of trimers observed in the other known structures of the catalytic subunit. The central channel of the catalytic subunit contains a sulfate ion and a K{sup +} ion as well as a glycerol molecule at its entrance. It is possible that it is involved in channeling carbamoyl phosphate (CP) to the active site of the enzyme. A second sulfate ion near Arg164 is near the second CP position in the wild-type Escherichia coli ATCase structure complexed with CP. It is suggested that this position may also be in the path that CP takes when binding to the active site in a partial diffusion process at 310 K. Additional biochemical studies of carbamoylation and the molecular organization of this enzyme in M. jannaschii will provide further insight into these points.

  9. Structure of the catalytic chain of Methanococcus jannaschii aspartate transcarbamoylase in a hexagonal crystal form: insights into the path of carbamoyl phosphate to the active site of the enzyme

    PubMed Central

    Vitali, Jacqueline; Singh, Aditya K.; Soares, Alexei S.; Colaneri, Michael J.

    2012-01-01

    Crystals of the catalytic chain of Methanococcus jannaschii aspartate trans­carbamoylase (ATCase) grew in the presence of the regulatory chain in the hexagonal space group P6322, with one monomer per asymmetric unit. This is the first time that crystals with only one monomer in the asymmetric unit have been obtained; all known structures of the catalytic subunit contain several crystallographically independent monomers. The symmetry-related chains form the staggered dimer of trimers observed in the other known structures of the catalytic subunit. The central channel of the catalytic subunit contains a sulfate ion and a K+ ion as well as a glycerol molecule at its entrance. It is possible that it is involved in channeling carbamoyl phosphate (CP) to the active site of the enzyme. A second sulfate ion near Arg164 is near the second CP position in the wild-type Escherichia coli ATCase structure complexed with CP. It is suggested that this position may also be in the path that CP takes when binding to the active site in a partial diffusion process at 310 K. Additional biochemical studies of carbamoylation and the molecular organization of this enzyme in M. janna­schii will provide further insight into these points. PMID:22691781

  10. Improved catalytic activity of laser generated bimetallic and trimetallic nanoparticles.

    PubMed

    Singh, Rina; Soni, R K

    2014-09-01

    We report synthesis of silver nanoparticles, bimetallic (Al2O3@Ag) nanoparticles and trimetallic (Al2O3@AgAu) nanoparticles by nanosecond pulse laser ablation (PLA) in deionized water. Two-step laser ablation methodologies were adopted for the synthesis of bi- and tri-metallic nanoparticles. In this method a silver or gold target was ablated in colloidal solution of γ-alumina nanoparticles prepared by PLA. The TEM image analysis of bimetallic and trimetallic particles reveals deposition of fine silver particles and Ag-Au alloy particles, respectively, on large alumina particles. The laser generated nanoparticles were tested for catalytic reduction of 4-nitrophenol to 4-aminophenol and showed excellent catalytic behaviour. The catalytic rate was greatly improved by incorporation of additional metal in silver nanoparticles. The catalytic efficiency of trimetallic Al2O3@AgAu for reduction of 4-nitrophenol to 4-aminophenol was remarkably enhanced and the catalytic reaction was completed in just 5 sec. Even at very low concentration, both Al2O3@Ag nanoparticles and Al2O3@AgAu nanoparticles showed improved rate of catalytic reduction than monometallic silver nanoparticles. Our results demonstrate that alumina particles in the solution not only provide the active sites for particle dispersion but also improve the catalytic activity. PMID:25924343

  11. A Phosphoenzyme Mimic, Overlapping Catalytic Sites and Reaction Coordinate Motion for Human NAMPT

    SciTech Connect

    Burgos, E.; Ho, M; Almo, S; Schramm, V

    2009-01-01

    Nicotinamide phosphoribosyltransferase (NAMPT) is highly evolved to capture nicotinamide (NAM) and replenish the nicotinamide adenine dinucleotide (NAD+) pool during ADP-ribosylation and transferase reactions. ATP-phosphorylation of an active-site histidine causes catalytic activation, increasing NAM affinity by 160,000. Crystal structures of NAMPT with catalytic site ligands identify the phosphorylation site, establish its role in catalysis, demonstrate unique overlapping ATP and phosphoribosyltransferase sites, and establish reaction coordinate motion. NAMPT structures with beryllium fluoride indicate a covalent H247-BeF3- as the phosphohistidine mimic. Activation of NAMPT by H247-phosphorylation causes stabilization of the enzyme-phosphoribosylpyrophosphate complex, permitting efficient capture of NAM. Reactant and product structures establish reaction coordinate motion for NAMPT to be migration of the ribosyl anomeric carbon from the pyrophosphate leaving group to the nicotinamide-N1 while the 5-phosphoryl group, the pyrophosphate moiety, and the nicotinamide ring remain fixed in the catalytic site.

  12. Catalytic glucose isomerization by porous coordination polymers with open metal sites.

    PubMed

    Akiyama, George; Matsuda, Ryotaro; Sato, Hiroshi; Kitagawa, Susumu

    2014-10-01

    Highly efficient catalytic isomerization reactions from glucose to fructose in aqueous media using porous coordination polymers (PCPs) or metal-organic frameworks (MOFs) is reported for the first time. The catalytic activity of PCPs functionalized with -NH2, -(CH3)2, -NO2, and -SO3H groups on the pore surface is systematically tested. The catalytic activity can be tuned by the acidity of open metal sites (OMSs) by modifying the organic linkers with the functional groups. As a result, it is demonstrated that MIL-101 functionalized with -SO3H not only shows high conversion of glucose but also selectively produces fructose. Further, catalytic one-pot conversion of amylose to fructose is achieved, thanks to the high stability of the framework in an acidic solution. These results show that MOF/PCP compounds having OMSs are promising materials for various useful heterogeneous catalytic reactions, in particular in the biomass field. PMID:25080129

  13. Ultrafine Nanoparticle-Supported Ru Nanoclusters with Ultrahigh Catalytic Activity.

    PubMed

    Zhu, Lihua; Jiang, Yingying; Zheng, Jinbao; Zhang, Nuowei; Yu, Changlin; Li, Yunhua; Pao, Chih-Wen; Chen, Jeng-Lung; Jin, Chuanhong; Lee, Jyh-Fu; Zhong, Chuan-Jian; Chen, Bing H

    2015-09-01

    The design of an ideal heterogeneous catalyst for hydrogenation reaction is to impart the catalyst with synergetic surface sites active cooperatively toward different reaction species. Herein a new strategy is presented for the creation of such a catalyst with dual active sites by decorating metal and metal oxide nanoparticles with ultrafine nanoclusters at atomic level. This strategy is exemplified by the design and synthesis of Ru nanoclusters supported on Ni/NiO nanoparticles. This Ru-nanocluster/Ni/NiO-nanoparticle catalyst is shown to exhibit ultrahigh catalytic activity for benzene hydrogenation reaction, which is 55 times higher than Ru-Ni alloy or Ru on Ni catalysts. The nanoclusters-on-nanoparticles are characterized by high-resolution transmission electron microscope, Cs-corrected high angle annular dark field-scanning transmission electron microscopy, elemental mapping, high-sensitivity low-energy ion scattering, and X-ray absorption spectra. The atomic-scale nanocluster-nanoparticle structural characteristics constitute the basis for creating the catalytic synergy of the surface sites, where Ru provides hydrogen adsorption and dissociation site, Ni acts as a "bridge" for transferring H species to benzene adsorbed and activated at NiO site, which has significant implications to multifunctional nanocatalysts design for wide ranges of catalytic reactions. PMID:26081741

  14. Lanthanide Metal-Organic Frameworks with Six-Coordinated Ln(III) Ions and Free Functional Organic Sites for Adsorptions and Extensive Catalytic Activities

    NASA Astrophysics Data System (ADS)

    Zhu, Yu; Zhu, Min; Xia, Li; Wu, Yunlong; Hua, Hui; Xie, Jimin

    2016-07-01

    Three chelating-amino-functionalized lanthanide metal-organic frameworks, Y-DDQ, Dy-DDQ and Eu-DDQ, were synthesized with a flexible dicarboxylate ligand based on quinoxaline (H2DDQ = N, N‧-dibenzoic acid-2,3-diaminoquinoxaline). The three-dimensional framework is constructed by the H2DDQ linkers connecting the zigzag ladders, showing a net of sra topology. In the structures, one kind of Ln(III) ions metal centers are six-coordinated and thus can potentially behave as open metal sites (OMSs), while the free chelating amino groups can act as free functional organic sites (FOSs). The N2 and Ar adsorption behaviors indicate that these Ln-DDQ exhibits stable microporous frameworks with high surface area after remove of the solvents. Owing to presence of OMSs and FOSs, these MOFs show good ability of CO2, dyes captures and Lewis acid catalyst for cyanosilylation reaction. In view of the existing FOSs in the framework, Pd NPs were immobilized onto the MOFs through graft interactions between free chelating amino groups and metal ions precursor using postsynthetic modification. The well dispersed Pd@Ln-DDQs exhibit efficient and recyclable catalytic reduction of 4-nitrophenol to 4-aminophenol, and they can also act as an excellent catalyst for Suzuki-Miyaura cross-coupling reactions with the exposed Pd NPs.

  15. Lanthanide Metal-Organic Frameworks with Six-Coordinated Ln(III) Ions and Free Functional Organic Sites for Adsorptions and Extensive Catalytic Activities.

    PubMed

    Zhu, Yu; Zhu, Min; Xia, Li; Wu, Yunlong; Hua, Hui; Xie, Jimin

    2016-01-01

    Three chelating-amino-functionalized lanthanide metal-organic frameworks, Y-DDQ, Dy-DDQ and Eu-DDQ, were synthesized with a flexible dicarboxylate ligand based on quinoxaline (H2DDQ = N, N'-dibenzoic acid-2,3-diaminoquinoxaline). The three-dimensional framework is constructed by the H2DDQ linkers connecting the zigzag ladders, showing a net of sra topology. In the structures, one kind of Ln(III) ions metal centers are six-coordinated and thus can potentially behave as open metal sites (OMSs), while the free chelating amino groups can act as free functional organic sites (FOSs). The N2 and Ar adsorption behaviors indicate that these Ln-DDQ exhibits stable microporous frameworks with high surface area after remove of the solvents. Owing to presence of OMSs and FOSs, these MOFs show good ability of CO2, dyes captures and Lewis acid catalyst for cyanosilylation reaction. In view of the existing FOSs in the framework, Pd NPs were immobilized onto the MOFs through graft interactions between free chelating amino groups and metal ions precursor using postsynthetic modification. The well dispersed Pd@Ln-DDQs exhibit efficient and recyclable catalytic reduction of 4-nitrophenol to 4-aminophenol, and they can also act as an excellent catalyst for Suzuki-Miyaura cross-coupling reactions with the exposed Pd NPs. PMID:27431731

  16. Lanthanide Metal-Organic Frameworks with Six-Coordinated Ln(III) Ions and Free Functional Organic Sites for Adsorptions and Extensive Catalytic Activities

    PubMed Central

    Zhu, Yu; Zhu, Min; Xia, Li; Wu, Yunlong; Hua, Hui; Xie, Jimin

    2016-01-01

    Three chelating-amino-functionalized lanthanide metal-organic frameworks, Y-DDQ, Dy-DDQ and Eu-DDQ, were synthesized with a flexible dicarboxylate ligand based on quinoxaline (H2DDQ = N, N′-dibenzoic acid-2,3-diaminoquinoxaline). The three-dimensional framework is constructed by the H2DDQ linkers connecting the zigzag ladders, showing a net of sra topology. In the structures, one kind of Ln(III) ions metal centers are six-coordinated and thus can potentially behave as open metal sites (OMSs), while the free chelating amino groups can act as free functional organic sites (FOSs). The N2 and Ar adsorption behaviors indicate that these Ln-DDQ exhibits stable microporous frameworks with high surface area after remove of the solvents. Owing to presence of OMSs and FOSs, these MOFs show good ability of CO2, dyes captures and Lewis acid catalyst for cyanosilylation reaction. In view of the existing FOSs in the framework, Pd NPs were immobilized onto the MOFs through graft interactions between free chelating amino groups and metal ions precursor using postsynthetic modification. The well dispersed Pd@Ln-DDQs exhibit efficient and recyclable catalytic reduction of 4-nitrophenol to 4-aminophenol, and they can also act as an excellent catalyst for Suzuki-Miyaura cross-coupling reactions with the exposed Pd NPs. PMID:27431731

  17. Treatment of activated carbon to enhance catalytic activity for reduction of nitric oxide with ammonia

    SciTech Connect

    Ku, B.J.; Rhee, H.K. . Dept. of Chemical Engineering); Lee, J.K.; Park, D. )

    1994-11-01

    Catalytic activity of activated carbon treated with various techniques was examined in a fixed bed reactor for the reduction of nitric oxide with ammonia at 150 C. Activated carbon derived from coconut shell impregnated with an aqueous solution of ammonium sulfate, further treated with sulfuric acid, dried at 120 C, and then heated in an inert gas stream at 400 C, showed the highest catalytic activity within the range of experimental conditions. The enhancement of catalytic activity of modified activated carbon could be attributed to the increase in the amount of oxygen function groups which increased the adsorption site for ammonia. Catalytic activity of activated carbons depended on the surface area and the oxygen content as well.

  18. Tunable plasmonic nanoparticles with catalytically active high-index facets.

    PubMed

    Jing, Hao; Zhang, Qingfeng; Large, Nicolas; Yu, Chunmei; Blom, Douglas A; Nordlander, Peter; Wang, Hui

    2014-06-11

    Noble metal nanoparticles have been of tremendous interest due to their intriguing size- and shape-dependent plasmonic and catalytic properties. Combining tunable plasmon resonances with superior catalytic activities on the same metallic nanoparticle, however, has long been challenging because nanoplasmonics and nanocatalysis typically require nanoparticles in two drastically different size regimes. Here, we demonstrate that creation of high-index facets on subwavelength metallic nanoparticles provides a unique approach to the integration of desired plasmonic and catalytic properties on the same nanoparticle. Through site-selective surface etching of metallic nanocuboids whose surfaces are dominated by low-index facets, we have controllably fabricated nanorice and nanodumbbell particles, which exhibit drastically enhanced catalytic activities arising from the catalytically active high-index facets abundant on the particle surfaces. The nanorice and nanodumbbell particles also possess appealing tunable plasmonic properties that allow us to gain quantitative insights into nanoparticle-catalyzed reactions with unprecedented sensitivity and detail through time-resolved plasmon-enhanced spectroscopic measurements. PMID:24842375

  19. Tunable Plasmonic Nanoparticles with Catalytically Active High-Index Facets

    NASA Astrophysics Data System (ADS)

    Jing, Hao; Large, Nicolas; Zhang, Qinfeng; Nordlander, Peter; Wang, Hui

    2015-03-01

    Noble metal nanoparticles have been of tremendous interest due to their intriguing size- and shape-dependent plasmonic and catalytic properties. Combining tunable plasmon resonances with superior catalytic activities on the same metallic nanoparticle, however, has long been challenging because nanoplasmonics and nanocatalysis typically require nanoparticles in two drastically different size regimes. Here, we demonstrate that creation of high-index facets on subwavelength metallic nanoparticles provides a unique approach to the integration of desired plasmonic and catalytic properties on the same nanoparticle. Through site-selective surface etching of metallic nanocuboids whose surfaces are dominated by low-index facets, we have controllably fabricated nanorice and nanodumbbell shaped particles, which exhibit drastically enhanced catalytic activities arising from the catalytically active high-index facets abundant on the particle surfaces. The nanorice and nanodumbbell particles also possess appealing tunable plasmonic properties that allow us to gain quantitative insights into nanoparticle-catalyzed reactions with unprecedented sensitivity and detail through time-resolved plasmon-enhanced spectroscopic measurements. Past affiliation: Rice University.

  20. Site directed immobilization of glucose-6-phosphate dehydrogenase via thiol-disulfide interchange: influence on catalytic activity of cysteines introduced at different positions.

    PubMed

    Simons, J R; Mosisch, M; Torda, A E; Hilterhaus, L

    2013-08-10

    This study shows the effect of site-directed enzyme immobilization upon the enzyme activity of covalently bound glucose-6-phosphate dehydrogenase from Leuconostoc mesenteroides. Immobilization points were introduced at sterically accessible sites in order to control the protein's orientation and twice as much activity was recovered in comparison to conventionally immobilized enzyme. Immobilization of G6PDH via genetically engineered cysteine provided a simple, but effective method to control the immobilization process. G6PDH variants with cysteine close to the active center (L218C), close to the dimer interface (D205C) as well as far from the active center (D453C) showed changes in activity and the efficacy of immobilization. PMID:23770076

  1. Correlations between surface structure and catalytic activity/selectivity

    SciTech Connect

    Goodman, D.W.

    1992-10-01

    Objective is to address the keys to understanding the relation between surface structure and catalytic activity/selectivity. Of concern are questions related to enhanced catalytic properties of mixed-metal catalysts and critical active site requirements for molecular synthesis and rearrangement. The experimental approach utilizes a microcatalytic reactor contiguous to a surface analysis system, an arrangement which allows in vacuo transfer of the catalyst from one chamber to the other. Surface techniques being used include Auger (AES), UV and X-ray photoemission spectroscopy (UPS and XPS), temperature programmed desorption (TPD), low energy electron diffraction (LEED), high resolution electron energy loss spectroscopy (HREELS) and infrared reflection-absorption spectroscopy (IRAS). Our research program builds upon our previous experience relating the results of single crystal kinetic measurements with the results obtained with supported analogs. As well we are exploiting our recent work on the preparation, the characterization, and the determination of the catalytic properties of ultra-thin metal and metal oxide films. The program is proceeding toward the study of the unique catalytic properties of ultrathin metal films; the investigation of the critical ensemble size requirements for principal catalytic reaction types; and the modelling of supported catalysts using ultra-thin planar oxide surfaces.

  2. The role of the K-channel and the active-site tyrosine in the catalytic mechanism of cytochrome c oxidase.

    PubMed

    Sharma, Vivek; Wikström, Mårten

    2016-08-01

    The active site of cytochrome c oxidase (CcO) comprises an oxygen-binding heme, a nearby copper ion (CuB), and a tyrosine residue that is covalently linked to one of the histidine ligands of CuB. Two proton-conducting pathways are observed in CcO, namely the D- and the K-channels, which are used to transfer protons either to the active site of oxygen reduction (substrate protons) or for pumping. Proton transfer through the D-channel is very fast, and its role in efficient transfer of both substrate and pumped protons is well established. However, it has not been fully clear why a separate K-channel is required, apparently for the supply of substrate protons only. In this work, we have analysed the available experimental and computational data, based on which we provide new perspectives on the role of the K-channel. Our analysis suggests that proton transfer in the K-channel may be gated by the protonation state of the active-site tyrosine (Tyr244) and that the neutral radical form of this residue has a more general role in the CcO mechanism than thought previously. This article is part of a Special Issue entitled 'EBEC 2016: 19th European Bioenergetics Conference, Riva del Garda, Italy, July 2-6, 2016', edited by Prof. Paolo Bernardi. PMID:26898520

  3. Homology modelling and structural analysis of human arylamine N-acetyltransferase NAT1: evidence for the conservation of a cysteine protease catalytic domain and an active-site loop.

    PubMed Central

    Rodrigues-Lima, F; Deloménie, C; Goodfellow, G H; Grant, D M; Dupret, J M

    2001-01-01

    Arylamine N-acetyltransferases (EC 2.3.1.5) (NATs) catalyse the biotransformation of many primary arylamines, hydrazines and their N-hydroxylated metabolites, thereby playing an important role in both the detoxification and metabolic activation of numerous xenobiotics. The recently published crystal structure of the Salmonella typhimurium NAT (StNAT) revealed the existence of a cysteine protease-like (Cys-His-Asp) catalytic triad. In the present study, a three-dimensional homology model of human NAT1, based upon the crystal structure of StNAT [Sinclair, Sandy, Delgoda, Sim and Noble (2000) Nat. Struct. Biol. 7, 560-564], is demonstrated. Alignment of StNAT and NAT1, together with secondary structure predictions, have defined a consensus region (residues 29-131) in which 37% of the residues are conserved. Homology modelling provided a good quality model of the corresponding region in human NAT1. The location of the catalytic triad was found to be identical in StNAT and NAT1. Comparison of active-site structural elements revealed that a similar length loop is conserved in both species (residues 122-131 in NAT1 model and residues 122-133 in StNAT). This observation may explain the involvement of residues 125, 127 and 129 in human NAT substrate selectivity. Our model, and the fact that cysteine protease inhibitors do not affect the activity of NAT1, suggests that human NATs may have adapted a common catalytic mechanism from cysteine proteases to accommodate it for acetyl-transfer reactions. PMID:11368758

  4. Glu311 and Arg337 Stabilize a Closed Active-site Conformation and Provide a Critical Catalytic Base and Countercation for Green Bioluminescence in Beetle Luciferases.

    PubMed

    Viviani, V R; Simões, A; Bevilaqua, V R; Gabriel, G V M; Arnoldi, F G C; Hirano, T

    2016-08-30

    Beetle luciferases elicit the emission of different bioluminescence colors from green to red. Whereas firefly luciferases emit yellow-green light and are pH-sensitive, undergoing a typical red-shift at acidic pH and higher temperatures and in the presence of divalent heavy metals, click beetle and railroadworm luciferases emit a wider range of colors from green to red but are pH-independent. Despite many decades of study, the structural determinants and mechanisms of bioluminescence colors and pH sensitivity remain enigmatic. Here, through modeling studies, site-directed mutagenesis, and spectral and kinetic studies using recombinant luciferases from the three main families of bioluminescent beetles that emit different colors of light (Macrolampis sp2 firefly, Phrixotrix hirtus railroadworm, and Pyrearinus termitilluminans click beetle), we investigated the role of E311 and R337 in bioluminescence color determination. All mutations of these residues in firefly luciferase produced red mutants, indicating that the preservation of opposite charges and the lengths of the side chains of E311 and R337 are essential for keeping a salt bridge that stabilizes a closed hydrophobic conformation favorable for green light emission. Kinetic studies indicate that residue R337 is important for binding luciferin and creating a positively charged environment around excited oxyluciferin phenolate. In Pyrearinus green-emitting luciferase, the R334A mutation causes a 27 nm red-shift, whereas in Phrixotrix red-emitting luciferase, the L334R mutation causes a blue-shift that is no longer affected by guanidine. These results provide compelling evidence that the presence of arginine at position 334 is essential for blue-shifting the emission spectra of most beetle luciferases. Therefore, residues E311 and R337 play both structural and catalytic roles in bioluminescence color determination, by stabilizing a closed hydrophobic conformation favorable for green light emission, and also

  5. Human holocarboxylase synthetase with a start site at methionine-58 is the predominant nuclear variant of this protein and has catalytic activity

    SciTech Connect

    Bao, Baolong; Wijeratne, Subhashinee S.K.; Rodriguez-Melendez, Rocio; Zempleni, Janos

    2011-08-19

    Highlights: {yields} Unambiguous evidence is provided that methionine-58 serves as an in-frame alternative translation site for holocarboxylase synthetase (HLCS58). {yields} Full-length HLCS and HLCS58 enter the nucleus, but HLCS58 is the predominant variant. {yields} HLCS58 has biological activity as biotin protein ligase. -- Abstract: Holocarboxylase synthetase (HLCS) catalyzes the covalent binding of biotin to both carboxylases in extranuclear structures and histones in cell nuclei, thereby mediating important roles in intermediary metabolism, gene regulation, and genome stability. HLCS has three putative translational start sites (methionine-1, -7, and -58), but lacks a strong nuclear localization sequence that would explain its participation in epigenetic events in the cell nucleus. Recent evidence suggests that small quantities of HLCS with a start site in methionine-58 (HLCS58) might be able to enter the nuclear compartment. We generated the following novel insights into HLCS biology. First, we generated a novel HLCS fusion protein vector to demonstrate that methionine-58 is a functional translation start site in human cells. Second, we used confocal microscopy and western blots to demonstrate that HLCS58 enters the cell nucleus in meaningful quantities, and that full-length HLCS localizes predominantly in the cytoplasm but may also enter the nucleus. Third, we produced recombinant HLCS58 to demonstrate its biological activity toward catalyzing the biotinylation of both carboxylases and histones. Collectively, these observations are consistent with roles of HLCS58 and full-length HLCS in nuclear events. We conclude this report by proposing a novel role for HLCS in epigenetic events, mediated by physical interactions between HLCS and other chromatin proteins as part of a larger multiprotein complex that mediates gene repression.

  6. Targeting the cyclin-binding groove site to inhibit the catalytic activity of CDK2/cyclin A complex using p27(KIP1)-derived peptidomimetic inhibitors.

    PubMed

    Karthiga, Arumugasamy; Tripathi, Sunil Kumar; Shanmugam, Ramasamy; Suryanarayanan, Venkatesan; Singh, Sanjeev Kumar

    2015-01-01

    Functionally activated cyclin-dependent kinase 2 (CDK2)/cyclin A complex has been validated as an interesting therapeutic target to develop the efficient antineoplastic drug based on the cell cycle arrest. Cyclin A binds to CDK2 and activates the kinases as well as recruits the substrate and inhibitors using a hydrophobic cyclin-binding groove (CBG). Blocking the cyclin substrate recruitment on CBG is an alternative approach to override the specificity hurdle of the currently available ATP site targeting CDK2 inhibitors. Greater understanding of the interaction of CDK2/cyclin A complex with p27 (negative regulator) reveals that the Leu-Phe-Gly (LFG) motif region of p27 binds with the CBG site of cyclin A to arrest the malignant cell proliferation that induces apoptosis. In the present study, Replacement with Partial Ligand Alternatives through Computational Enrichment (REPLACE) drug design strategies have been applied to acquire LFG peptide-derived peptidomimetics library. The peptidomimetics function is equivalent with respect to substrate p27 protein fashion but does not act as an ATP antagonist. The combined approach of molecular docking, molecular dynamics (MD), and molecular electrostatic potential and ADME/T prediction were carried out to evaluate the peptidomimetics. Resultant interaction and electrostatic potential maps suggested that smaller substituent is desirable at the position of phenyl ring to interact with Trp217, Arg250, and Gln254 residues in the active site. The best docked poses were refined by the MD simulations which resulted in conformational changes. After equilibration, the structure of the peptidomimetic and receptor complex was stable. The results revealed that the various substrate protein-derived peptidomimetics could serve as perfect leads against CDK2 protein. PMID:25584078

  7. Catalytic Ethanol Dehydration over Different Acid-activated Montmorillonite Clays.

    PubMed

    Krutpijit, Chadaporn; Jongsomjit, Bunjerd

    2016-01-01

    In the present study, the catalytic dehydration of ethanol to obtain ethylene over montmorillonite clays (MMT) with mineral acid activation including H2SO4 (SA-MMT), HCl (HA-MMT) and HNO3 (NA-MMT) was investigated at temperature range of 200 to 400°C. It revealed that HA-MMT exhibited the highest catalytic activity. Ethanol conversion and ethylene selectivity were found to increase with increased reaction temperature. At 400°C, the HA-MMT yielded 82% of ethanol conversion having 78% of ethylene yield. At lower temperature (i.e. 200 to 300°C), diethyl ether (DEE) was a major product. The highest activity obtained from HA-MMT can be attributed to an increase of weak acid sites and acid density by the activation of MMT with HCl. It can be also proven by various characterization techniques that in most case, the main structure of MMT did not alter by acid activation (excepted for NA-MMT). Upon the stability test for 72 h during the reaction, the MMT and HA-MMT showed only slight deactivation due to carbon deposition. Hence, the acid activation of MMT by HCl is promising to enhance the catalytic dehydration of ethanol. PMID:27041515

  8. Catalytic Activities Of [GADV]-Peptides

    NASA Astrophysics Data System (ADS)

    Oba, Takae; Fukushima, Jun; Maruyama, Masako; Iwamoto, Ryoko; Ikehara, Kenji

    2005-10-01

    We have previously postulated a novel hypothesis for the origin of life, assuming that life on the earth originated from “[GADV]-protein world”, not from the “RNA world” (see Ikehara's review, 2002). The [GADV]-protein world is constituted from peptides and proteins with random sequences of four amino acids (glycine [G], alanine [A], aspartic acid [D] and valine [V]), which accumulated by pseudo-replication of the [GADV]-proteins. To obtain evidence for the hypothesis, we produced [GADV]-peptides by repeated heat-drying of the amino acids for 30 cycles ([GADV]-P30) and examined whether the peptides have some catalytic activities or not. From the results, it was found that the [GADV]-P30 can hydrolyze several kinds of chemical bonds in molecules, such as umbelliferyl-β-D-galactoside, glycine-p-nitroanilide and bovine serum albumin. This suggests that [GADV]-P30 could play an important role in the accumulation of [GADV]-proteins through pseudo-replication, leading to the emergence of life. We further show that [GADV]-octapaptides with random sequences, but containing no cyclic compounds as diketepiperazines, have catalytic activity, hydrolyzing peptide bonds in a natural protein, bovine serum albumin. The catalytic activity of the octapeptides was much higher than the [GADV]-P30 produced through repeated heat-drying treatments. These results also support the [GADV]-protein-world hypothesis of the origin of life (see Ikehara's review, 2002). Possible steps for the emergence of life on the primitive earth are presented.

  9. Oxidative Dehydrogenation on Nanocarbon: Intrinsic Catalytic Activity and Structure-Function Relationships.

    PubMed

    Qi, Wei; Liu, Wei; Guo, Xiaoling; Schlögl, Robert; Su, Dangsheng

    2015-11-01

    Physical and chemical insights into the nature and quantity of the active sites and the intrinsic catalytic activity of nanocarbon materials in alkane oxidative dehydrogenation (ODH) reactions are reported using a novel in situ chemical titration process. A study on the structure-function relationship reveals that the active sites are identical both in nature and function on various nanocarbon catalysts. Additionally, the quantity of the active sites could be used as a metric to normalize the reaction rates, and thus to evaluate the intrinsic activity of nanocarbon catalysts. The morphology of the nanocarbon catalysts at the microscopic scale exhibits a minor influence on their intrinsic ODH catalytic activity. The number of active sites calculated from the titration process indicates the number of catalytic centers that are active (that is, working) under the reaction conditions. PMID:26388451

  10. Catalytic mechanism of active-site serine beta-lactamases: role of the conserved hydroxy group of the Lys-Thr(Ser)-Gly triad.

    PubMed Central

    Dubus, A; Wilkin, J M; Raquet, X; Normark, S; Frère, J M

    1994-01-01

    The role of the conserved hydroxy group of the Lys-Thr(Ser)-Gly [KT(S)G] triad has been studied for a class A and a class C beta-lactamase by site-directed mutagenesis. Surprisingly, the disappearance of this functional group had little impact on the penicillinase activity of both enzymes. The cephalosporinase activity was much more affected for the class A S235A (Ser235-->Ala) and the class C T316V (Thr315-->Val) mutants, but the class C T316A mutant was less impaired. Studies were extended to beta-lactams, where the carboxy group on C-3 of penicillins or C-4 of cephalosporins had been modified. The effects of the mutations were the same on these compounds as on the unmodified regular penicillins and cephalosporins. The results are compared with those obtained with a similar mutant (T299V) of the Streptomyces R61 DD-peptidase. With this enzyme the mutation also affected the interactions with penicillins and severely decreased the peptidase activity. The strict conservation of the hydroxy group on the second residue of the KT(S)G triad is thus much more easy to understand for the DD-peptidase and the penicillin-binding proteins than for beta-lactamases, especially those of class C. Images Figure 1 PMID:8042993

  11. Thrombomodulin Binding Selects the Catalytically Active Form of Thrombin.

    PubMed

    Handley, Lindsey D; Treuheit, Nicholas A; Venkatesh, Varun J; Komives, Elizabeth A

    2015-11-01

    Human α-thrombin is a serine protease with dual functions. Thrombin acts as a procoagulant, cleaving fibrinogen to make the fibrin clot, but when bound to thrombomodulin (TM), it acts as an anticoagulant, cleaving protein C. A minimal TM fragment consisting of the fourth, fifth, and most of the sixth EGF-like domain (TM456m) that has been prepared has much improved solubility, thrombin binding capacity, and anticoagulant activity versus those of previous TM456 constructs. In this work, we compare backbone amide exchange of human α-thrombin in three states: apo, D-Phe-Pro-Arg-chloromethylketone (PPACK)-bound, and TM456m-bound. Beyond causing a decreased level of amide exchange at their binding sites, TM and PPACK both cause a decreased level of amide exchange in other regions including the γ-loop and the adjacent N-terminus of the heavy chain. The decreased level of amide exchange in the N-terminus of the heavy chain is consistent with the historic model of activation of serine proteases, which involves insertion of this region into the β-barrel promoting the correct conformation of the catalytic residues. Contrary to crystal structures of thrombin, hydrogen-deuterium exchange mass spectrometry results suggest that the conformation of apo-thrombin does not yet have the N-terminus of the heavy chain properly inserted for optimal catalytic activity, and that binding of TM allosterically promotes the catalytically active conformation. PMID:26468766

  12. Structural Basis for Catalytic Activation of a Serine Recombinase

    SciTech Connect

    Keenholtz, Ross A.; Rowland, Sally-J.; Boocock, Martin R.; Stark, W. Marshall; Rice, Phoebe A.

    2014-10-02

    Sin resolvase is a site-specific serine recombinase that is normally controlled by a complex regulatory mechanism. A single mutation, Q115R, allows the enzyme to bypass the entire regulatory apparatus, such that no accessory proteins or DNA sites are required. Here, we present a 1.86 {angstrom} crystal structure of the Sin Q115R catalytic domain, in a tetrameric arrangement stabilized by an interaction between Arg115 residues on neighboring subunits. The subunits have undergone significant conformational changes from the inactive dimeric state previously reported. The structure provides a new high-resolution view of a serine recombinase active site that is apparently fully assembled, suggesting roles for the conserved active site residues. The structure also suggests how the dimer-tetramer transition is coupled to assembly of the active site. The tetramer is captured in a different rotational substate than that seen in previous hyperactive serine recombinase structures, and unbroken crossover site DNA can be readily modeled into its active sites.

  13. Site-Directed Mutagenesis of Human Cytosolic Sulfotransferase (SULT) 2B1b to Phospho-mimetic Ser348Asp Results in an Isoform With Increased Catalytic Activity

    PubMed Central

    Salman, Emily D.; He, Dongning; Runge-Morris, Melissa; Kocarek, Thomas A.; Falany, Charles N.

    2011-01-01

    Human SULT2B1b is distinct from other SULT isoforms due to the presence of unique amino (N)- and carboxy (C)-terminal peptides. Using site-directed mutagenesis, it was determined that phosphorylation of Ser348 was associated with nuclear localization. To investigate the effects of this phosphorylation of Ser348 on activity and cellular localization, an in silico molecular mimic was generated by mutating Ser348 to an Asp. The Asp residue mimics the shape and charge of a phospho-Ser and homology models of SULT2B1b-phospho-S348 and SULT2B1b-S348D suggest a similar significant structural rearrangement in the C-terminal peptide. To evaluate the functional consequences of this post-translational modification and predicted rearrangement, 6His-SULT2B1b-S348D was synthesized, expressed, purified and characterized. The 6His-SULT2B1b-S348D has a specific activity for DHEA sulfation ten-fold higher than recombinant 6His-SULT2B1b (209.6 and 21.8 pmol·min−1·mg−1, respectively). Similar to native SULT2B1b, gel filtration chromatography showed SULT2B1b-S348D was enzymatically active as a homodimer. Stability assays comparing SULT2B1b and SUL2B1b-S348 demonstrated that SULT2B1b is 60% less thermostable than SULT2B1b-348D. The increased stability and sulfation activity allowed for better characterization of the sulfation kinetics for putative substrates as well as the determination of dissociation constants that were difficult to obtain with wild-type (WT) 6His-SULT2B1b. The KDs for DHEA and PAPS binding to 6His-SULT2B1b-S348D were 650 ± 7 nM and 265 ± 4 nM, respectively, whereas KDs for binding of substrates to the WT enzyme could not be determined. Characterization of the molecular mimic SULT2B1b-S348D provides a better understanding for the role of the unique structure of SULT2B1b and its effect on sulfation activity, and has allowed for improved kinetic characterization of the SULT2B1b enzyme. PMID:21855633

  14. Tunable Molecular MoS2 Edge-Site Mimics for Catalytic Hydrogen Production.

    PubMed

    Garrett, Benjamin R; Polen, Shane M; Click, Kevin A; He, Mingfu; Huang, Zhongjie; Hadad, Christopher M; Wu, Yiying

    2016-04-18

    Molybdenum sulfides represent state-of-the-art, non-platinum electrocatalysts for the hydrogen evolution reaction (HER). According to the Sabatier principle, the hydrogen binding strength to the edge active sites should be neither too strong nor too weak. Therefore, it is of interest to develop a molecular motif that mimics the catalytic sites structurally and possesses tunable electronic properties that influence the hydrogen binding strength. Furthermore, molecular mimics will be important for providing mechanistic insight toward the HER with molybdenum sulfide catalysts. In this work, a modular method to tune the catalytic properties of the S-S bond in MoO(S2)2L2 complexes is described. We studied the homogeneous electrocatalytic hydrogen production performance metrics of three catalysts with different bipyridine substitutions. By varying the electron-donating abilities, we present the first demonstration of using the ligand to tune the catalytic properties of the S-S bond in molecular MoS2 edge-site mimics. This work can shed light on the relationship between the structure and electrocatalytic activity of molecular MoS2 catalysts and thus is of broad importance from catalytic hydrogen production to biological enzyme functions. PMID:27022836

  15. Role of support-nanoalloy interactions in the atomic-scale structural and chemical ordering for tuning catalytic sites

    SciTech Connect

    Yang, Lefu; Shan, Shiyao; Loukrakpam, Rameshwori; Petkov, Valeri; Ren, Yang; Wanjala, Bridgid N.; Engelhard, Mark H.; Luo, Jin; Yin, Jun; Chen, Yongsheng; Zhong, Chuan-Jian

    2012-09-12

    The understanding of the atomic-scale structural and chemical ordering in supported nanosized alloy particles is fundamental for achieving active catalysts by design. This report shows how such knowledge can be obtained by a combination of techniques including x-ray photoelectron spectroscopy and synchrotron radiation based x-ray fine structure absorption spectroscopy and high-energy x-ray diffraction coupled to atomic pair distribution function analysis, and how the support-nanoalloy interaction influences the catalytic activity of a ternary nanoalloy (platinum-nickel-cobalt) particles on three different supports: carbon, silica and titania. The reaction of carbon monoxide with oxygen is employed as a probe of the catalytic activity. This ternary composition, in combination with the different support materials, is demonstrated to be capable of fine-tuning the catalytic activity and stability. The support-nanoalloy interaction is shown to influence structural and chemical ordering in the nanoparticles, leading to support-tunable active sites on the nanoalloys for oxygen activation in the catalytic oxidation of carbon monoxide. A nickel/cobalt-tuned catalytic site on the surface of nanoalloy was revealed for oxygen activation, which differs from the traditional oxygen-activation sites known for oxide-supported noble metal catalysts. The discovery of such support-nanoalloy interaction enabled oxygen-activation sites introduces a very promising strategy for designing active catalysts in heterogeneous catalysis.

  16. Catalytic Activity of a Binary Informational Macromolecule

    NASA Technical Reports Server (NTRS)

    Reader, John S.; Joyce, Gerald F.

    2003-01-01

    RNA molecules are thought to have played a prominent role in the early history of life on Earth based on their ability both to encode genetic information and to exhibit catalytic function. The modern genetic alphabet relies on two sets of complementary base pairs to store genetic information. However, due to the chemical instability of cytosine, which readily deaminates to uracil, a primitive genetic system composed of the bases A, U, G and C may have been difficult to establish. It has been suggested that the first genetic material instead contained only a single base-pairing unie'. Here we show that binary informational macromolecules, containing only two different nucleotide subunits, can act as catalysts. In vitro evolution was used to obtain ligase ribozymes composed of only 2,6-diaminopurine and uracil nucleotides, which catalyze the template-directed joining of two RNA molecules, one bearing a 5'-triphosphate and the other a 3'-hydroxyl. The active conformation of the fastest isolated ribozyme had a catalytic rate that was about 36,000-fold faster than the uncatalyzed rate of reaction. This ribozyme is specific for the formation of biologically relevant 3',5'-phosphodiester linkages.

  17. Long-range electrostatics-induced two-proton transfer captured by neutron crystallography in an enzyme catalytic site

    DOE PAGESBeta

    Gerlits, Oksana; Wymore, Troy; Das, Amit; Shen, Chen -Hsiang; Parks, Jerry M.; Smith, Jeremy C.; Weiss, Kevin L.; Keen, David A.; Blakeley, Matthew P.; Louis, John M.; et al

    2016-03-09

    Neutron crystallography was used to directly locate two protons before and after a pH-induced two-proton transfer between catalytic aspartic acid residues and the hydroxy group of the bound clinical drug darunavir, located in the catalytic site of enzyme HIV-1 protease. The two-proton transfer is triggered by electrostatic effects arising from protonation state changes of surface residues far from the active site. The mechanism and pH effect are supported by quantum mechanics/molecular mechanics (QM/MM) calculations. The low-pH proton configuration in the catalytic site is deemed critical for the catalytic action of this enzyme and may apply more generally to other asparticmore » proteases. Neutrons therefore represent a superb probe to obtain structural details for proton transfer reactions in biological systems at a truly atomic level.« less

  18. Long-Range Electrostatics-Induced Two-Proton Transfer Captured by Neutron Crystallography in an Enzyme Catalytic Site.

    PubMed

    Gerlits, Oksana; Wymore, Troy; Das, Amit; Shen, Chen-Hsiang; Parks, Jerry M; Smith, Jeremy C; Weiss, Kevin L; Keen, David A; Blakeley, Matthew P; Louis, John M; Langan, Paul; Weber, Irene T; Kovalevsky, Andrey

    2016-04-11

    Neutron crystallography was used to directly locate two protons before and after a pH-induced two-proton transfer between catalytic aspartic acid residues and the hydroxy group of the bound clinical drug darunavir, located in the catalytic site of enzyme HIV-1 protease. The two-proton transfer is triggered by electrostatic effects arising from protonation state changes of surface residues far from the active site. The mechanism and pH effect are supported by quantum mechanics/molecular mechanics (QM/MM) calculations. The low-pH proton configuration in the catalytic site is deemed critical for the catalytic action of this enzyme and may apply more generally to other aspartic proteases. Neutrons therefore represent a superb probe to obtain structural details for proton transfer reactions in biological systems at a truly atomic level. PMID:26958828

  19. Catalytically active single-atom niobium in graphitic layers.

    PubMed

    Zhang, Xuefeng; Guo, Junjie; Guan, Pengfei; Liu, Chunjing; Huang, Hao; Xue, Fanghong; Dong, Xinglong; Pennycook, Stephen J; Chisholm, Matthew F

    2013-01-01

    Carbides of groups IV through VI (Ti, V and Cr groups) have long been proposed as substitutes for noble metal-based electrocatalysts in polymer electrolyte fuel cells. However, their catalytic activity has been extremely limited because of the low density and stability of catalytically active sites. Here we report the excellent performance of a niobium-carbon structure for catalysing the cathodic oxygen reduction reaction. A large number of single niobium atoms and ultra small clusters trapped in graphitic layers are directly identified using state-of-the-art aberration-corrected scanning transmission electron microscopy. This structure not only enhances the overall conductivity for accelerating the exchange of ions and electrons, but it suppresses the chemical/thermal coarsening of the active particles. Experimental results coupled with theory calculations reveal that the single niobium atoms incorporated within the graphitic layers produce a redistribution of d-band electrons and become surprisingly active for O2 adsorption and dissociation, and also exhibit high stability. PMID:23715283

  20. Noble metal ionic sites for catalytic hydrogen combustion: spectroscopic insights.

    PubMed

    Deshpande, Parag A; Madras, Giridhar

    2011-01-14

    A catalytic hydrogen combustion reaction was carried out over noble metal catalysts substituted in ZrO(2) and TiO(2) in ionic form. The catalysts were synthesized by the solution combustion technique. The compounds showed high activity and CO tolerance for the reaction. The activity of Pd and Pt ion substituted TiO(2) was comparable and was higher than Pd and Pt ion substituted ZrO(2). The mechanisms of the reaction over the two supports were proposed by making use of the X-ray photoelectron spectroscopy and FT infrared spectroscopic observations. The reaction over ZrO(2) supported catalysts was proposed to take place by the utilization of the surface hydroxyl groups while the reaction over TiO(2) supported catalysts was hypothesized to be a hybrid mechanism utilizing surface hydroxyl groups and the lattice oxygen. PMID:21060910

  1. Paramagnetic 1H and 13C NMR studies on cobalt-substituted human carbonic anhydrase I carboxymethylated at active site histidine-200: molecular basis for the changes in catalytic properties induced by the modification.

    PubMed

    Khalifah, R G; Rogers, J I; Harmon, P; Morely, P J; Carroll, S B

    1984-07-01

    Using bromo[1-13C]acetate to modify N tau of His-200 of human carbonic anhydrase isozyme I leads to the introduction of a useful 13C NMR probe into the active site. To complement our previous diamagnetic NMR studies with this probe, we have now succeeded in directly observing the paramagnetically perturbed resonance of the carboxylate in the cobalt-substituted modified enzyme above pH 8. In the pH range 8-10, the resonance undergoes a pH-dependent slow-exchange process, with the more alkaline form having a much smaller pseudocontact shift and a narrower line width. Below pH 8, the resonance apparently undergoes a very large paramagnetic downfield shift that was estimated by extrapolation. An ionization of approximate pK of 6 appears to control this process. Paramagnetic spin-relaxation studies on the resonance under conditions where it was directly observed yielded distance measurements between the carboxylate carbon and the active site cobalt ion. In inhibitor complexes, this distance was in the range of 5-7 A. In the absence of inhibitors, the distance was approximately 3.0-3.2 A at pH 7.9, consistent with the coordination of the carboxylate to the metal. However, at pH 10, the distance was increased to 4.8 A. These distance determinations were aided by relaxation measurements of a paramagnetically shifted proton resonance at 60-65 ppm downfield assigned by others to a proton of a ligand histidine of metal and confirmed by us to be 5.2 +/- 0.1 A from the metal. Our findings provide a molecular basis for the observed changes in catalytic properties that accompany the carboxymethylation. PMID:6432037

  2. Interface dynamics explain assembly dependency of influenza neuraminidase catalytic activity

    PubMed Central

    von Grafenstein, Susanne; Wallnoefer, Hannes G.; Kirchmair, Johannes; Fuchs, Julian E.; Huber, Roland G.; Schmidtke, Michaela; Sauerbrei, Andreas; Rollinger, Judith M.; Liedl, Klaus R.

    2015-01-01

    Influenza virus neuraminidase (iNA) is a homotetrameric surface protein of the influenza virus and an established target for antiviral drugs. In contrast to neuraminidases (NAs) of other biological systems (non-iNAs), enzymatic activity of iNA is only observed in a quaternary assembly and iNA needs the tetramerization to mediate enzymatic activity. Obviously, differences on a molecular level between iNA and non-iNAs are responsible for this intriguing observation. Comparison between protein structures and multiple sequence alignment allow the identification of differences in amino acid composition in crucial regions of the enzyme, such as next to the conserved D151 and the 150-loop. These differences in amino acid sequence and protein tetramerization are likely to alter the dynamics of the system. Therefore, we performed molecular dynamics simulations to investigate differences in the molecular flexibility of monomers, dimers, and tetramers of iNAs of subtype N1 (avian 2004, pandemic 1918 and pandemic 2009 iNA) and as comparison the non-iNA monomer from Clostridium perfringens. We show that conformational transitions of iNA are crucially influenced by its assembly state. The protein–protein interface induces a complex hydrogen-bonding network between the 110-helix and the 150-loop, which consequently stabilizes the structural arrangement of the binding site. Therefore, we claim that these altered dynamics are responsible for the dependence of iNA’s catalytic activity on the tetrameric assembly. Only the tetramerization-induced balance between stabilization and altered local flexibility in the binding site provides the appropriate arrangement of key residues for iNA’s catalytic activity. PMID:24279589

  3. Catalytic improvement and structural analysis of atrazine chlorohydrolase by site-saturation mutagenesis.

    PubMed

    Guo, Yuan; Zhao, Panjie; Zhang, Wenhao; Li, Xiaolong; Chen, Xiwen; Chen, Defu

    2016-07-01

    To improve the catalytic activity of atrazine chlorohydrolase (AtzA), amino acid residues involved in substrate binding (Gln71) and catalytic efficiency (Val12, Ile393, and Leu395) were targeted to generate site-saturation mutagenesis libraries. Seventeen variants were obtained through Haematococcus pluvialis-based screening, and their specific activities were 1.2-5.2-fold higher than that of the wild type. For these variants, Gln71 tended to be substituted by hydrophobic amino acids, Ile393 and Leu395 by polar ones, especially arginine, and Val12 by alanine, respectively. Q71R and Q71M significantly decreased the Km by enlarging the substrate-entry channel and affecting N-ethyl binding. Mutations at sites 393 and 395 significantly increased the kcat/Km, probably by improving the stability of the dual β-sheet domain and the whole enzyme, owing to hydrogen bond formation. In addition, the contradictory relationship between the substrate affinity improvement by Gln71 mutation and the catalytic efficiency improvement by the dual β-sheet domain modification was discussed. PMID:27010688

  4. Modeling the heterogeneous catalytic activity of a single nanoparticle using a first passage time distribution formalism

    NASA Astrophysics Data System (ADS)

    Das, Anusheela; Chaudhury, Srabanti

    2015-11-01

    Metal nanoparticles are heterogeneous catalysts and have a multitude of non-equivalent, catalytic sites on the nanoparticle surface. The product dissociation step in such reaction schemes can follow multiple pathways. Proposed here for the first time is a completely analytical theoretical framework, based on the first passage time distribution, that incorporates the effect of heterogeneity in nanoparticle catalysis explicitly by considering multiple, non-equivalent catalytic sites on the nanoparticle surface. Our results show that in nanoparticle catalysis, the effect of dynamic disorder is manifested even at limiting substrate concentrations in contrast to an enzyme that has only one well-defined active site.

  5. Functional Identification of Catalytic Metal Ion Binding Sites within RNA

    PubMed Central

    2005-01-01

    The viability of living systems depends inextricably on enzymes that catalyze phosphoryl transfer reactions. For many enzymes in this class, including several ribozymes, divalent metal ions serve as obligate cofactors. Understanding how metal ions mediate catalysis requires elucidation of metal ion interactions with both the enzyme and the substrate(s). In the Tetrahymena group I intron, previous work using atomic mutagenesis and quantitative analysis of metal ion rescue behavior identified three metal ions (MA, MB, and MC) that make five interactions with the ribozyme substrates in the reaction's transition state. Here, we combine substrate atomic mutagenesis with site-specific phosphorothioate substitutions in the ribozyme backbone to develop a powerful, general strategy for defining the ligands of catalytic metal ions within RNA. In applying this strategy to the Tetrahymena group I intron, we have identified the pro-SP phosphoryl oxygen at nucleotide C262 as a ribozyme ligand for MC. Our findings establish a direct connection between the ribozyme core and the functionally defined model of the chemical transition state, thereby extending the known set of transition-state interactions and providing information critical for the application of the recent group I intron crystallographic structures to the understanding of catalysis. PMID:16092891

  6. An effective approach for modifying carbonaceous materials with niobium single sites to improve their catalytic properties.

    PubMed

    Bozzi, A S; Lavall, R L; Souza, T E; Pereira, M C; de Souza, P P; De Abreu, H A; De Oliveira, A; Ortega, P F R; Paniago, R; Oliveira, L C A

    2015-12-14

    In this paper we show a very simple route for the incorporation of catalytically active niobium species on the surface of carbon materials, such as graphene oxide, carbon nanotubes and activated carbon. Some existing methods of incorporating a transition metal on a support have involved co-precipitation or wet impregnation, to obtain the corresponding oxides. These methods, however, cause reduction in the specific area of the support and can also form large metal oxide particles with loss of metal exposure. Therefore, here we present a novel way to add catalytically active species on the surfaces of different types of carbon through the formation of interaction complexes between the metal precursor and the functional groups of the carbon matrix. Because of the excellent catalytic properties exhibited by the niobium species we choose the NH4[NbO(C2O4)2(H2O)2]·2H2O salt as the model precursor. The characterization by XPS reveals the presence of the niobium species indicated by the displacement of the peaks between 206-212 eV related to the oxalate species according to the spectrum from pure niobium oxalate. Images obtained by TEM and SEM show the typical morphologies of carbonaceous materials without the niobium oxide formation signal, which indicates the presence of niobium complexes as isolated sites on the carbon surfaces. This new class of materials exhibited excellent properties as catalysts for pollutant oxidation. The presence of Nb promotes the catalytic activation of H2O2 generating hydroxyl radicals in situ, which allows their use in the organic compound oxidation processes. Tests for DBT oxidation indicate that Nb significantly improves the removal of such pollutants in biphasic reactions with removal around 90% under the tested conditions. Theoretical calculations showed that the most favorable adsorption model is an ionic complex presenting a ΔG = -108.7 kcal mol(-1) for the whole adsorption process. PMID:26514577

  7. Catalytic activities of zeolite compounds for decomposing aqueous ozone.

    PubMed

    Kusuda, Ai; Kitayama, Mikito; Ohta, Yoshio

    2013-12-01

    The advanced oxidation process (AOP), chemical oxidation using aqueous ozone in the presence of appropriate catalysts to generate highly reactive oxygen species, offers an attractive option for removing poorly biodegradable pollutants. Using the commercial zeolite powders with various Si/Al ratios and crystal structures, their catalytic activities for decomposing aqueous ozone were evaluated by continuously flowing ozone to water containing the zeolite powders. The hydrophilic zeolites (low Si/Al ratio) with alkali cations in the crystal structures were found to possess high catalytic activity for decomposing aqueous ozone. The hydrophobic zeolite compounds (high Si/Al ratio) were found to absorb ozone very well, but to have no catalytic activity for decomposing aqueous ozone. Their catalytic activities were also evaluated by using the fixed bed column method. When alkali cations were removed by acid rinsing or substituted by alkali-earth cations, the catalytic activities was significantly deteriorated. These results suggest that the metal cations on the crystal surface of the hydrophilic zeolite would play a key role for catalytic activity for decomposing aqueous ozone. PMID:25078817

  8. Structures of the Wild-Type And Activated Catalytic Domains of Brachydanio Rerio Polo-Like Kinase 1 (Plk1): Changes in the Active-Site Conformation And Interactions With Ligands

    SciTech Connect

    Elling, R.A.; Fucini, R.V.; Romanowski, M.J.

    2009-05-18

    Polo-like kinase 1 (Plk1) is a member of a family of serine/threonine kinases involved in the regulation of cell-cycle progression and cytokinesis and is an attractive target for the development of anticancer therapeutics. A zebrafish homolog of the human Plk1 (hPlk1) kinase domain (KD) was identified that can be expressed in large quantities in bacteria and crystallizes readily, whether in a wild-type form or as a variant containing the activating Thr196-->Asp substitution, in one space group and under similar conditions both in the absence and presence of active-site compounds. This construct was validated by testing a panel of hPlk1 inhibitors against human and zebrafish proteins and it was shown that the selected small molecules inhibited the homologs with a high degree of correlation. Crystal structures of ligand-free wild-type and activated zebrafish Plk1 (zPlk1) KDs revealed the organization of the secondary structural elements around the active site and demonstrated that the activation segment was disordered in the activated form of the domain but possessed a well defined secondary structure in the wild-type enzyme. The cocrystal structure of wild-type zPlk1 KD with ADP documented the hydrolysis of ATP and revealed the phosphorylation site. The cocrystal structure of the activated KD with wortmannin, a covalent inhibitor of Plk1 and PI3 kinases, showed the binding mode of the small molecule to the enzyme and may facilitate the design of more potent Plk1 inhibitors. The work presented in this study establishes the zPlk1 KD as a useful tool for rapid low- and high-throughput structure-based screening and drug discovery of compounds specific for this mitotic target.

  9. Probes of the Catalytic Site of Cysteine Dioxygenase

    SciTech Connect

    Chai,S.; Bruyere, J.; Maroney, M.

    2006-01-01

    The first major step of cysteine catabolism, the oxidation of cysteine to cysteine sulfinic acid, is catalyzed by cysteine dioxygenase (CDO). In the present work, we utilize recombinant rat liver CDO and cysteine derivatives to elucidate structural parameters involved in substrate recognition and x-ray absorption spectroscopy to probe the interaction of the active site iron center with cysteine. Kinetic studies using cysteine structural analogs show that most are inhibitors and that a terminal functional group bearing a negative charge (e.g. a carboxylate) is required for binding. The substrate-binding site has no stringent restrictions with respect to the size of the amino acid. Lack of the amino or carboxyl groups at the a-carbon does not prevent the molecules from interacting with the active site. In fact, cysteamine is shown to be a potent activator of the enzyme without being a substrate. CDO was also rendered inactive upon complexation with the metal-binding inhibitors azide and cyanide. Unlike many non-heme iron dioxygenases that employ a-keto acids as cofactors, CDO was shown to be the only dioxygenase known to be inhibited by {alpha}-ketoglutarate.

  10. Key residues at the riboflavin kinase catalytic site of the bifunctional riboflavin kinase/FMN adenylyltransferase from Corynebacterium ammoniagenes.

    PubMed

    Serrano, Ana; Frago, Susana; Herguedas, Beatriz; Martínez-Júlvez, Marta; Velázquez-Campoy, Adrián; Medina, Milagros

    2013-01-01

    Many known prokaryotic organisms depend on a single bifunctional enzyme, encoded by the RibC of RibF gene and named FAD synthetase (FADS), to convert Riboflavin (RF), first into FMN and then into FAD. The reaction occurs through the sequential action of two activities present on a single polypeptide chain where the N-terminus is responsible for the ATP:FMN adenylyltransferase (FMNAT) activity and the C-terminus for the ATP: riboflavin kinase (RFK) activity. Sequence and structural analysis suggest that T208, N210 and E268 at the C-terminus RFK module of Corynebacterium ammoniagenes FADS (CaFADS) might be key during RF phosphorylation. The effect of site-directed mutagenesis on the RFK activity, as well as on substrates and products binding, indicates that T208 and N210 provide the RFK active-site geometry for binding and catalysis, while E268 might be involved in the catalytic step as catalytic base. These data additionally suggest concerted conformational changes at the RFK module of CaFADS during its activity. Mutations at the RFK site also modulate the binding parameters at the FMNAT active site of CaFADS, altering the catalytic efficiency in the transformation of FMN into FAD. This observation supports the hypothesis that the hexameric assembly previously revealed by the crystal structure of CaFADS might play a functional role during catalysis. PMID:22892871

  11. Size-dependent catalytic activity of supported metal clusters

    NASA Astrophysics Data System (ADS)

    Xu, Z.; Xiao, F.-S.; Purnell, S. K.; Alexeev, O.; Kawi, S.; Deutsch, S. E.; Gates, B. C.

    1994-11-01

    BECAUSE catalysis by metals is a surface phenomenon, many technological catalysts contain small (typically nanometre-sized) supported metal particles with a large fraction of the atoms exposed1. Many reactions, such as hydrocarbon hydrogenations, are structure-insensitive, proceeding at approximately the same rate on metal particles of various sizes provided that they are larger than about 1 nm and show bulk-like metallic behaviour1. But it is not known whether the catalytic properties of metal particles become size-dependent as the particles become so small that they are no longer metallic in character. Here we investigate the catalytic behaviour of precisely defined clusters of just four and six iridium atoms on solid supports. We find that the Ir4 and Ir6 clusters differ in catalytic activity both from each other and from metallic Ir particles. This raises the possibility of tailoring the catalytic behaviour of metal clusters by controlling the cluster size.

  12. Toward Understanding the Catalytic Mechanism of Human Paraoxonase 1: Site-Specific Mutagenesis at Position 192

    PubMed Central

    Aggarwal, Geetika; Prajapati, Rameshwar; Tripathy, Rajan K.; Bajaj, Priyanka; Iyengar, A. R. Satvik; Sangamwar, Abhay T.; Pande, Abhay H.

    2016-01-01

    Human paraoxonase 1 (h-PON1) is a serum enzyme that can hydrolyze a variety of substrates. The enzyme exhibits anti-inflammatory, anti-oxidative, anti-atherogenic, anti-diabetic, anti-microbial and organophosphate-hydrolyzing activities. Thus, h-PON1 is a strong candidate for the development of therapeutic intervention against a variety conditions in human. However, the crystal structure of h-PON1 is not solved and the molecular details of how the enzyme hydrolyzes different substrates are not clear yet. Understanding the catalytic mechanism(s) of h-PON1 is important in developing the enzyme for therapeutic use. Literature suggests that R/Q polymorphism at position 192 in h-PON1 dramatically modulates the substrate specificity of the enzyme. In order to understand the role of the amino acid residue at position 192 of h-PON1 in its various hydrolytic activities, site-specific mutagenesis at position 192 was done in this study. The mutant enzymes were produced using Escherichia coli expression system and their hydrolytic activities were compared against a panel of substrates. Molecular dynamics simulation studies were employed on selected recombinant h-PON1 (rh-PON1) mutants to understand the effect of amino acid substitutions at position 192 on the structural features of the active site of the enzyme. Our results suggest that, depending on the type of substrate, presence of a particular amino acid residue at position 192 differentially alters the micro-environment of the active site of the enzyme resulting in the engagement of different subsets of amino acid residues in the binding and the processing of substrates. The result advances our understanding of the catalytic mechanism of h-PON1. PMID:26829396

  13. Characterization of papaya peptidase A as a cysteine proteinase of Carica papaya L. with active-centre properties that differ from those of papain by using 2,2'-dipyridyl disulphide and 4-chloro-7-nitrobenzofurazan as reactivity probes. Use of two-protonic-state electrophiles in the identification of catalytic-site thiol groups.

    PubMed Central

    Baines, B S; Brocklehurst, K

    1982-01-01

    1. The proteinase papaya peptidase A, one of the major components of the latex of Carica papaya L., was shown to contain 1 thiol group per molecule; this thiol group is essential for catalytic activity and is part of the catalytic site. 2. The usefulness of two-protonic-state reactivity probes coupled with modification/activity-loss data in assigning a thiol group as an integral part of the catalytic site as against merely 'essential' for activity is discussed. 3. The active centre of papaya peptidase A was investigated by using 2,2'-dipyridyl disulphide and 4-chloro-7-nitrobenzofurazan as reactivity probes. The presence in the enzyme in weakly acidic media of an interactive system containing a nucleophile S atom (pKI3.9,pKII7.9) was demonstrated. 5. Papaya peptidase A resembles ficin (EC 3.4.22.3) and actinidin (the cysteine proteinase from Actinidin chinenis) in that it does not appear to possess a carboxy group able to influence the reactivity of the thiol group by change of ionization state at pH values of about 4, a situation that contrasts markedly with that which obtains in papain. 6. Implications of the results for possible variations in cysteine proteinase mechanism are discussed. PMID:6751321

  14. The active sites of supported silver particle catalysts in formaldehyde oxidation.

    PubMed

    Chen, Yaxin; Huang, Zhiwei; Zhou, Meijuan; Hu, Pingping; Du, Chengtian; Kong, Lingdong; Chen, Jianmin; Tang, Xingfu

    2016-08-01

    Surface silver atoms with upshifted d-orbitals are identified as the catalytically active sites in formaldehyde oxidation by correlating their activity with the number of surface silver atoms, and the degree of the d-orbital upshift governs the catalytic performance of the active sites. PMID:27406403

  15. Mechanism of the reaction catalyzed by mandelate racemase. 2. Crystal structure of mandelate racemase at 2.5-A resolution: identification of the active site and possible catalytic residues.

    PubMed

    Neidhart, D J; Howell, P L; Petsko, G A; Powers, V M; Li, R S; Kenyon, G L; Gerlt, J A

    1991-09-24

    The crystal structure of mandelate racemase (MR) has been solved at 3.0-A resolution by multiple isomorphous replacement and subsequently refined against X-ray diffraction data to 2.5-A resolution by use of both molecular dynamics refinement (XPLOR) and restrained least-squares refinement (PROLSQ). The current crystallographic R-factor for this structure is 18.3%. MR is composed of two major structural domains and a third, smaller, C-terminal domain. The N-terminal domain has an alpha + beta topology consisting of a three-stranded antiparallel beta-sheet followed by an antiparallel four alpha-helix bundle. The central domain is a singly wound parallel alpha/beta-barrel composed of eight central strands of beta-sheet and seven alpha-helices. The C-terminal domain consists of an irregular L-shaped loop with several short sections of antiparallel beta-sheet and two short alpha-helices. This C-terminal domain partially covers the junction between the major domains and occupies a region of the central domain that is filled by an eight alpha-helix in all other known parallel alpha/beta-barrels except for the barrel domain in muconate lactonizing enzyme (MLE) [Goldman, A., Ollis, D. L., & Steitz, T. A. (1987) J. Mol. Biol. 194, 143] whose overall polypeptide fold and amino acid sequence are strikingly similar to those of MR [Neidhart, D. J., Kenyon, G. L., Gerlt, J. A., & Petsko, G. A. (1990) Nature 347, 692]. In addition, the crystal structure reveals that, like MLE, MR is tightly packed as an octamer of identical subunits. The active site of MR is located between the two major domains, at the C-terminal ends of the beta-strands in the alpha/beta-barrel domain. The catalytically essential divalent metal ion is ligated by three side-chain carboxyl groups contributed by residues of the central beta-sheet. A model of a productive substrate complex of MR has been constructed on the basis of difference Fourier analysis at 3.5-A resolution of a complex between MR and (R

  16. Identification of methionine as a possible precursor to the selenocysteine catalytic site of glutathione peroxidase

    SciTech Connect

    Chung, C.K.

    1985-01-01

    The selenium (Se) moiety of glutathione peroxidase (GSHPx) occurs as selenocysteine and is present at the catalytic active site of the enzyme which catalyzes the reduction of hydrogen peroxides and lipid peroxides. The presence of this unusual amino acid at the active site raises the question as to the origin of the carbon skeleton of Se-cysteine. ICR Swiss mice were fed a Se deficient diet for 50 days and then were fed a Se adequate diet (1 ppm Se as SeO/sub 3/). Mice were i.p. injected with either (U-/sup 14/C) methionine, serine, or alanine (0.5 ..mu..Ci/0.1 ml/mouse/day) for 25 days. Recovered GSHPx activity in liver and blood was carboxymethylated (CM) with iodoacetic acid. CM-GSHPx was partially purified by column chromatography. /sup 14/C-GSHPx fractions were collected, lyophilized, and hydrolyzed. /sup 14/C-amino acids were separated by TLC and ion-exchange chromatography. TLC (phenol, cyclohexane, acetic acid, and water (90;6.5;3.5;8)) revealed a GSHPx /sup 14/C-amino acid derived from U-/sup 14/C-methionine, but not from serine or alanine corresponding to CM-selenocysteine (R/sub f/; 0.16). Ion-exchange chromatography of U-/sup 14/C-methionine labeled GSHPx hydrolyzate revealed two radio carbon ninhydrin positive peaks corresponding to /sup 14/C-CM-selenocysteine and /sup 14/C-methionine. No corresponding /sup 14/C-labeled peaks were observed for CM-selenocysteine derived from U-/sup 14/C serine or alanine. The results suggest that methionine may contribute a portion of the carbon skeleton to selenocysteine which may include an alternative metabolic pathway. Animal studies demonstrated that GSHPx activity is increased by methionine supplementation may be due to its contribution of carbon source to the catalytic site of the enzyme.

  17. Disruption of the aldolase A tetramer into catalytically active monomers.

    PubMed

    Beernink, P T; Tolan, D R

    1996-05-28

    The fructose-1,6-bisphosphate aldolase (EC 4.1.2.13) homotetramer has been destabilized by site-directed mutagenesis at the two different subunit interfaces. A double mutant aldolase, Q125D/E224A, sediments as two distinct species, characteristic of a slow equilibrium, with velocities expected for the monomer and tetramer. The aldolase monomer is shown to be catalytically active following isolation from sucrose density gradients. The isolated aldolase monomer had 72% of the specific activity of the wild-type enzyme and a slightly lower Michaelis constant, clearly indicating that the quaternary structure is not required for catalysis. Cross-linking of the isolated monomer confirmed that it does not rapidly reequilibrate with the tetramer following isolation. There was a substantial difference between the tetramer and monomer in their inactivation by urea. The stability toward both urea and thermal inactivation of these oligomeric variants suggests a role for the quaternary structure in maintaining the stability of aldolase, which may be an important role of quaternary structure in many proteins. PMID:8643582

  18. [A structure-activity study of a catalytic antiidiotypic antibody to the human erythrocyte acetylcholinesterase].

    PubMed

    Aleksandrova, E S; Koralevski, F; Titov, M I; Demin, A V; Kozyr', A V; Kolesnikov, A V; Tramontano, A; Paul, S; Thomas, D; Gabibov, A G; Gnuchev, N V; Friboulet, A

    2002-01-01

    The catalytic monoclonal antibody 9A8 (MA 9A8), antiidiotypic to the antibody AE-2 (MA AE2) produced to the active site of acetyl cholinesterase from human erythrocytes, was subjected to a structure-function study. The specific binding of MA 9A8 to MA AE2 (K 2.26 x 10(9) M-1) was shown by the method of surface plasmon resonance, and the functional activity of MA 9A8 was demonstrated. Unlike acetyl cholinesterase, this antibody specifically reacted with the irreversible phosphonate inhibitors of esterases. A peptide map of MA 9A8 was analyzed by MALDI mass spectrometry. The Ser99 residue of its heavy chain was shown to be within the active site of the catalytic antibody. A computer modeling of the MA 9A8 active site suggested the existence of a catalytic dyad formed by Ser99 and His35. A comparison of the tertiary structures of the MA 9A8 and the 17E8 monoclonal antibody, which also exhibited an esterase activity and was produced to the stable analogue of the reaction transition state, indicated a practically complete coincidence of the structures of their presumed active sites. PMID:11962233

  19. HIPK2 catalytic activity and subcellular localization are regulated by activation-loop Y354 autophosphorylation.

    PubMed

    Siepi, Francesca; Gatti, Veronica; Camerini, Serena; Crescenzi, Marco; Soddu, Silvia

    2013-06-01

    HIPK2 (homeodomain-interacting protein kinase-2) binds to and phosphorylates, at Ser and Thr residues, a large number of targets involved in cell division and cell fate decision in response to different physiological or stress stimuli. Inactivation of HIPK2 has been observed in human and mouse cancers supporting its role as a tumor suppressor. Despite the biological relevance of this kinase, very little is known on how HIPK2 becomes catalytically active. Based on sequence homologies, HIPK2 has been taxonomically classified as a subfamily member of the dual-specificity tyrosine-regulated kinases (DYRKs) and the activation-loop Y354 of HIPK2 has been found phosphorylated in different cells; however, the relevance of this Y phosphorylation is presently unknown. Here, we show that HIPK2, which is extensively phosphorylated at S/T sites throughout its functional domains, becomes catalytically active by autophosphorylation at the activation-loop Y354. In particular, we found that, in analogy to DYRKs, HIPK2-Y354 phosphorylation is an autocatalytic event and its prevention, through Y354 substitution with non-phosphorylatable amino acids or by using the kinase inhibitor purvalanol A, induces a strong reduction of the HIPK2 S/T-kinase activity on different substrates. Interestingly, at variance from DYRKs, inhibition of HIPK2-Y354 phosphorylation induces a strong out-of-target Y-kinase activity in cis and a strong cytoplasmic relocalization of the kinase. Together, these results demonstrate that the catalytic activity, substrate specificity, and subcellular localization of HIPK2 are regulated by autophosphorylation of its activation-loop Y354. PMID:23485397

  20. HIPK2 catalytic activity and subcellular localization are regulated by activation-loop Y354 autophosphorylation

    PubMed Central

    Siepi, Francesca; Gatti, Veronica; Camerini, Serena; Crescenzi, Marco; Soddu, Silvia

    2013-01-01

    HIPK2 (homeodomain-interacting protein kinase-2) binds to and phosphorylates, at Ser and Thr residues, a large number of targets involved in cell division and cell fate decision in response to different physiological or stress stimuli. Inactivation of HIPK2 has been observed in human and mouse cancers supporting its role as a tumor suppressor. Despite the biological relevance of this kinase, very little is known on how HIPK2 becomes catalytically active. Based on sequence homologies, HIPK2 has been taxonomically classified as a subfamily member of the dual-specificity tyrosine-regulated kinases (DYRKs) and the activation-loop Y354 of HIPK2 has been found phosphorylated in different cells; however, the relevance of this Y phosphorylation is presently unknown. Here, we show that HIPK2, which is extensively phosphorylated at S/T sites throughout its functional domains, becomes catalytically active by autophosphorylation at the activation-loop Y354. In particular, we found that, in analogy to DYRKs, HIPK2-Y354 phosphorylation is an autocatalytic event and its prevention, through Y354 substitution with non-phosphorylatable amino acids or by using the kinase inhibitor purvalanol A, induces a strong reduction of the HIPK2 S/T-kinase activity on different substrates. Interestingly, at variance from DYRKs, inhibition of HIPK2-Y354 phosphorylation induces a strong out-of-target Y-kinase activity in cis and a strong cytoplasmic relocalization of the kinase. Together, these results demonstrate that the catalytic activity, substrate specificity, and subcellular localization of HIPK2 are regulated by autophosphorylation of its activation-loop Y354. PMID:23485397

  1. Structural stability and catalytic activity of lanthanum-based perovskites

    SciTech Connect

    Sergey N. Rashkeev; Lucia M. Petkovic

    2011-05-01

    Perovskite-type oxide materials with a general formula La(1-x)A(x)Fe(1-y)Co(y)O(3-delta), where A is an alkaline earth metal Sr or Ba have been studied as cathode materials for catalytic reduction of oxygen in solid oxide fuel cells (SOFC), as well as combustion catalysts. In this study, we use a combination of temperature programmed reduction measurements, X-ray diffraction, carbon black catalytic oxidation measurements, and first-principles, density-functional-theory (DFT) calculations to elucidate the main processes that contribute into the structural stability and catalytic activity for soot oxidation of these materials. In particular, we investigate the dynamics of the structure reconstruction with oxygen loss during the regulated increase of the temperature. The calculations are in good qualitative agreement with catalytic experiments and allow identify special combinations of the perovskite chemical composition and local surface structures for which one could expect the highest catalytic activity for the soot oxidation process.

  2. Engineering a hyper-catalytic enzyme by photo-activated conformation modulation

    SciTech Connect

    Agarwal, Pratul K

    2012-01-01

    Enzyme engineering for improved catalysis has wide implications. We describe a novel chemical modification of Candida antarctica lipase B that allows modulation of the enzyme conformation to promote catalysis. Computational modeling was used to identify dynamical enzyme regions that impact the catalytic mechanism. Surface loop regions located distal to active site but showing dynamical coupling to the reaction were connected by a chemical bridge between Lys136 and Pro192, containing a derivative of azobenzene. The conformational modulation of the enzyme was achieved using two sources of light that alternated the azobenzene moiety in cis and trans conformations. Computational model predicted that mechanical energy from the conformational fluctuations facilitate the reaction in the active-site. The results were consistent with predictions as the activity of the engineered enzyme was found to be enhanced with photoactivation. Preliminary estimations indicate that the engineered enzyme achieved 8-52 fold better catalytic activity than the unmodulated enzyme.

  3. Structural Characterization of the Catalytic Sites of Mononuclear Nonheme Fe Hydroxylases Using ²H-ESEEM.

    PubMed

    McCracken, John

    2015-01-01

    Aromatic amino acid hydroxylases are members of a larger group of enzymes that use a mononuclear nonheme Fe center to catalyze a variety of thermodynamically challenging reactions in which O2 is used in the oxidative transformation of substrates. The hydroxylase enzymes are catalytically active in the ferrous oxidation state and are high-spin. To render the catalytic site EPR-active, we have used nitric oxide (NO) as a surrogate for substrate O2 to form an S=3/2 paramagnetic center. While the continuous-wave (cw)-EPR spectra of NO-enzyme adducts are rather generic, they provide electron spin echo envelope modulation (ESEEM) data that are rich with structural information derived from ligand hyperfine couplings. This chapter will focus on (2)H-ESEEM spectroscopy, an approach that we have taken for assigning these spectra and harvesting the unique information on Fe(II) coordination chemistry that they provide. While these spectroscopic measurements are routine, an emphasis will be placed on the analysis of cw-EPR and (2)H-ESEEM data using an unconstrained nonlinear optimization approach. These analysis methods are based on simple custom "scripts" that run in the MATLAB environment and that use EasySpin, a public-domain EPR simulation package, as their calculation engine. The examples provided here use a strategy that can be adapted for the treatment of most EPR measurements. PMID:26478489

  4. Active Site and Remote Contributions to Catalysis in Methylthioadenosine Nucleosidases

    PubMed Central

    Thomas, Keisha; Cameron, Scott A.; Almo, Steven C.; Burgos, Emmanuel S.; Gulab, Shivali A.; Schramm, Vern L.

    2015-01-01

    5′-Methylthioadenosine/S-adenosyl-L-homocysteine nucleosidases (MTANs) catalyze the hydrolysis of 5′-methylthioadenosine to adenine and 5-methylthioribose. The amino acid sequences of the MTANs from Vibrio cholerae (VcMTAN) and Escherichia coli (EcMTAN) are 60% identical and 75% similar. Protein structure folds and kinetic properties are similar. However, binding of transition-state analogues is dominated by favorable entropy in VcMTAN and by enthalpy in EcMTAN. Catalytic sites of VcMTAN and EcMTAN in contact with reactants differ by two residues; Ala113 and Val153 in VcMTAN are Pro113 and Ile152, respectively, in EcMTAN. We mutated the VcMTAN catalytic site residues to match those of EcMTAN in anticipation of altering its properties toward EcMTAN. Inhibition of VcMTAN by transition-state analogues required filling both active sites of the homodimer. However, in the Val153Ile mutant or double mutants, transition-state analogue binding at one site caused complete inhibition. Therefore, a single amino acid, Val153, alters the catalytic site cooperativity in VcMTAN. The transition-state analogue affinity and thermodynamics in mutant VcMTAN became even more unlike those of EcMTAN, the opposite of expectations from catalytic site similarity; thus, catalytic site contacts in VcMTAN are unable to recapitulate the properties of EcMTAN. X-ray crystal structures of EcMTAN, VcMTAN, and a multiple-site mutant of VcMTAN most closely resembling EcMTAN in catalytic site contacts show no major protein conformational differences. The overall protein architectures of these closely related proteins are implicated in contributing to the catalytic site differences. PMID:25806409

  5. Surface-mediated synthesis of dimeric rhodium catalysts on MgO: tracking changes in the nuclearity and ligand environment of the catalytically active sites by X-ray absorption and infrared spectroscopies.

    PubMed

    Yardimci, Dicle; Serna, Pedro; Gates, Bruce C

    2013-01-21

    The preparation of dinuclear rhodium clusters and their use as catalysts is challenging because these clusters are unstable, evolving readily into species with higher nuclearities. We now present a novel synthetic route to generate rhodium dimers on the surface of MgO by a stoichiometrically simple surface-mediated reaction involving [Rh(C(2)H(4))(2)] species and H(2). X-ray absorption and IR spectra were used to characterize the changes in the nuclearity of the essentially molecular surface species as they formed, including the ligands on the rhodium and the metal-support interactions. The support plays a key role in stabilizing the dinuclear rhodium species, allowing the incorporation of small ligands (ethyl, hydride, and/or CO) and enabling a characterization of the catalytic performance of the supported species for the hydrogenation of ethylene as a function of the metal nuclearity and ligand environment. A change in the nuclearity from one to two Rh atoms leads to a 58-fold increase in the catalytic activity for ethylene hydrogenation, a reaction involving unsaturated, but stable, dimeric rhodium species. PMID:23208893

  6. Pair interaction of catalytically active colloids: from assembly to escape

    NASA Astrophysics Data System (ADS)

    Sharifi-Mood, Nima; Mozaffari, Ali; Córdova-Figueroa, Ubaldo M.

    2016-07-01

    The dynamics and pair trajectory of two self-propelled colloids are reported. The autonomous motions of the colloids are due to a catalytic chemical reaction taking place asymmetrically on their surfaces that generates a concentration gradient of interactive solutes around the particles and actuate particle propulsion. We consider two spherical particles with symmetric catalytic caps extending over the local polar angles $\\theta^1_{cap}$ and $\\theta^2_{cap}$ from the centers of active sectors in an otherwise quiescent fluid. A combined analytical-numerical technique was developed to solve the coupled mass transfer equation and the hydrodynamics in the Stokes flow regime. The ensuing pair trajectory of the colloids is controlled by the reacting coverages $\\theta^j_{cap}$ and their initial relative orientation with respect to each other. Our analysis indicates two possible scenarios for pair trajectories of catalytic self-propelled particles: either the particles approach, come into contact and assemble or they interact and move away from each other (escape). For arbitrary motions of the colloids, it is found that the direction of particle rotations is the key factor in determining the escape or assembly scenario. Based on the analysis, a phase diagram is sketched for the pair trajectory of the catalytically active particles as a function of active coverages and their initial relative orientations. We believe this study has important implications in elucidation of collective behaviors of auotophoretically self-propelled colloids.

  7. A Structure-Based Approach for Detection of Thiol Oxidoreductases and Their Catalytic Redox-Active Cysteine Residues

    PubMed Central

    Marino, Stefano M.; Gladyshev, Vadim N.

    2009-01-01

    Cysteine (Cys) residues often play critical roles in proteins, for example, in the formation of structural disulfide bonds, metal binding, targeting proteins to the membranes, and various catalytic functions. However, the structural determinants for various Cys functions are not clear. Thiol oxidoreductases, which are enzymes containing catalytic redox-active Cys residues, have been extensively studied, but even for these proteins there is little understanding of what distinguishes their catalytic redox Cys from other Cys functions. Herein, we characterized thiol oxidoreductases at a structural level and developed an algorithm that can recognize these enzymes by (i) analyzing amino acid and secondary structure composition of the active site and its similarity to known active sites containing redox Cys and (ii) calculating accessibility, active site location, and reactivity of Cys. For proteins with known or modeled structures, this method can identify proteins with catalytic Cys residues and distinguish thiol oxidoreductases from the enzymes containing other catalytic Cys types. Furthermore, by applying this procedure to Saccharomyces cerevisiae proteins containing conserved Cys, we could identify the majority of known yeast thiol oxidoreductases. This study provides insights into the structural properties of catalytic redox-active Cys and should further help to recognize thiol oxidoreductases in protein sequence and structure databases. PMID:19424433

  8. Structure of the catalytic sites in Fe/N/C-catalysts for O2-reduction in PEM fuel cells

    PubMed Central

    Kramm, Ulrike I.; Herranz, Juan; Larouche, Nicholas; Arruda, Thomas M.; Lefèvre, Michel; Jaouen, Frédéric; Bogdanoff, Peter; Fiechter, Sebastian; Abs-Wurmbach, Irmgard; Mukerjee, Sanjeev; Dodelet, Jean-Pol

    2012-01-01

    Fe-based catalytic sites for the reduction of oxygen in acidic medium have been identified by 57Fe Mössbauer spectroscopy of Fe/N/C catalysts containing 0.03 to 1.55 wt% Fe, which were prepared by impregnation of iron acetate on carbon black followed by heat-treatment in NH3 at 950°C. Four different Fe-species were detected at all iron concentrations: three doublets assigned to molecular FeN4-like sites with their ferrous ion in low (D1), medium (D2) or high spin state (D3), and two other doublets assigned to a single Fe-species (D4 and D5) consisting of surface oxidized nitride nanoparticles (FexN, with x≤2.1). A fifth Fe-species appears only in those catalysts with Fe-contents ≥ 0.27 wt%. It is characterized by a very broad singlet, which has been assigned to incomplete FeN4-like sites that quickly dissolve in contact with an acid. Among the five Fe-species identified in these catalysts, only D1 and D3 display catalytic activity for the oxygen reduction reaction (ORR) in the acid medium, with D3 featuring a composite structure with a protonated neighbour basic nitrogen and being by far the most active species, with an estimated turn over frequency for the ORR of 11.4 e− site−1 s−1 at 0.8V vs RHE. Moreover, all D1 sites and between 1/2 to 2/3 of the D3 sites are acid-resistant. A scheme for the mechanism of site formation upon heat-treatment is also proposed. This identification of the ORR-active sites in these catalysts is of crucial importance to design strategies to improve the catalytic activity and stability of these materials. PMID:22824866

  9. Catalytic site remodelling of the DOT1L methyltransferase by selective inhibitors

    SciTech Connect

    Yu, Wenyu; Chory, Emma J.; Wernimont, Amy K.; Tempel, Wolfram; Scopton, Alex; Federation, Alexander; Marineau, Jason J.; Qi, Jun; Barsyte-Lovejoy, Dalia; Yi, Joanna; Marcellus, Richard; Iacob, Roxana E.; Engen, John R.; Griffin, Carly; Aman, Ahmed; Wienholds, Erno; Li, Fengling; Pineda, Javier; Estiu, Guillermina; Shatseva, Tatiana; Hajian, Taraneh; Al-awar, Rima; Dick, John E.; Vedadi, Masoud; Brown, Peter J.; Arrowsmith, Cheryl H.; Bradner, James E.; Schapira, Matthieu

    2012-12-18

    Selective inhibition of protein methyltransferases is a promising new approach to drug discovery. An attractive strategy towards this goal is the development of compounds that selectively inhibit binding of the cofactor, S-adenosylmethionine, within specific protein methyltransferases. Here we report the three-dimensional structure of the protein methyltransferase DOT1L bound toEPZ004777, the first S-adenosylmethionine-competitive inhibitor of a protein methyltransferase with in vivo efficacy. This structure and those of four new analogues reveal remodelling of the catalytic site. EPZ004777 and a brominated analogue, SGC0946, inhibit DOT1L in vitro and selectively kill mixed lineage leukaemia cells, in which DOT1L is aberrantly localized via interaction with an oncogenic MLL fusion protein. These data provide important new insight into mechanisms of cell-active S-adenosylmethionine-competitive protein methyltransferase inhibitors, and establish a foundation for the further development of drug-like inhibitors of DOT1L for cancer therapy.

  10. Structural Basis for the Catalytic Activity of Human SER/THR Protein Phosphatase-5

    NASA Technical Reports Server (NTRS)

    Swingle, M. R.; Honkanen, R.; Ciszak, E.

    2004-01-01

    Serinekhreonine protein phosphatase-5 (PP5) affects many signaling networks that regulate cell growth. Here we report the 1.6 Angstrom resolution crystal structure of PP5 catalytic domain with metal and phosphate ions in the active site. The structure reveals a mechanism for PPS-mediated catalysis that requires the precise positioning of two metal ions within a conserved Asp(sup 271)-M(sub 1),-M(sub 2)-His(sup 427)-W(sup 2)-His(sup 304)-Asp(sup 274) catalytic motif, and provides a structural basis for the exceptional catalytic proficiency of protein phosphatases placing them among the most powerful catalysts. Resolution of the entire C-terminus revealed a novel subdomain, and the structure of PP5 should aid development of specific inhibitors.

  11. Role of conserved Met112 residue in the catalytic activity and stability of ketosteroid isomerase.

    PubMed

    Cha, Hyung Jin; Jang, Do Soo; Jeong, Jae-Hee; Hong, Bee Hak; Yun, Young Sung; Shin, Eun Ju; Choi, Kwan Yong

    2016-10-01

    Ketosteroid isomerase (3-oxosteroid Δ(5)-Δ(4)-isomerase, KSI) from Pseudomonas putida catalyzes allylic rearrangement of the 5,6-double bond of Δ(5)-3-ketosteroid to 4,5-position by stereospecific intramolecular transfer of a proton. The active site of KSI is formed by several hydrophobic residues and three catalytic residues (Tyr14, Asp38, and Asp99). In this study, we investigated the role of a hydrophobic Met112 residue near the active site in the catalysis, steroid binding, and stability of KSI. Replacing Met112 with alanine (yields M112A) or leucine (M112L) decreased the kcat by 20- and 4-fold, respectively. Compared with the wild type (WT), M112A and M112L KSIs showed increased KD values for equilenin, an intermediate analogue; these changes suggest that loss of packing at position 112 might lead to unfavorable steroid binding, thereby resulting in decreased catalytic activity. Furthermore, M112A and M112L mutations reduced melting temperature (Tm) by 6.4°C and 2.5°C, respectively. These changes suggest that favorable packing in the core is important for the maintenance of stability in KSI. The M112K mutation decreased kcat by 2000-fold, compared with the WT. In M112K KSI structure, a new salt bridge was formed between Asp38 and Lys112. This bridge could change the electrostatic potential of Asp38, and thereby contribute to the decreased catalytic activity. The M112K mutation also decreased the stability by reducing Tm by 4.1°C. Our data suggest that the Met112 residue may contribute to the catalytic activity and stability of KSI by providing favorable hydrophobic environments and compact packing in the catalytic core. PMID:27375051

  12. Pivalase catalytic antibodies: towards abzymatic activation of prodrugs.

    PubMed

    Bensel, N; Reymond, M T; Reymond, J L

    2001-11-01

    Screening of monoclonal-antibody libraries generated against the tert-butyl phosphonate hapten 2 and the chloromethyl phosphonate hapten 3 with pivaloyloxymethyl-umbelliferone 1 as a fluorogenic substrate led to the isolation of eleven catalytic antibodies with rate accelerations around kcat/ kuncat = 10(3). The antibodies are not inhibited by the product and accept different acyloxymethyl derivatives of acidic phenols as substrates. The highest activity was found for the bulky, chemically less-reactive pivaloyloxymethyl group: there is no activity with acetoxymethyl or acetyl esters. This difference might reflect the preference of the immune system for hydrophobic interactions in binding and catalysis. Pivalase catalytic antibodies might be useful for activating orally available pivaloyloxymethyl prodrugs. PMID:11757652

  13. Phosphorylation Modulates Catalytic Activity of Mycobacterial Sirtuins

    PubMed Central

    Yadav, Ghanshyam S.; Ravala, Sandeep K.; Malhotra, Neha; Chakraborti, Pradip K.

    2016-01-01

    Sirtuins are NAD+-dependent deacetylases involved in the regulation of diverse cellular processes and are conserved throughout phylogeny. Here we report about in vitro transphosphorylation of the only NAD+-dependent deacetylase (mDAC) present in the genome of Mycobacterium tuberculosis by eukaryotic-type Ser/Thr kinases, particularly PknA. The phosphorylated mDAC displayed decreased deacetylase activity compared to its unphosphorylated counterpart. Mass-spectrometric study identified seven phosphosites in mDAC; however, mutational analysis highlighted major contribution of Thr-214 for phosphorylation of the protein. In concordance to this observation, variants of mDAC substituting Thr-214 with either Ala (phospho-ablated) or Glu (phosphomimic) exhibited significantly reduced deacetylase activity suggesting phosphorylation mediated control of enzymatic activity. To assess the role of phosphorylation towards functionality of mDAC, we opted for a sirtuin knock-out strain of Escherichia coli (Δdac), where interference of endogenous mycobacterial kinases could be excluded. The Δdac strain in nutrient deprived acetate medium exhibited compromised growth and complementation with mDAC reversed this phenotype. The phospho-ablated or phosphomimic variant, on the other hand, was unable to restore the functionality of mDAC indicating the role of phosphorylation per se in the process. We further over-expressed mDAC or mDAC-T214A as His-tagged protein in M. smegmatis, where endogenous eukaryotic-type Ser/Thr kinases are present. Anti-phosphothreonine antibody recognized both mDAC and mDAC-T214A proteins in western blotting. However, the extent of phosphorylation as adjudged by scanning the band intensity, was significantly low in the mutant protein (mDAC-T214A) compared to that of the wild-type (mDAC). Furthermore, expression of PknA in the mDAC complemented Δdac strain was able to phosphorylate M. tuberculosis sirtuin. The growth profile of this culture in acetate medium was

  14. SWI/SNF-mutant cancers depend on catalytic and non-catalytic activity of EZH2.

    PubMed

    Kim, Kimberly H; Kim, Woojin; Howard, Thomas P; Vazquez, Francisca; Tsherniak, Aviad; Wu, Jennifer N; Wang, Weishan; Haswell, Jeffrey R; Walensky, Loren D; Hahn, William C; Orkin, Stuart H; Roberts, Charles W M

    2015-12-01

    Human cancer genome sequencing has recently revealed that genes that encode subunits of SWI/SNF chromatin remodeling complexes are frequently mutated across a wide variety of cancers, and several subunits of the complex have been shown to have bona fide tumor suppressor activity. However, whether mutations in SWI/SNF subunits result in shared dependencies is unknown. Here we show that EZH2, a catalytic subunit of the polycomb repressive complex 2 (PRC2), is essential in all tested cancer cell lines and xenografts harboring mutations of the SWI/SNF subunits ARID1A, PBRM1, and SMARCA4, which are several of the most frequently mutated SWI/SNF subunits in human cancer, but that co-occurrence of a Ras pathway mutation is correlated with abrogation of this dependence. Notably, we demonstrate that SWI/SNF-mutant cancer cells are primarily dependent on a non-catalytic role of EZH2 in the stabilization of the PRC2 complex, and that they are only partially dependent on EZH2 histone methyltransferase activity. These results not only reveal a shared dependency of cancers with genetic alterations in SWI/SNF subunits, but also suggest that EZH2 enzymatic inhibitors now in clinical development may not fully suppress the oncogenic activity of EZH2. PMID:26552009

  15. SWI/SNF mutant cancers depend upon catalytic and non–catalytic activity of EZH2

    PubMed Central

    Kim, Kimberly H.; Kim, Woojin; Howard, Thomas P.; Vazquez, Francisca; Tsherniak, Aviad; Wu, Jennifer N.; Wang, Weishan; Haswell, Jeffrey R.; Walensky, Loren D.; Hahn, William C.; Orkin, Stuart H.; Roberts, Charles W. M.

    2016-01-01

    Human cancer genome sequencing has recently revealed that genes encoding subunits of SWI/SNF chromatin remodeling complexes are frequently mutated across a wide variety of cancers, and several subunits of the complex have been shown to have bona fide tumor suppressor activity1. However, whether mutations in SWI/SNF subunits result in shared dependencies is unknown. Here we show that EZH2, a catalytic subunit of the Polycomb repressive complex 2 (PRC2), is essential in all tested cancer cell lines and xenografts harboring mutations of the SWI/SNF subunits ARID1A, PBRM1, and SMARCA4, which are several of the most frequently mutated SWI/SNF subunits in human cancer but that co–occurrence of a Ras pathway mutation correlates with abrogation of this dependence. Surprisingly, we demonstrate that SWI/SNF mutant cancer cells are primarily dependent upon a non–catalytic role of EZH2 in stabilization of the PRC2 complex, and only partially dependent on EZH2 histone methyltransferase activity. These results not only reveal a shared dependency of cancers with genetic alterations in SWI/SNF subunits, but also suggest that EZH2 enzymatic inhibitors now in clinical development may not fully suppress the oncogenic activity of EZH2. PMID:26552009

  16. Phosphorylation of Leukotriene C4 Synthase at Serine 36 Impairs Catalytic Activity.

    PubMed

    Ahmad, Shabbir; Ytterberg, A Jimmy; Thulasingam, Madhuranayaki; Tholander, Fredrik; Bergman, Tomas; Zubarev, Roman; Wetterholm, Anders; Rinaldo-Matthis, Agnes; Haeggström, Jesper Z

    2016-08-26

    Leukotriene C4 synthase (LTC4S) catalyzes the formation of the proinflammatory lipid mediator leukotriene C4 (LTC4). LTC4 is the parent molecule of the cysteinyl leukotrienes, which are recognized for their pathogenic role in asthma and allergic diseases. Cellular LTC4S activity is suppressed by PKC-mediated phosphorylation, and recently a downstream p70S6k was shown to play an important role in this process. Here, we identified Ser(36) as the major p70S6k phosphorylation site, along with a low frequency site at Thr(40), using an in vitro phosphorylation assay combined with mass spectrometry. The functional consequences of p70S6k phosphorylation were tested with the phosphomimetic mutant S36E, which displayed only about 20% (20 μmol/min/mg) of the activity of WT enzyme (95 μmol/min/mg), whereas the enzyme activity of T40E was not significantly affected. The enzyme activity of S36E increased linearly with increasing LTA4 concentrations during the steady-state kinetics analysis, indicating poor lipid substrate binding. The Ser(36) is located in a loop region close to the entrance of the proposed substrate binding pocket. Comparative molecular dynamics indicated that Ser(36) upon phosphorylation will pull the first luminal loop of LTC4S toward the neighboring subunit of the functional homotrimer, thereby forming hydrogen bonds with Arg(104) in the adjacent subunit. Because Arg(104) is a key catalytic residue responsible for stabilization of the glutathione thiolate anion, this phosphorylation-induced interaction leads to a reduction of the catalytic activity. In addition, the positional shift of the loop and its interaction with the neighboring subunit affect active site access. Thus, our mutational and kinetic data, together with molecular simulations, suggest that phosphorylation of Ser(36) inhibits the catalytic function of LTC4S by interference with the catalytic machinery. PMID:27365393

  17. Multiple Glycogen-binding Sites in Eukaryotic Glycogen Synthase Are Required for High Catalytic Efficiency toward Glycogen

    SciTech Connect

    Baskaran, Sulochanadevi; Chikwana, Vimbai M.; Contreras, Christopher J.; Davis, Keri D.; Wilson, Wayne A.; DePaoli-Roach, Anna A.; Roach, Peter J.; Hurley, Thomas D.

    2012-12-10

    Glycogen synthase is a rate-limiting enzyme in the biosynthesis of glycogen and has an essential role in glucose homeostasis. The three-dimensional structures of yeast glycogen synthase (Gsy2p) complexed with maltooctaose identified four conserved maltodextrin-binding sites distributed across the surface of the enzyme. Site-1 is positioned on the N-terminal domain, site-2 and site-3 are present on the C-terminal domain, and site-4 is located in an interdomain cleft adjacent to the active site. Mutation of these surface sites decreased glycogen binding and catalytic efficiency toward glycogen. Mutations within site-1 and site-2 reduced the V{sub max}/S{sub 0.5} for glycogen by 40- and 70-fold, respectively. Combined mutation of site-1 and site-2 decreased the V{sub max}/S{sub 0.5} for glycogen by >3000-fold. Consistent with the in vitro data, glycogen accumulation in glycogen synthase-deficient yeast cells ({Delta}gsy1-gsy2) transformed with the site-1, site-2, combined site-1/site-2, or site-4 mutant form of Gsy2p was decreased by up to 40-fold. In contrast to the glycogen results, the ability to utilize maltooctaose as an in vitro substrate was unaffected in the site-2 mutant, moderately affected in the site-1 mutant, and almost completely abolished in the site-4 mutant. These data show that the ability to utilize maltooctaose as a substrate can be independent of the ability to utilize glycogen. Our data support the hypothesis that site-1 and site-2 provide a 'toehold mechanism,' keeping glycogen synthase tightly associated with the glycogen particle, whereas site-4 is more closely associated with positioning of the nonreducing end during catalysis.

  18. Effective catalytic media using graphitic nitrogen-doped site in graphene for a non-aqueous Li-O2 battery: A density functional theory study

    NASA Astrophysics Data System (ADS)

    Yun, Kyung-Han; Hwang, Yubin; Chung, Yong-Chae

    2015-03-01

    The cell performance of lithium-oxygen batteries using nitrogen doped graphene as a catalytic cathode has been validated in recent research, but the cathode reaction mechanism of lithium and oxygen still remains unclear. Since the oxygen reduction reaction (ORR) mechanism by ionic lithium and catalytic surface is predicted to be distinct for different defective sites such as graphitic, pyridinic, and pyrrolic, it is necessary to observe the behavior of ionic lithium and oxygen gas at each defective site in nitrogen doped graphene. In this study, density functional theory (DFT) calculations are adopted to analyze at an atomic scale how effectively each defective site acts as a catalytic cathode. Interestingly, unlike pyridinic or pyrrolic N is known to be the most effective catalytic site for ORR in fuel cells. Among the other defective sites, it is found that the graphitic N site is the most effective catalytic media activating ORR by ionic lithium in lithium-oxygen batteries due to the electron accepting the reaction of Li-O formation by the graphitic N site.

  19. Support Effects on the Catalytic Activity of Graphene-Supported Pt13 Nanoclusters for CO Oxidation

    NASA Astrophysics Data System (ADS)

    Fampiou, Ioanna; Ramasubramaniam, Ashwin

    2015-03-01

    Sub-nanometer Pt nanoparticles supported on graphene are shown to exhibit increased stability, uniform dispersion and increased tolerance to CO poisoning, making them attractive candidates as electrocatalysts for fuel-cell electrodes. A fundamental understanding of support effects on the catalytic activity of the nanoparticles is important for effective catalyst design. In this study, we use density functional theory to investigate support effects on the catalytic activity for CO oxidation on Pt13 nanoclusters supported at point defects (vacancies, divacancies) in graphene in the high CO-coverage regime. Our results suggest that support defects are crucial in stabilizing the clusters on the support at high CO cluster coverage, preventing sintering and catalyst loss. By sampling the CO oxidation reaction at various surface sites on graphene-supported and free Pt13 nanoclusters, we show that strong cluster-support interactions can substantially reduce the barrier for CO oxidation on supported versus free nanoclusters, by more than 0.5 eV. Our results suggest that defect engineering of graphene supports could serve to enhance the catalytic activity of sub-nanometer Pt nanoclusters, allowing for tuning of catalytic properties through cluster-support interactions. We acknowledge support by U.S. DOE under Award Number DE-SC0010610 and computational resources by NERSC, supported by the Office of Science, U.S DOE under Contract No. DE-AC02-05CH11231.

  20. Expression and purification of correctly processed, active human TACE catalytic domain in Saccharomyces cerevisiae.

    PubMed

    Clarke, H R; Wolfson, M F; Rauch, C T; Castner, B J; Huang, C P; Gerhart, M J; Johnson, R S; Cerretti, D P; Paxton, R J; Price, V L; Black, R A

    1998-06-01

    Human tumor necrosis factor-alpha (TNF alpha) converting enzyme (TACE) releases soluble TNF alpha from cells. It is a member of the adamalysin family of metalloproteases. A truncated form of TACE cDNA was expressed in Saccharomyces cerevisiae and purified to homogeneity in order to study TACE structure and function. Recombinant TACE was expressed as a preproprotein including the pro- and catalytic (PROCAT) domains fused to the yeast alpha-factor leader. A C-terminal immunoreactive FLAG peptide was added for Western blot detection and anti-FLAG antibody column purification. We constructed two glycosylation mutant PROCAT TACE isoforms to facilitate purification. A PROCAT isoform, mutated to eliminate two N-linked glycosylation sites, was buffer exchanged and purified to homogeneity by ion exchange chromatography and an anti-FLAG antibody affinity step. N-terminal sequence analysis showed that the mutant preproprotein was processed in yeast at the furin protease cleavage site and yielded an active catalytic domain which has TNF alpha peptide-specific protease activity. Mass spectrometry of the purified catalytic domain showed that removal of both N-linked sites results in a homogeneous sized polypeptide lacking further posttranslational modifications. PMID:9631522

  1. Differences in Catalytic Sites for CO Oxidation and Propylene Epoxidation on Au Nanoparticles

    SciTech Connect

    Lee, W.S.; Stach, E.; Zhang, R.; Akatay, M.C.; Baertsch, C.D.; Ribeiro, F.H.; Delgass, W.N.

    2011-08-29

    Sintering and increased Au loading of Au/TS-1 causes the rate of CO oxidation per mole of Au to increase, whereas that for epoxidation of propylene in O{sub 2} and H{sub 2} decreases. This opposite trend in rate behavior shows that the catalytic sites for the two reactions must be different.

  2. Guiding Catalytically Active Particles with Chemically Patterned Surfaces

    NASA Astrophysics Data System (ADS)

    Uspal, W. E.; Popescu, M. N.; Dietrich, S.; Tasinkevych, M.

    2016-07-01

    Catalytically active Janus particles suspended in solution create gradients in the chemical composition of the solution along their surfaces, as well as along any nearby container walls. The former leads to self-phoresis, while the latter gives rise to chemiosmosis, providing an additional contribution to self-motility. Chemiosmosis strongly depends on the molecular interactions between the diffusing chemical species and the wall. We show analytically, using an approximate "point-particle" approach, that by chemically patterning a planar substrate one can direct the motion of Janus particles: the induced chemiosmotic flows can cause particles to either "dock" at the chemical step between the two materials or follow a chemical stripe. These theoretical predictions are confirmed by full numerical calculations. Generically, docking occurs for particles which tend to move away from their catalytic caps, while stripe following occurs in the opposite case. Our analysis reveals the physical mechanisms governing this behavior.

  3. Comprehensive Characterization of AMP-Activated Protein Kinase Catalytic Domain by Top-Down Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Yu, Deyang; Peng, Ying; Ayaz-Guner, Serife; Gregorich, Zachery R.; Ge, Ying

    2016-02-01

    AMP-activated protein kinase (AMPK) is a serine/threonine protein kinase that is essential in regulating energy metabolism in all eukaryotic cells. It is a heterotrimeric protein complex composed of a catalytic subunit (α) and two regulatory subunits (β and γ). C-terminal truncation of AMPKα at residue 312 yielded a protein that is active upon phosphorylation of Thr172 in the absence of β and γ subunits, which is refered to as the AMPK catalytic domain and commonly used to substitute for the AMPK heterotrimeric complex in in vitro kinase assays. However, a comprehensive characterization of the AMPK catalytic domain is lacking. Herein, we expressed a His-tagged human AMPK catalytic domin (denoted as AMPKΔ) in E. coli, comprehensively characterized AMPKΔ in its basal state and after in vitro phosphorylation using top-down mass spectrometry (MS), and assessed how phosphorylation of AMPKΔ affects its activity. Unexpectedly, we found that bacterially-expressed AMPKΔ was basally phosphorylated and localized the phosphorylation site to the His-tag. We found that AMPKΔ had noticeable basal activity and was capable of phosphorylating itself and its substrates without activating phosphorylation at Thr172. Moreover, our data suggested that Thr172 is the only site phosphorylated by its upstream kinase, liver kinase B1, and that this phosphorylation dramatically increases the kinase activity of AMPKΔ. Importantly, we demonstrated that top-down MS in conjunction with in vitro phosphorylation assay is a powerful approach for monitoring phosphorylation reaction and determining sequential order of phosphorylation events in kinase-substrate systems.

  4. A single iron site confined in a graphene matrix for the catalytic oxidation of benzene at room temperature

    PubMed Central

    Deng, Dehui; Chen, Xiaoqi; Yu, Liang; Wu, Xing; Liu, Qingfei; Liu, Yun; Yang, Huaixin; Tian, Huanfang; Hu, Yongfeng; Du, Peipei; Si, Rui; Wang, Junhu; Cui, Xiaoju; Li, Haobo; Xiao, Jianping; Xu, Tao; Deng, Jiao; Yang, Fan; Duchesne, Paul N.; Zhang, Peng; Zhou, Jigang; Sun, Litao; Li, Jianqi; Pan, Xiulian; Bao, Xinhe

    2015-01-01

    Coordinatively unsaturated (CUS) iron sites are highly active in catalytic oxidation reactions; however, maintaining the CUS structure of iron during heterogeneous catalytic reactions is a great challenge. Here, we report a strategy to stabilize single-atom CUS iron sites by embedding highly dispersed FeN4 centers in the graphene matrix. The atomic structure of FeN4 centers in graphene was revealed for the first time by combining high-resolution transmission electron microscopy/high-angle annular dark-field scanning transmission electron microscopy with low-temperature scanning tunneling microscopy. These confined single-atom iron sites exhibit high performance in the direct catalytic oxidation of benzene to phenol at room temperature, with a conversion of 23.4% and a yield of 18.7%, and can even proceed efficiently at 0°C with a phenol yield of 8.3% after 24 hours. Both experimental measurements and density functional theory calculations indicate that the formation of the Fe═O intermediate structure is a key step to promoting the conversion of benzene to phenol. These findings could pave the way toward highly efficient nonprecious catalysts for low-temperature oxidation reactions in heterogeneous catalysis and electrocatalysis. PMID:26665170

  5. E2 superfamily of ubiquitin-conjugating enzymes: constitutively active or activated through phosphorylation in the catalytic cleft

    PubMed Central

    Valimberti, Ilaria; Tiberti, Matteo; Lambrughi, Matteo; Sarcevic, Boris; Papaleo, Elena

    2015-01-01

    Protein phosphorylation is a modification that offers a dynamic and reversible mechanism to regulate the majority of cellular processes. Numerous diseases are associated with aberrant regulation of phosphorylation-induced switches. Phosphorylation is emerging as a mechanism to modulate ubiquitination by regulating key enzymes in this pathway. The molecular mechanisms underpinning how phosphorylation regulates ubiquitinating enzymes, however, are elusive. Here, we show the high conservation of a functional site in E2 ubiquitin-conjugating enzymes. In catalytically active E2s, this site contains aspartate or a phosphorylatable serine and we refer to it as the conserved E2 serine/aspartate (CES/D) site. Molecular simulations of substrate-bound and -unbound forms of wild type, mutant and phosphorylated E2s, provide atomistic insight into the role of the CES/D residue for optimal E2 activity. Both the size and charge of the side group at the site play a central role in aligning the substrate lysine toward E2 catalytic cysteine to control ubiquitination efficiency. The CES/D site contributes to the fingerprint of the E2 superfamily. We propose that E2 enzymes can be divided into constitutively active or regulated families. E2s characterized by an aspartate at the CES/D site signify constitutively active E2s, whereas those containing a serine can be regulated by phosphorylation. PMID:26463729

  6. Spectroscopic properties and the catalytic activity of new organo-lead supramolecular coordination polymer containing quinoxaline

    NASA Astrophysics Data System (ADS)

    Etaiw, Safaa El-din H.; Abdou, Safaa N.

    2015-01-01

    The 3D-supramolecular coordination polymer (SCP) 3∞[ Cu2(CN)3(Me3Pb)(qox)], 1, as the first example of the CuCN SCP containing the (Me3Pb) fragment, was explored to investigate its catalytic and photo-catalytic activities. The structure of 1 contains two chemically identical but crystallographically different [Cu2(CN)3ṡMe3Pbṡqox]2 units with four Cu(I) sites assuming distorted TP-3 geometry. Two non-linear chains of equal abundance are formed producing corrugated parallel chains which are connected laterally by quinoxaline creating 2D-layers which are arranged parallel in an (AB⋯AB⋯AB)n fashion forming 3D-network. IR, mass, electronic absorption and fluorescence spectra are also investigated. The SCP 1 is diamagnetic and exhibits good catalytic and photo-catalytic activities for the degradation of methylene blue (MB). The reaction is first order with respect to MB dye. The irradiation of the reaction with UV-light enhanced the rate of MB mineralization. The efficiency of recycled the 1 and the mechanism of degradation of MB dye were investigated.

  7. Spectroscopic properties and the catalytic activity of new organo-lead supramolecular coordination polymer containing quinoxaline.

    PubMed

    Etaiw, Safaa El-din H; Abdou, Safaa N

    2015-01-25

    The 3D-supramolecular coordination polymer (SCP) (3)∞[ Cu2(CN)3(Me3Pb)(qox)], 1, as the first example of the CuCN SCP containing the (Me3Pb) fragment, was explored to investigate its catalytic and photo-catalytic activities. The structure of 1 contains two chemically identical but crystallographically different [Cu2(CN)3⋅Me3Pb⋅qox]2 units with four Cu(I) sites assuming distorted TP-3 geometry. Two non-linear chains of equal abundance are formed producing corrugated parallel chains which are connected laterally by quinoxaline creating 2D-layers which are arranged parallel in an (AB⋯AB⋯AB)n fashion forming 3D-network. IR, mass, electronic absorption and fluorescence spectra are also investigated. The SCP 1 is diamagnetic and exhibits good catalytic and photo-catalytic activities for the degradation of methylene blue (MB). The reaction is first order with respect to MB dye. The irradiation of the reaction with UV-light enhanced the rate of MB mineralization. The efficiency of recycled the 1 and the mechanism of degradation of MB dye were investigated. PMID:25124847

  8. Anacardic acid inhibits the catalytic activity of matrix metalloproteinase-2 and matrix metalloproteinase-9.

    PubMed

    Omanakuttan, Athira; Nambiar, Jyotsna; Harris, Rodney M; Bose, Chinchu; Pandurangan, Nanjan; Varghese, Rebu K; Kumar, Geetha B; Tainer, John A; Banerji, Asoke; Perry, J Jefferson P; Nair, Bipin G

    2012-10-01

    Cashew nut shell liquid (CNSL) has been used in traditional medicine for the treatment of a wide variety of pathophysiological conditions. To further define the mechanism of CNSL action, we investigated the effect of cashew nut shell extract (CNSE) on two matrix metalloproteinases, MMP-2/gelatinase A and MMP-9/gelatinase B, which are known to have critical roles in several disease states. We observed that the major constituent of CNSE, anacardic acid, markedly inhibited the gelatinase activity of 3T3-L1 cells. Our gelatin zymography studies on these two secreted gelatinases, present in the conditioned media from 3T3-L1 cells, established that anacardic acid directly inhibited the catalytic activities of both MMP-2 and MMP-9. Our docking studies suggested that anacardic acid binds into the MMP-2/9 active site, with the carboxylate group of anacardic acid chelating the catalytic zinc ion and forming a hydrogen bond to a key catalytic glutamate side chain and the C15 aliphatic group being accommodated within the relatively large S1' pocket of these gelatinases. In agreement with the docking results, our fluorescence-based studies on the recombinant MMP-2 catalytic core domain demonstrated that anacardic acid directly inhibits substrate peptide cleavage in a dose-dependent manner, with an IC₅₀ of 11.11 μM. In addition, our gelatinase zymography and fluorescence data confirmed that the cardol-cardanol mixture, salicylic acid, and aspirin, all of which lack key functional groups present in anacardic acid, are much weaker MMP-2/MMP-9 inhibitors. Our results provide the first evidence for inhibition of gelatinase catalytic activity by anacardic acid, providing a novel template for drug discovery and a molecular mechanism potentially involved in CNSL therapeutic action. PMID:22745359

  9. Anacardic Acid Inhibits the Catalytic Activity of Matrix Metalloproteinase-2 and Matrix Metalloproteinase-9

    PubMed Central

    Omanakuttan, Athira; Nambiar, Jyotsna; Harris, Rodney M.; Bose, Chinchu; Pandurangan, Nanjan; Varghese, Rebu K.; Kumar, Geetha B.; Tainer, John A.; Banerji, Asoke; Perry, J. Jefferson P.

    2012-01-01

    Cashew nut shell liquid (CNSL) has been used in traditional medicine for the treatment of a wide variety of pathophysiological conditions. To further define the mechanism of CNSL action, we investigated the effect of cashew nut shell extract (CNSE) on two matrix metalloproteinases, MMP-2/gelatinase A and MMP-9/gelatinase B, which are known to have critical roles in several disease states. We observed that the major constituent of CNSE, anacardic acid, markedly inhibited the gelatinase activity of 3T3-L1 cells. Our gelatin zymography studies on these two secreted gelatinases, present in the conditioned media from 3T3-L1 cells, established that anacardic acid directly inhibited the catalytic activities of both MMP-2 and MMP-9. Our docking studies suggested that anacardic acid binds into the MMP-2/9 active site, with the carboxylate group of anacardic acid chelating the catalytic zinc ion and forming a hydrogen bond to a key catalytic glutamate side chain and the C15 aliphatic group being accommodated within the relatively large S1′ pocket of these gelatinases. In agreement with the docking results, our fluorescence-based studies on the recombinant MMP-2 catalytic core domain demonstrated that anacardic acid directly inhibits substrate peptide cleavage in a dose-dependent manner, with an IC50 of 11.11 μM. In addition, our gelatinase zymography and fluorescence data confirmed that the cardol-cardanol mixture, salicylic acid, and aspirin, all of which lack key functional groups present in anacardic acid, are much weaker MMP-2/MMP-9 inhibitors. Our results provide the first evidence for inhibition of gelatinase catalytic activity by anacardic acid, providing a novel template for drug discovery and a molecular mechanism potentially involved in CNSL therapeutic action. PMID:22745359

  10. Catalytic Activity of Supported Metal Particles for Sulfuric Acid Decomposition Reaction

    SciTech Connect

    Sergey N. Rashkeev; Daniel M. Ginosar; Lucia M. Petkovic; Helen H. Farrell

    2007-08-01

    Production of hydrogen by splitting water in thermochemical water-splitting cycles, such as the sulfur-based group that employs the catalytic decomposition of sulfuric acid into SO2 and O2 is of considerable interest. Most of these processes occur at high temperatures (T = 1,000 K) and exposes catalysts to the extreme conditions such as steam, oxygen, and acid vapor that severely damage these catalysts within a short time. To develop an understanding of the factors that cause catalyst deactivation, we performed density-functional-theory (DFT)-based first-principles calculations and computer simulations for transition metal (TM) particles positioned on the two types of substrate (?-alumina and TiO2-rutile). The catalytic activity of the considered systems is defined by several factors, namely: (i) The efficiency of detaching oxygen atoms from the sulfur-containing species SOn (n = 1,2,3). The breaking of the S-O bonds may occur at both the substrate and the transition metal cluster. However, the bond-breaking at the substrate is endothermic (and takes about 1.5 eV per bond) while at low-coordinated metal atom of a cluster it is exothermic (with energy gain of about 0.5 eV per bond). This explains why the presence of transition metal clusters is necessary for catalytic activity; (ii) The ability of the cluster to “clean” itself, i.e., to eliminate oxygen from its surface, in order to regain the catalytically active sites and to continue the process. We found that the clusters of Pd and Pt with the size = 2-3 nm are more efficient in this process (at T = 1,000 K) than the clusters of other TM’s considered (Rh, Ir, Ru, and Os); (iii) The ability of the cluster to keep its size to avoid sintering (that reduces the number of low-coordinated catalytically active sites at the surface of the cluster). We found that the sintering of Rh, Ir, Ru, and Os clusters is significantly suppressed in comparison with the sintering of Pd and Pt clusters of the same size (the

  11. Crystal structure of the catalytic domain of human bile salt activated lipase.

    PubMed Central

    Terzyan, S.; Wang, C. S.; Downs, D.; Hunter, B.; Zhang, X. C.

    2000-01-01

    Bile-salt activated lipase (BAL) is a pancreatic enzyme that digests a variety of lipids in the small intestine. A distinct property of BAL is its dependency on bile salts in hydrolyzing substrates of long acyl chains or bulky alcoholic motifs. A crystal structure of the catalytic domain of human BAL (residues 1-538) with two surface mutations (N186D and A298D), which were introduced in attempting to facilitate crystallization, has been determined at 2.3 A resolution. The crystal form belongs to space group P2(1)2(1)2(1) with one monomer per asymmetric unit, and the protein shows an alpha/beta hydrolase fold. In the absence of bound bile salt molecules, the protein possesses a preformed catalytic triad and a functional oxyanion hole. Several surface loops around the active site are mobile, including two loops potentially involved in substrate binding (residues 115-125 and 270-285). PMID:11045623

  12. Catalytic activity of platinum on ruthenium electrodes with modified (electro)chemical states.

    PubMed

    Park, Kyung-Won; Sung, Yung-Eun

    2005-07-21

    Using Pt on Ru thin-film electrodes with various (electro)chemical states designed by the sputtering method, the effect of Ru states on the catalytic activity of Pt was investigated. The chemical and electrochemical properties of Pt/Ru thin-film samples were confirmed by X-ray photoelectron spectroscopy (XPS) and cyclic voltammetry. In addition, Pt nanoparticles on Ru metal or oxide for an actual fuel cell system showed an effect of Ru states on the catalytic activity of Pt in methanol electrooxidation. Finally, it was concluded that such an enhancement of methanol electrooxidation on the Pt is responsible for Ru metallic and/or oxidation sites compared to pure Pt without any Ru state. PMID:16852701

  13. Selective nitrogen doping in graphene: Enhanced catalytic activity for the oxygen reduction reaction

    NASA Astrophysics Data System (ADS)

    Wang, Xianlong; Hou, Zhufeng; Ikeda, Takashi; Huang, Sheng-Feng; Terakura, Kiyoyuki; Boero, Mauro; Oshima, Masaharu; Kakimoto, Masa-Aki; Miyata, Seizo

    2011-12-01

    The structural and electronic properties of N-doped zigzag graphene ribbons with various ratios of dihydrogenated to monohydrogenated edge carbons are investigated within the density functional theory framework. We find that the stability of graphitic N next to the edge, which is claimed to play important roles in the catalytic activity in our previous work, will be enhanced with increasing the concentration of dihydrogenated carbons. Furthermore, the dihydrogenated edge carbons turn out to be easily converted into monohydrogenated ones in the presence of oxygen molecules at room temperature. Based on our results, we propose a possible way to enhance the oxygen reduction catalytic activity of N-doped graphene by controlling the degrees of hydrogenation of edge carbons. The characteristic features in the x-ray absorption and emission spectra for each specific N site considered here will also be given.

  14. A Supramolecularly Activated Radical Cation for Accelerated Catalytic Oxidation.

    PubMed

    Jiao, Yang; Li, Wan-Lu; Xu, Jiang-Fei; Wang, Guangtong; Li, Jun; Wang, Zhiqiang; Zhang, Xi

    2016-07-25

    Tuning the activity of radicals is crucial for radical reactions and radical-based materials. Herein, we report a supramolecular strategy to accelerate the Fenton reaction through the construction of supramolecularly activated radical cations. As a proof of the concept, cucurbit[7]uril (CB[7]) was introduced, through host-guest interactions, onto each side of a derivative of 1,4-diketopyrrolo[3,4-c]pyrrole (DPP), a model dye for Fenton oxidation. The DPP radical cation, the key intermediate in the oxidation process, was activated by the electrostatically negative carbonyl groups of CB[7]. The activation induced a drastic decrease in the apparent activation energy and greatly increased the reaction rate. This facile supramolecular strategy is a promising method for promoting radical reactions. It may also open up a new route for the catalytic oxidation of organic pollutants for water purification and widen the realm of supramolecular catalysis. PMID:27273046

  15. Highly Selective Synthesis of Catalytically Active Monodisperse Rhodium Nanocubes

    SciTech Connect

    Zhang, Y.; Grass, M.E.; Kuhn, J.N.; Tao, F.; Habas, S.E.; Huang, W.; Yang, P.; Somorjai, G.A.

    2009-02-21

    Synthesis of monodisperse and shape-controlled colloidal inorganic nanocrystals (NCs) is of increasing scientific interest and technological significance. Recently, shape control of Pt, Pd, Ag, Au, and Rh NCs has been obtained by tuning growth kinetics in various solution-phase approaches, including modified polyol methods, seeded growth by polyol reduction, thermolysis of organometallics, and micelle techniques. Control of reduction kinetics of the noble metal precursors and regulation of the relative growth rates of low-index planes (i.e. {l_brace}100{r_brace} and {l_brace}111{r_brace}) via selective adsorption of selected chemical species are two keys for achieving shape modification of noble metal NCs. One application for noble metal NCs of well-defined shape is in understanding how NC faceting (determines which crystallographic planes are exposed) affects catalytic performance. Rh NCs are used in many catalytic reactions, including hydrogenation, hydroformylation, hydrocarbonylation, and combustion reactions. Shape manipulation of Rh NCs may be important in understanding how faceting on the nanoscale affects catalytic properties, but such control is challenging and there are fewer reports on the shape control of Rh NCs compared to other noble metals. Xia and coworkers obtained Rh multipods exhibiting interesting surface plasmonic properties by a polyol approach. The Somorjai and Tilley groups synthesized crystalline Rh multipods, cubes, horns and cuboctahedra, via polyol seeded growth. Son and colleagues prepared catalytically active monodisperse oleylamine-capped tetrahedral Rh NCs for the hydrogenation of arenes via an organometallic route. More recently, the Somorjai group synthesized sizetunable monodisperse Rh NCs using a one-step polyol technique. In this Communication, we report the highly selective synthesis of catalytically active, monodisperse Rh nanocubes of < 10 nm by a seedless polyol method. In this approach, Br{sup -} ions from trimethyl

  16. Catalytic site inhibition of insulin-degrading enzyme by a small molecule induces glucose intolerance in mice

    SciTech Connect

    Deprez-Poulain, Rebecca; Hennuyer, Nathalie; Bosc, Damien; Liang, Wenguang G.; Enée, Emmanuelle; Marechal, Xavier; Charton, Julie; Totobenazara, Jane; Berte, Gonzague; Jahklal, Jouda; Verdelet, Tristan; Dumont, Julie; Dassonneville, Sandrine; Woitrain, Eloise; Gauriot, Marion; Paquet, Charlotte; Duplan, Isabelle; Hermant, Paul; Cantrelle, François- Xavier; Sevin, Emmanuel; Culot, Maxime; Landry, Valerie; Herledan, Adrien; Piveteau, Catherine; Lippens, Guy; Leroux, Florence; Tang, Wei-Jen; van Endert, Peter; Staels, Bart; Deprez, Benoit

    2015-09-23

    Insulin-degrading enzyme (IDE) is a protease that cleaves insulin and other bioactive peptides such as amyloid-β. Knockout and genetic studies have linked IDE to Alzheimer’s disease and type-2 diabetes. As the major insulin-degrading protease, IDE is a candidate drug target in diabetes. Here we have used kinetic target-guided synthesis to design the first catalytic site inhibitor of IDE suitable for in vivo studies (BDM44768). Crystallographic and small angle X-ray scattering analyses show that it locks IDE in a closed conformation. Among a panel of metalloproteases, BDM44768 selectively inhibits IDE. Acute treatment of mice with BDM44768 increases insulin signalling and surprisingly impairs glucose tolerance in an IDE-dependent manner. These results confirm that IDE is involved in pathways that modulate short-term glucose homeostasis, but casts doubt on the general usefulness of the inhibition of IDE catalytic activity to treat diabetes.

  17. Catalytic site inhibition of insulin-degrading enzyme by a small molecule induces glucose intolerance in mice.

    PubMed

    Deprez-Poulain, Rebecca; Hennuyer, Nathalie; Bosc, Damien; Liang, Wenguang G; Enée, Emmanuelle; Marechal, Xavier; Charton, Julie; Totobenazara, Jane; Berte, Gonzague; Jahklal, Jouda; Verdelet, Tristan; Dumont, Julie; Dassonneville, Sandrine; Woitrain, Eloise; Gauriot, Marion; Paquet, Charlotte; Duplan, Isabelle; Hermant, Paul; Cantrelle, François-Xavier; Sevin, Emmanuel; Culot, Maxime; Landry, Valerie; Herledan, Adrien; Piveteau, Catherine; Lippens, Guy; Leroux, Florence; Tang, Wei-Jen; van Endert, Peter; Staels, Bart; Deprez, Benoit

    2015-01-01

    Insulin-degrading enzyme (IDE) is a protease that cleaves insulin and other bioactive peptides such as amyloid-β. Knockout and genetic studies have linked IDE to Alzheimer's disease and type-2 diabetes. As the major insulin-degrading protease, IDE is a candidate drug target in diabetes. Here we have used kinetic target-guided synthesis to design the first catalytic site inhibitor of IDE suitable for in vivo studies (BDM44768). Crystallographic and small angle X-ray scattering analyses show that it locks IDE in a closed conformation. Among a panel of metalloproteases, BDM44768 selectively inhibits IDE. Acute treatment of mice with BDM44768 increases insulin signalling and surprisingly impairs glucose tolerance in an IDE-dependent manner. These results confirm that IDE is involved in pathways that modulate short-term glucose homeostasis, but casts doubt on the general usefulness of the inhibition of IDE catalytic activity to treat diabetes. PMID:26394692

  18. Catalytic site inhibition of insulin-degrading enzyme by a small molecule induces glucose intolerance in mice

    PubMed Central

    Deprez-Poulain, Rebecca; Hennuyer, Nathalie; Bosc, Damien; Liang, Wenguang G.; Enée, Emmanuelle; Marechal, Xavier; Charton, Julie; Totobenazara, Jane; Berte, Gonzague; Jahklal, Jouda; Verdelet, Tristan; Dumont, Julie; Dassonneville, Sandrine; Woitrain, Eloise; Gauriot, Marion; Paquet, Charlotte; Duplan, Isabelle; Hermant, Paul; Cantrelle, François- Xavier; Sevin, Emmanuel; Culot, Maxime; Landry, Valerie; Herledan, Adrien; Piveteau, Catherine; Lippens, Guy; Leroux, Florence; Tang, Wei-Jen; van Endert, Peter; Staels, Bart; Deprez, Benoit

    2015-01-01

    Insulin-degrading enzyme (IDE) is a protease that cleaves insulin and other bioactive peptides such as amyloid-β. Knockout and genetic studies have linked IDE to Alzheimer's disease and type-2 diabetes. As the major insulin-degrading protease, IDE is a candidate drug target in diabetes. Here we have used kinetic target-guided synthesis to design the first catalytic site inhibitor of IDE suitable for in vivo studies (BDM44768). Crystallographic and small angle X-ray scattering analyses show that it locks IDE in a closed conformation. Among a panel of metalloproteases, BDM44768 selectively inhibits IDE. Acute treatment of mice with BDM44768 increases insulin signalling and surprisingly impairs glucose tolerance in an IDE-dependent manner. These results confirm that IDE is involved in pathways that modulate short-term glucose homeostasis, but casts doubt on the general usefulness of the inhibition of IDE catalytic activity to treat diabetes. PMID:26394692

  19. Catalytically and biologically active silver nanoparticles synthesized using essential oil.

    PubMed

    Vilas, Vidya; Philip, Daizy; Mathew, Joseph

    2014-11-11

    There are numerous reports on phytosynthesis of silver nanoparticles and various phytochemicals are involved in the reduction and stabilization. Pure explicit phytosynthetic protocol for catalytically and biologically active silver nanoparticles is of importance as it is an environmentally benign green method. This paper reports the use of essential oil of Myristica fragrans enriched in terpenes and phenyl propenes in the reduction and stabilization. FTIR spectra of the essential oil and the synthesized biogenic silver nanoparticles are in accordance with the GC-MS spectral analysis reports. Nanosilver is initially characterized by an intense SPR band around 420 nm, followed by XRD and TEM analysis revealing the formation of 12-26 nm sized, highly pure, crystalline silver nanoparticles. Excellent catalytic and bioactive potential of the silver nanoparticles is due to the surface modification. The chemocatalytic potential of nanosilver is exhibited by the rapid reduction of the organic pollutant, para nitro phenol and by the degradation of the thiazine dye, methylene blue. Significant antibacterial activity of the silver colloid against Gram positive, Staphylococcus aureus (inhibition zone--12 mm) and Gram negative, Escherichia coli (inhibition zone--14 mm) is demonstrated by Agar-well diffusion method. Strong antioxidant activity of the biogenic silver nanoparticles is depicted through NO scavenging, hydrogen peroxide scavenging, reducing power, DPPH and total antioxidant activity assays. PMID:24956490

  20. Catalytically and biologically active silver nanoparticles synthesized using essential oil

    NASA Astrophysics Data System (ADS)

    Vilas, Vidya; Philip, Daizy; Mathew, Joseph

    2014-11-01

    There are numerous reports on phytosynthesis of silver nanoparticles and various phytochemicals are involved in the reduction and stabilization. Pure explicit phytosynthetic protocol for catalytically and biologically active silver nanoparticles is of importance as it is an environmentally benign green method. This paper reports the use of essential oil of Myristica fragrans enriched in terpenes and phenyl propenes in the reduction and stabilization. FTIR spectra of the essential oil and the synthesized biogenic silver nanoparticles are in accordance with the GC-MS spectral analysis reports. Nanosilver is initially characterized by an intense SPR band around 420 nm, followed by XRD and TEM analysis revealing the formation of 12-26 nm sized, highly pure, crystalline silver nanoparticles. Excellent catalytic and bioactive potential of the silver nanoparticles is due to the surface modification. The chemocatalytic potential of nanosilver is exhibited by the rapid reduction of the organic pollutant, para nitro phenol and by the degradation of the thiazine dye, methylene blue. Significant antibacterial activity of the silver colloid against Gram positive, Staphylococcus aureus (inhibition zone - 12 mm) and Gram negative, Escherichia coli (inhibition zone - 14 mm) is demonstrated by Agar-well diffusion method. Strong antioxidant activity of the biogenic silver nanoparticles is depicted through NO scavenging, hydrogen peroxide scavenging, reducing power, DPPH and total antioxidant activity assays.

  1. Active site specificity of plasmepsin II.

    PubMed Central

    Westling, J.; Cipullo, P.; Hung, S. H.; Saft, H.; Dame, J. B.; Dunn, B. M.

    1999-01-01

    Members of the aspartic proteinase family of enzymes have very similar three-dimensional structures and catalytic mechanisms. Each, however, has unique substrate specificity. These distinctions arise from variations in amino acid residues that line the active site subsites and interact with the side chains of the amino acids of the peptides that bind to the active site. To understand the unique binding preferences of plasmepsin II, an enzyme of the aspartic proteinase class from the malaria parasite, Plasmodium falciparum, chromogenic octapeptides having systematic substitutions at various positions in the sequence were analyzed. This enabled the design of new, improved substrates for this enzyme (Lys-Pro-Ile-Leu-Phe*Nph-Ala/Glu-Leu-Lys, where * indicates the cleavage point). Additionally, the crystal structure of plasmepsin II was analyzed to explain the binding characteristics. Specific amino acids (Met13, Ser77, and Ile287) that were suspected of contributing to active site binding and specificity were chosen for site-directed mutagenesis experiments. The Met13Glu and Ile287Glu single mutants and the Met13Glu/Ile287Glu double mutant gain the ability to cleave substrates containing Lys residues. PMID:10548045

  2. A classical enzyme active center motif lacks catalytic competence until modulated electrostatically.

    PubMed

    Pinitglang, S; Watts, A B; Patel, M; Reid, J D; Noble, M A; Gul, S; Bokth, A; Naeem, A; Patel, H; Thomas, E W; Sreedharan, S K; Verma, C; Brocklehurst, K

    1997-08-19

    The cysteine proteinase superfamily is a source of natural structural variants of value in the investigation of mechanism. It has long been considered axiomatic that catalytic competence of these enzymes mirrors the generation of the ubiquitous catalytic site imidazolium-thiolate ion pair. We here report definitive evidence from kinetic studies supported by electrostatic potential calculations, however, that at least for some of these enzymes the ion pair state which provides the nucleophilic and acid-base chemistry is essentially fully developed at low pH where the enzymes are inactive. Catalytic competence requires an additional protonic dissociation with a common pKa value close to 4 possibly from the Glu50 cluster to control ion pair geometry. The pH dependence of the second-order rate constant (k) for the reactions of the catalytic site thiol groups with 4,4'-dipyrimidyl disulfide is shown to provide the pKa values for the formation and deprotonation of the (Cys)-S-/(His)-Im+H ion pair state. Analogous study of the reactions with 2,2'-dipyridyl disulfide reveals other kinetically influential ionizations, and all of these pKa values are compared with those observed in the pH dependence of kcat/Km for the catalyzed hydrolysis of N-acetylphenylalanylglycine 4-nitroanilide. The discrepancy between the pKa value for ion pair formation and the common pKa value close to 4 related to generation of catalytic activity is particularly marked for ficin (pKa 2.49 +/- 0.02) and caricain (pKa 2.88 +/- 0.02) but exists also for papain (pKa 3.32 +/- 0.01). PMID:9254592

  3. Determinants of ligand binding and catalytic activity in the myelin enzyme 2',3'-cyclic nucleotide 3'-phosphodiesterase.

    PubMed

    Raasakka, Arne; Myllykoski, Matti; Laulumaa, Saara; Lehtimäki, Mari; Härtlein, Michael; Moulin, Martine; Kursula, Inari; Kursula, Petri

    2015-01-01

    2',3'-cyclic nucleotide 3'-phosphodiesterase (CNPase) is an enzyme highly abundant in the central nervous system myelin of terrestrial vertebrates. The catalytic domain of CNPase belongs to the 2H phosphoesterase superfamily and catalyzes the hydrolysis of nucleoside 2',3'-cyclic monophosphates to nucleoside 2'-monophosphates. The detailed reaction mechanism and the essential catalytic amino acids involved have been described earlier, but the roles of many amino acids in the vicinity of the active site have remained unknown. Here, several CNPase catalytic domain mutants were studied using enzyme kinetics assays, thermal stability experiments, and X-ray crystallography. Additionally, the crystal structure of a perdeuterated CNPase catalytic domain was refined at atomic resolution to obtain a detailed view of the active site and the catalytic mechanism. The results specify determinants of ligand binding and novel essential residues required for CNPase catalysis. For example, the aromatic side chains of Phe235 and Tyr168 are crucial for substrate binding, and Arg307 may affect active site electrostatics and regulate loop dynamics. The β5-α7 loop, unique for CNPase in the 2H phosphoesterase family, appears to have various functions in the CNPase reaction mechanism, from coordinating the nucleophilic water molecule to providing a binding pocket for the product and being involved in product release. PMID:26563764

  4. alpha-lytic protease can exist in two separately stable conformations with different His57 mobilities and catalytic activities.

    PubMed

    Haddad, Kristin Coffman; Sudmeier, James L; Bachovchin, Daniel A; Bachovchin, William W

    2005-01-25

    alpha-Lytic protease is a bacterial serine protease widely studied as a model system of enzyme catalysis. Here we report that lyophilization induces a structural change in the enzyme that is not reversed by redissolution in water. The structural change reduces the mobility of the active-site histidine residue and the catalytic activity of the enzyme. The application of mild pressure to solutions of the altered enzyme reverses the lyophilization-induced structural change and restores the mobility of the histidine residue and the enzyme's catalytic activity. This effect of lyophilization permits a unique opportunity for investigating the relationship between histidine ring dynamics and catalytic activity. The results demonstrate that His57 in resting enzymes is more mobile than previously thought, especially when protonated. The histidine motion and its correlation to enzyme activity lend support to the reaction-driven ring flip hypothesis. PMID:15657134

  5. α-Lytic protease can exist in two separately stable conformations with different His57 mobilities and catalytic activities

    PubMed Central

    Haddad, Kristin Coffman; Sudmeier, James L.; Bachovchin, Daniel A.; Bachovchin, William W.

    2005-01-01

    α-Lytic protease is a bacterial serine protease widely studied as a model system of enzyme catalysis. Here we report that lyophilization induces a structural change in the enzyme that is not reversed by redissolution in water. The structural change reduces the mobility of the active-site histidine residue and the catalytic activity of the enzyme. The application of mild pressure to solutions of the altered enzyme reverses the lyophilization-induced structural change and restores the mobility of the histidine residue and the enzyme's catalytic activity. This effect of lyophilization permits a unique opportunity for investigating the relationship between histidine ring dynamics and catalytic activity. The results demonstrate that His57 in resting enzymes is more mobile than previously thought, especially when protonated. The histidine motion and its correlation to enzyme activity lend support to the reaction-driven ring flip hypothesis. PMID:15657134

  6. Atomically-thin two-dimensional sheets for understanding active sites in catalysis.

    PubMed

    Sun, Yongfu; Gao, Shan; Lei, Fengcai; Xie, Yi

    2015-02-01

    Catalysis can speed up chemical reactions and it usually occurs on the low coordinated steps, edges, terraces, kinks and corner atoms that are often called "active sites". However, the atomic level interplay between active sites and catalytic activity is still an open question, owing to the large difference between idealized models and real catalysts. This stimulates us to pursue a suitable material model for studying the active sites-catalytic activity relationship, in which the atomically-thin two-dimensional sheets could serve as an ideal model, owing to their relatively simple type of active site and the ultrahigh fraction of active sites that are comparable to the overall atoms. In this tutorial review, we focus on the recent progress in disclosing the factors that affect the activity of reactive sites, including characterization of atomic coordination number, structural defects and disorder in ultrathin two-dimensional sheets by X-ray absorption fine structure spectroscopy, positron annihilation spectroscopy, electron spin resonance and high resolution transmission electron microscopy. Also, we overview their applications in CO catalytic oxidation, photocatalytic water splitting, electrocatalytic oxygen and hydrogen evolution reactions, and hence highlight the atomic level interplay among coordination number, structural defects/disorder, active sites and catalytic activity in the two-dimensional sheets with atomic thickness. Finally, we also present the major challenges and opportunities regarding the role of active sites in catalysis. We believe that this review provides critical insights for understanding the catalysis and hence helps to develop new catalysts with high catalytic activity. PMID:25382246

  7. Catalytic Intramolecular Ketone Alkylation with Olefins by Dual Activation.

    PubMed

    Lim, Hee Nam; Dong, Guangbin

    2015-12-01

    Two complementary methods for catalytic intramolecular ketone alkylation reactions with unactivated olefins, resulting in Conia-ene-type reactions, are reported. The transformations are enabled by dual activation of both the ketone and the olefin and are atom-economical as stoichiometric oxidants or reductants are not required. Assisted by Kool's aniline catalyst, the reaction conditions can be both pH- and redox-neutral. A broad range of functional groups are thus tolerated. Whereas the rhodium catalysts are effective for the formation of five-membered rings, a ruthenium-based system that affords the six-membered ring products was also developed. PMID:26486569

  8. Structures of bacterial kynurenine formamidase reveal a crowded binuclear zinc catalytic site primed to generate a potent nucleophile

    PubMed Central

    Díaz-Sáez, Laura; Srikannathasan, Velupillai; Zoltner, Martin; Hunter, William N.

    2014-01-01

    Tryptophan is an important precursor for chemical entities that ultimately support the biosynthesis of key metabolites. The second stage of tryptophan catabolism is catalysed by kynurenine formamidase, an enzyme that is different between eukaryotes and prokaryotes. In the present study, we characterize the catalytic properties and present the crystal structures of three bacterial kynurenine formamidases. The structures reveal a new amidase protein fold, a highly organized and distinctive binuclear Zn2+ catalytic centre in a confined, hydrophobic and relatively rigid active site. The structure of a complex with 2-aminoacetophenone delineates aspects of molecular recognition extending to the observation that the substrate itself may be conformationally restricted to assist binding in the confined space of the active site and for subsequent processing. The cations occupy a crowded environment, and, unlike most Zn2+-dependent enzymes, there is little scope to increase co-ordination number during catalysis. We propose that the presence of a bridging water/hydroxide ligand in conjunction with the placement of an active site histidine supports a distinctive amidation mechanism. PMID:24942958

  9. Activity of catalytic silver nanoparticles modulated by capping agent hydrophobicity.

    PubMed

    Janani, Seralathan; Stevenson, Priscilla; Veerappan, Anbazhagan

    2014-05-01

    In this paper, a facile in situ method is reported for the preparation of catalytic silver nanoparticles (AgNPs) using N-acyl tyramine (NATA) with variable hydrophobic acyl length. Scanning electron microscopic analysis shows that NATA exists initially as larger aggregates in alkaline aqueous solution. The addition of AgNO3 dissociates these larger aggregate and subsequently promotes the formation of self-assembled NATA and AgNPs. Characterization of AgNPs using UV-vis spectroscopy, scanning electron microscope and transmission electron microscope revealed that the hydrophobic acyl chain length of NATA does not influence the particle size, shape and morphology. All NATA-AgNPs yielded relatively identical values in full width at half-maximum (FWHM) analysis, indicating that the AgNPs prepared with NATA are relatively polydispersed at all tested acyl chain lengths. These nanoparticles are able to efficiently catalyze the reduction of 4-nitro phenol to 4-amino phenol, 2-nitro aniline to 1,2-diamino benzene, 2,4,6-trinitro phenol to 2,4,6-triamino phenol by NaBH4 in an aqueous environment. The reduction reaction rate is determined to be pseudo-first order and the apparent rate constant is linearly dependent on the hydrophobic acyl chain length of the NATA. All reaction kinetics presented an induction period, which is dependent on the N-acyl chain length, indicating that the hydrophobic effects play a critical role in bringing the substrate to the metal nanoparticle surface to induce the catalytic reaction. In this study, however, the five catalytic systems have similar size and polydispersity, differing only in terms of capping agent hydrophobicity, and shows different catalytic activity with respect to the alkyl chain length of the capping agent. As discussed, the ability to modulate the metal nanoparticles catalytic property, by modifying the capping agent hydrophobicity represents a promising future for developing an efficient nanocatalyst without altering the size

  10. Cwc2 and its human homologue RBM22 promote an active conformation of the spliceosome catalytic centre

    PubMed Central

    Rasche, Nicolas; Dybkov, Olexandr; Schmitzová, Jana; Akyildiz, Berktan; Fabrizio, Patrizia; Lührmann, Reinhard

    2012-01-01

    RNA-structural elements play key roles in pre-mRNA splicing catalysis; yet, the formation of catalytically competent RNA structures requires the assistance of spliceosomal proteins. We show that the S. cerevisiae Cwc2 protein functions prior to step 1 of splicing, and it is not required for the Prp2-mediated spliceosome remodelling that generates the catalytically active B* complex, suggesting that Cwc2 plays a more sophisticated role in the generation of a functional catalytic centre. In active spliceosomes, Cwc2 contacts catalytically important RNA elements, including the U6 internal stem-loop (ISL), and regions of U6 and the pre-mRNA intron near the 5′ splice site, placing Cwc2 at/near the spliceosome's catalytic centre. These interactions are evolutionarily conserved, as shown by studies with Cwc2's human counterpart RBM22, indicating that Cwc2/RBM22–RNA contacts are functionally important. We propose that Cwc2 induces an active conformation of the spliceosome's catalytic RNA elements. Thus, the function of RNA–RNA tertiary interactions within group II introns, namely to induce an active conformation of domain V, may be fulfilled by proteins that contact the functionally analogous U6-ISL, within the spliceosome. PMID:22246180

  11. Ultra-high electrochemical catalytic activity of MXenes

    PubMed Central

    Pan, Hui

    2016-01-01

    Cheap and abundant electrocatalysts for hydrogen evolution reactions (HER) have been widely pursued for their practical application in hydrogen-energy technologies. In this work, I present systematical study of the hydrogen evolution reactions on MXenes (Mo2X and W2X, X = C and N) based on density-functional-theory calculations. I find that their HER performances strongly depend on the composition, hydrogen adsorption configurations, and surface functionalization. I show that W2C monolayer has the best HER activity with near-zero overpotential at high hydrogen density among all of considered pure MXenes, and hydrogenation can efficiently enhance its catalytic performance in a wide range of hydrogen density further, while oxidization makes its activity reduced significantly. I further show that near-zero overpotential for HER on Mo2X monolayers can be achieved by oxygen functionalization. My calculations predict that surface treatment, such as hydrogenation and oxidization, is critical to enhance the catalytic performance of MXenes. I expect that MXenes with HER activity comparable to Pt in a wide range of hydrogen density can be realized by tuning composition and functionalizing, and promotes their applications into hydrogen-energy technologies. PMID:27604848

  12. Ultra-high electrochemical catalytic activity of MXenes.

    PubMed

    Pan, Hui

    2016-01-01

    Cheap and abundant electrocatalysts for hydrogen evolution reactions (HER) have been widely pursued for their practical application in hydrogen-energy technologies. In this work, I present systematical study of the hydrogen evolution reactions on MXenes (Mo2X and W2X, X = C and N) based on density-functional-theory calculations. I find that their HER performances strongly depend on the composition, hydrogen adsorption configurations, and surface functionalization. I show that W2C monolayer has the best HER activity with near-zero overpotential at high hydrogen density among all of considered pure MXenes, and hydrogenation can efficiently enhance its catalytic performance in a wide range of hydrogen density further, while oxidization makes its activity reduced significantly. I further show that near-zero overpotential for HER on Mo2X monolayers can be achieved by oxygen functionalization. My calculations predict that surface treatment, such as hydrogenation and oxidization, is critical to enhance the catalytic performance of MXenes. I expect that MXenes with HER activity comparable to Pt in a wide range of hydrogen density can be realized by tuning composition and functionalizing, and promotes their applications into hydrogen-energy technologies. PMID:27604848

  13. Catalytic Mesoporous Janus Nanomotors for Active Cargo Delivery

    PubMed Central

    2015-01-01

    We report on the synergy between catalytic propulsion and mesoporous silica nanoparticles (MSNPs) for the design of Janus nanomotors as active cargo delivery systems with sizes <100 nm (40, 65, and 90 nm). The Janus asymmetry of the nanomotors is given by electron beam (e-beam) deposition of a very thin platinum (2 nm) layer on MSNPs. The chemically powered Janus nanomotors present active diffusion at low H2O2 fuel concentration (i.e., <3 wt %). Their apparent diffusion coefficient is enhanced up to 100% compared to their Brownian motion. Due to their mesoporous architecture and small dimensions, they can load cargo molecules in large quantity and serve as active nanocarriers for directed cargo delivery on a chip. PMID:25844893

  14. Triggering activity of catalytic rod-like supramolecular polymers.

    PubMed

    Huerta, Elisa; van Genabeek, Bas; Lamers, Brigitte A G; Koenigs, Marcel M E; Meijer, E W; Palmans, Anja R A

    2015-02-23

    Supramolecular polymers based on benzene-1,3,5-tricarboxamides (BTAs) functionalized with an L- or D-proline moiety display high catalytic activity towards aldol reactions in water. High turnover frequencies (TOF) of up to 27×10(-4) s(-1) and excellent stereoselectivities (up to 96% de, up to 99% ee) were observed. In addition, the catalyst could be reused and remained active at catalyst loadings and substrate concentrations as low as 0.1 mol % and 50 mM, respectively. A temperature-induced conformational change in the supramolecular polymer triggers the high activity of the catalyst. The supramolecular polymer's helical sense in combination with the configuration of the proline (L- or D-) is responsible for the observed selectivity. PMID:25614098

  15. Catalytic mesoporous Janus nanomotors for active cargo delivery.

    PubMed

    Ma, Xing; Hahn, Kersten; Sanchez, Samuel

    2015-04-22

    We report on the synergy between catalytic propulsion and mesoporous silica nanoparticles (MSNPs) for the design of Janus nanomotors as active cargo delivery systems with sizes <100 nm (40, 65, and 90 nm). The Janus asymmetry of the nanomotors is given by electron beam (e-beam) deposition of a very thin platinum (2 nm) layer on MSNPs. The chemically powered Janus nanomotors present active diffusion at low H2O2 fuel concentration (i.e., <3 wt %). Their apparent diffusion coefficient is enhanced up to 100% compared to their Brownian motion. Due to their mesoporous architecture and small dimensions, they can load cargo molecules in large quantity and serve as active nanocarriers for directed cargo delivery on a chip. PMID:25844893

  16. Balancing the stability and the catalytic specificities of OP hydrolases with enhanced V-agent activities.

    PubMed

    Reeves, T E; Wales, M E; Grimsley, J K; Li, P; Cerasoli, D M; Wild, J R

    2008-06-01

    Rational site-directed mutagenesis and biophysical analyses have been used to explore the thermodynamic stability and catalytic capabilities of organophosphorus hydrolase (OPH) and its genetically modified variants. There are clear trade-offs in the stability of modifications that enhance catalytic activities. For example, the H254R/H257L variant has higher turnover numbers for the chemical warfare agents VX (144 versus 14 s(-1) for the native enzyme (wild type) and VR (Russian VX, 465 versus 12 s(-1) for wild type). These increases are accompanied by a loss in stability in which the total Gibb's free energy for unfolding is 19.6 kcal/mol, which is 5.7 kcal/mol less than that of the wild-type enzyme. X-ray crystallographic studies support biophysical data that suggest amino acid residues near the active site contribute to the chemical and thermal stability through hydrophobic and cation-pi interactions. The cation-pi interactions appear to contribute an additional 7 kcal/mol to the overall global stability of the enzyme. Using rational design, it has been possible to make amino acid changes in this region that restored the stability, yet maintained effective V-agent activities, with turnover numbers of 68 and 36 s(-1) for VX and VR, respectively. This study describes the first rationally designed, stability/activity balance for an OPH enzyme with a legitimate V-agent activity, and its crystal structure. PMID:18434422

  17. Origin of the catalytic activity of bovine seminal ribonuclease against double-stranded RNA

    NASA Technical Reports Server (NTRS)

    Opitz, J. G.; Ciglic, M. I.; Haugg, M.; Trautwein-Fritz, K.; Raillard, S. A.; Jermann, T. M.; Benner, S. A.

    1998-01-01

    Bovine seminal ribonuclease (RNase) binds, melts, and (in the case of RNA) catalyzes the hydrolysis of double-stranded nucleic acid 30-fold better under physiological conditions than its pancreatic homologue, the well-known RNase A. Reported here are site-directed mutagenesis experiments that identify the sequence determinants of this enhanced catalytic activity. These experiments have been guided in part by experimental reconstructions of ancestral RNases from extinct organisms that were intermediates in the evolution of the RNase superfamily. It is shown that the enhanced interactions between bovine seminal RNase and double-stranded nucleic acid do not arise from the increased number of basic residues carried by the seminal enzyme. Rather, a combination of a dimeric structure and the introduction of two glycine residues at positions 38 and 111 on the periphery of the active site confers the full catalytic activity of bovine seminal RNase against duplex RNA. A structural model is presented to explain these data, the use of evolutionary reconstructions to guide protein engineering experiments is discussed, and a new variant of RNase A, A(Q28L K31C S32C D38G E111G), which contains all of the elements identified in these experiments as being important for duplex activity, is prepared. This is the most powerful catalyst within this subfamily yet observed, some 46-fold more active against duplex RNA than RNase A.

  18. Catalytic activity of nuclease P1: Experiment and theory

    SciTech Connect

    Miller, J.H.; Falcone, J.M.; Shibata, M.; Box, H.C.

    1994-10-01

    Nuclease P1 from Penicillium citrinum is a zinc dependent glyco-enzyme that recognizes single stranded DNA and RNA as substrates and hydrolyzes the phosphate ester bond. Nuclease Pl seems to recognize particular conformations of the phosphodiester backbone and shows significant variation in the rate of hydrolytic activity depending upon which nucleosides are coupled by the phosphodiester bond. The efficiency of nuclease Pl in hydrolyzing the phosphodiester bonds of a substrate can be altered by modifications to one of the substrate bases induced by ionizing radiation or oxidative stress. Measurements have been made of the effect of several radiation induced lesions on the catalytic rate of nuclease Pl. A model of the structure of the enzyme has been constructed in order to better understand the binding and activity of this enzyme on various ssDNA substrates.

  19. The bifunctional active site of s-adenosylmethionine synthetase. Roles of the active site aspartates.

    PubMed

    Taylor, J C; Markham, G D

    1999-11-12

    S-Adenosylmethionine (AdoMet) synthetase catalyzes the biosynthesis of AdoMet in a unique enzymatic reaction. Initially the sulfur of methionine displaces the intact tripolyphosphate chain (PPP(i)) from ATP, and subsequently PPP(i) is hydrolyzed to PP(i) and P(i) before product release. The crystal structure of Escherichia coli AdoMet synthetase shows that the active site contains four aspartate residues. Aspartate residues Asp-16* and Asp-271 individually provide the sole protein ligand to one of the two required Mg(2+) ions (* denotes a residue from a second subunit); aspartates Asp-118 and Asp-238* are proposed to interact with methionine. Each aspartate has been changed to an uncharged asparagine, and the metal binding residues were also changed to alanine, to assess the roles of charge and ligation ability on catalytic efficiency. The resultant enzyme variants all structurally resemble the wild type enzyme as indicated by circular dichroism spectra and are tetramers. However, all have k(cat) reductions of approximately 10(3)-fold in AdoMet synthesis, whereas the MgATP and methionine K(m) values change by less than 3- and 8-fold, respectively. In the partial reaction of PPP(i) hydrolysis, mutants of the Mg(2+) binding residues have >700-fold reduced catalytic efficiency (k(cat)/K(m)), whereas the D118N and D238*N mutants are impaired less than 35-fold. The catalytic efficiency for PPP(i) hydrolysis by Mg(2+) site mutants is improved by AdoMet, like the wild type enzyme. In contrast AdoMet reduces the catalytic efficiency for PPP(i) hydrolysis by the D118N and D238*N mutants, indicating that the events involved in AdoMet activation are hindered in these methionyl binding site mutants. Ca(2+) uniquely activates the D271A mutant enzyme to 15% of the level of Mg(2+), in contrast to the approximately 1% Ca(2+) activation of the wild type enzyme. This indicates that the Asp-271 side chain size is a discriminator between the activating ability of Ca(2+) and the

  20. Metal active site elasticity linked to activation of homocysteine in methionine synthases

    SciTech Connect

    Koutmos, Markos; Pejchal, Robert; Bomer, Theresa M.; Matthews, Rowena G.; Smith, Janet L.; Ludwig, Martha L.

    2008-04-02

    Enzymes possessing catalytic zinc centers perform a variety of fundamental processes in nature, including methyl transfer to thiols. Cobalamin-independent (MetE) and cobalamin-dependent (MetH) methionine synthases are two such enzyme families. Although they perform the same net reaction, transfer of a methyl group from methyltetrahydrofolate to homocysteine (Hcy) to form methionine, they display markedly different catalytic strategies, modular organization, and active site zinc centers. Here we report crystal structures of zinc-replete MetE and MetH, both in the presence and absence of Hcy. Structural investigation of the catalytic zinc sites of these two methyltransferases reveals an unexpected inversion of zinc geometry upon binding of Hcy and displacement of an endogenous ligand in both enzymes. In both cases a significant movement of the zinc relative to the protein scaffold accompanies inversion. These structures provide new information on the activation of thiols by zinc-containing enzymes and have led us to propose a paradigm for the mechanism of action of the catalytic zinc sites in these and related methyltransferases. Specifically, zinc is mobile in the active sites of MetE and MetH, and its dynamic nature helps facilitate the active site conformational changes necessary for thiol activation and methyl transfer.

  1. TET2 Regulates Mast Cell Differentiation and Proliferation through Catalytic and Non-catalytic Activities.

    PubMed

    Montagner, Sara; Leoni, Cristina; Emming, Stefan; Della Chiara, Giulia; Balestrieri, Chiara; Barozzi, Iros; Piccolo, Viviana; Togher, Susan; Ko, Myunggon; Rao, Anjana; Natoli, Gioacchino; Monticelli, Silvia

    2016-05-17

    Dioxygenases of the TET family impact genome functions by converting 5-methylcytosine (5mC) in DNA to 5-hydroxymethylcytosine (5hmC). Here, we identified TET2 as a crucial regulator of mast cell differentiation and proliferation. In the absence of TET2, mast cells showed disrupted gene expression and altered genome-wide 5hmC deposition, especially at enhancers and in the proximity of downregulated genes. Impaired differentiation of Tet2-ablated cells could be relieved or further exacerbated by modulating the activity of other TET family members, and mechanistically it could be linked to the dysregulated expression of C/EBP family transcription factors. Conversely, the marked increase in proliferation induced by the loss of TET2 could be rescued exclusively by re-expression of wild-type or catalytically inactive TET2. Our data indicate that, in the absence of TET2, mast cell differentiation is under the control of compensatory mechanisms mediated by other TET family members, while proliferation is strictly dependent on TET2 expression. PMID:27160912

  2. Guiding catalytically active particles with chemically patterned surfaces

    NASA Astrophysics Data System (ADS)

    Uspal, William; Popescu, Mihail; Dietrich, Siegfried; Tasinkevych, Mykola

    Catalytically active Janus particles in solution create gradients in the chemical composition of the solution along their surfaces, as well as along any nearby container walls. The former leads to self-phoresis, while the latter gives rise to chemi-osmosis, providing an additional contribution to self-motility. Chemi-osmosis strongly depends on the molecular interactions between the diffusing chemical species and the wall. We show analytically, using an approximate ``point-particle'' approach, that by chemically patterning a planar substrate (e.g., by adsorbing two different materials) one can direct the motion of Janus particles: the induced chemi-osmotic flows can cause particles to either ``dock'' at a chemical step between the two materials, or to follow a chemical stripe. These theoretical predictions are confirmed by full numerical calculations. Generically, docking occurs for particles which tend to move away from their catalytic caps, while stripe-following occurs in the opposite case. Our analysis reveals the physical mechanisms governing this behavior.

  3. Studies Relevent to Catalytic Activation Co & other small Molecules

    SciTech Connect

    Ford, Peter C

    2005-02-22

    Detailed annual and triannual reports describing the progress accomplished during the tenure of this grant were filed with the Program Manager for Catalysis at the Office of Basic Energy Sciences. To avoid unnecessary duplication, the present report will provide a brief overview of the research areas that were sponsored by this grant and list the resulting publications and theses based on this DOE supported research. The scientific personnel participating in (and trained by) this grant's research are also listed. Research carried out under this DOE grant was largely concerned with the mechanisms of the homogeneous catalytic and photocatalytic activation of small molecules such as carbon monoxide, dihydrogen and various hydrocarbons. Much of the more recent effort has focused on the dynamics and mechanisms of reactions relevant to substrate carbonylations by homogeneous organometallic catalysts. A wide range of modern investigative techniques were employed, including quantitative fast reaction methodologies such as time-resolved optical (TRO) and time-resolved infrared (TRIR) spectroscopy and stopped flow kinetics. Although somewhat diverse, this research falls within the scope of the long-term objective of applying quantitative techniques to elucidate the dynamics and understand the principles of mechanisms relevant to the selective and efficient catalytic conversions of fundamental feedstocks to higher value materials.

  4. Catalytic combustion of dry carbon monoxide by external power activation

    NASA Astrophysics Data System (ADS)

    Treviño, C.; Prince, J. C.

    2000-03-01

    The catalytic combustion of dry carbon monoxide and air in a planar stagnation-point flow over a platinum foil with external power is studied in this paper. The reduced heterogeneous kinetics are modelled with the dissociative adsorption of the molecular oxygen and the non-dissociative adsorption of CO, together with a surface reaction of the Langmuir-Hinshelwood type and the desorption reaction of the adsorbed product, CO 2(s). The resulting governing equations have been numerically integrated and the whole S-shaped response curve has been obtained as a function of the mixture initial concentration. The critical conditions for the catalytic ignition and extinction are deduced using high activation energy asymptotics of the desorption kinetics of the most efficient adsorbed reactant, CO(s). We obtained a very good agreement between the numerical and asymptotic results for the ignition and extinction conditions. In general, the ignition process can be well modelled without reactant consumption, while extinction occurs in the partial diffusion-controlled regime, with a finite non-zero concentration of carbon monoxide close to the plate.

  5. Catalytic activity of unsaturated coordinated Cu-MOF to the hydroxylation of phenol

    NASA Astrophysics Data System (ADS)

    Jian, Lijuan; Chen, Chao; Lan, Fan; Deng, Shengjun; Xiao, Weiming; Zhang, Ning

    2011-05-01

    A 2D metal-organic framework [Cu 2 (BPTC) (Im) 4(H 2O) (DMF)] n ( 1) with unsaturated coordinated Cu(II) sites has been prepared under solvothermal condition, and applied to the hydroxylation of phenol after activating. The catalytic results indicate that 1a (the activated 1) exhibits an obvious activity for phenol hydroxylation at 40 °C for 4 h. Compared to the control experiments where the free Cu(II) (from Cu(OAc) 2 salt) has been utilized as the catalysts, 1a shows the higher selectivity to diphenols. This suggests that the coordinated environment of unsaturated coordinated Cu(II) sites in the 2D layer play the key role in the phenol hydroxylation.

  6. Copper metal-organic framework nanocrystal for plane effect nonenzymatic electro-catalytic activity of glucose.

    PubMed

    Liu, Yuanying; Zhang, Youjuan; Chen, Jing; Pang, Huan

    2014-10-01

    This work describes the first demonstration of nanocrystal plane dependent nonenzymatic electro-catalytic glucose activity of [Cu3(btc)2] nanocrystals with different shapes (nanocube, truncated cube, cuboctahedron, and octahedron). From electrochemical results, the obtained [Cu3(btc)2] nanocube modified electrode shows the best nonenzymatic electro-catalytic glucose activity. Interestingly, decreasing the {100} crystal planes from cubes to octahedra, changes the nonenzymatic electro-catalytic activity from highly sensitive to general. PMID:25123202

  7. Topological constraints of structural elements in regulation of catalytic activity in HDV-like self-cleaving ribozymes

    PubMed Central

    Webb, Chiu-Ho T.; Nguyen, Dang; Myszka, Marie; Lupták, Andrej

    2016-01-01

    Self-cleaving ribozymes fold into intricate structures, which orient active site groups into catalytically competent conformations. Most ribozyme families have distinct catalytic cores stabilized by tertiary interactions between domains peripheral to those cores. We show that large hepatitis delta virus (HDV)-like ribozymes are activated by peripheral domains that bring two helical segments, P1 and P2, into proximity – a “pinch” that results in rate acceleration by almost three orders of magnitude. Kinetic analysis of ribozymes with systematically altered length and stability of the peripheral domain revealed that about one third of its free energy of formation is used to lower an activation energy barrier, likely related to a rate-limiting conformational change leading to the pre-catalytic state. These findings provide a quantitative view of enzyme regulation by peripheral domains and may shed light on the energetics of allosteric regulation. PMID:27302490

  8. Topological constraints of structural elements in regulation of catalytic activity in HDV-like self-cleaving ribozymes.

    PubMed

    Webb, Chiu-Ho T; Nguyen, Dang; Myszka, Marie; Lupták, Andrej

    2016-01-01

    Self-cleaving ribozymes fold into intricate structures, which orient active site groups into catalytically competent conformations. Most ribozyme families have distinct catalytic cores stabilized by tertiary interactions between domains peripheral to those cores. We show that large hepatitis delta virus (HDV)-like ribozymes are activated by peripheral domains that bring two helical segments, P1 and P2, into proximity - a "pinch" that results in rate acceleration by almost three orders of magnitude. Kinetic analysis of ribozymes with systematically altered length and stability of the peripheral domain revealed that about one third of its free energy of formation is used to lower an activation energy barrier, likely related to a rate-limiting conformational change leading to the pre-catalytic state. These findings provide a quantitative view of enzyme regulation by peripheral domains and may shed light on the energetics of allosteric regulation. PMID:27302490

  9. Nicotinamide Cofactors Suppress Active-Site Labeling of Aldehyde Dehydrogenases.

    PubMed

    Stiti, Naim; Chandrasekar, Balakumaran; Strubl, Laura; Mohammed, Shabaz; Bartels, Dorothea; van der Hoorn, Renier A L

    2016-06-17

    Active site labeling by (re)activity-based probes is a powerful chemical proteomic tool to globally map active sites in native proteomes without using substrates. Active site labeling is usually taken as a readout for the active state of the enzyme because labeling reflects the availability and reactivity of active sites, which are hallmarks for enzyme activities. Here, we show that this relationship holds tightly, but we also reveal an important exception to this rule. Labeling of Arabidopsis ALDH3H1 with a chloroacetamide probe occurs at the catalytic Cys, and labeling is suppressed upon nitrosylation and oxidation, and upon treatment with other Cys modifiers. These experiments display a consistent and strong correlation between active site labeling and enzymatic activity. Surprisingly, however, labeling is suppressed by the cofactor NAD(+), and this property is shared with other members of the ALDH superfamily and also detected for unrelated GAPDH enzymes with an unrelated hydantoin-based probe in crude extracts of plant cell cultures. Suppression requires cofactor binding to its binding pocket. Labeling is also suppressed by ALDH modulators that bind at the substrate entrance tunnel, confirming that labeling occurs through the substrate-binding cavity. Our data indicate that cofactor binding adjusts the catalytic Cys into a conformation that reduces the reactivity toward chloroacetamide probes. PMID:26990764

  10. A redox 2-Cys mechanism regulates the catalytic activity of divergent cyclophilins.

    PubMed

    Campos, Bruna Medéia; Sforça, Mauricio Luis; Ambrosio, Andre Luis Berteli; Domingues, Mariane Noronha; Brasil de Souza, Tatiana de Arruda Campos; Barbosa, João Alexandre Ribeiro Gonçalvez; Paes Leme, Adriana Franco; Perez, Carlos Alberto; Whittaker, Sara Britt-Marie; Murakami, Mario Tyago; Zeri, Ana Carolina de Matos; Benedetti, Celso Eduardo

    2013-07-01

    The citrus (Citrus sinensis) cyclophilin CsCyp is a target of the Xanthomonas citri transcription activator-like effector PthA, required to elicit cankers on citrus. CsCyp binds the citrus thioredoxin CsTdx and the carboxyl-terminal domain of RNA polymerase II and is a divergent cyclophilin that carries the additional loop KSGKPLH, invariable cysteine (Cys) residues Cys-40 and Cys-168, and the conserved glutamate (Glu) Glu-83. Despite the suggested roles in ATP and metal binding, the functions of these unique structural elements remain unknown. Here, we show that the conserved Cys residues form a disulfide bond that inactivates the enzyme, whereas Glu-83, which belongs to the catalytic loop and is also critical for enzyme activity, is anchored to the divergent loop to maintain the active site open. In addition, we demonstrate that Cys-40 and Cys-168 are required for the interaction with CsTdx and that CsCyp binds the citrus carboxyl-terminal domain of RNA polymerase II YSPSAP repeat. Our data support a model where formation of the Cys-40-Cys-168 disulfide bond induces a conformational change that disrupts the interaction of the divergent and catalytic loops, via Glu-83, causing the active site to close. This suggests a new type of allosteric regulation in divergent cyclophilins, involving disulfide bond formation and a loop-displacement mechanism. PMID:23709667

  11. The Non-Catalytic Domains of Drosophila Katanin Regulate Its Abundance and Microtubule-Disassembly Activity

    PubMed Central

    Grode, Kyle D.; Rogers, Stephen L.

    2015-01-01

    Microtubule severing is a biochemical reaction that generates an internal break in a microtubule and regulation of microtubule severing is critical for cellular processes such as ciliogenesis, morphogenesis, and meiosis and mitosis. Katanin is a conserved heterodimeric ATPase that severs and disassembles microtubules, but the molecular determinants for regulation of microtubule severing by katanin remain poorly defined. Here we show that the non-catalytic domains of Drosophila katanin regulate its abundance and activity in living cells. Our data indicate that the microtubule-interacting and trafficking (MIT) domain and adjacent linker region of the Drosophila katanin catalytic subunit Kat60 cooperate to regulate microtubule severing in two distinct ways. First, the MIT domain and linker region of Kat60 decrease its abundance by enhancing its proteasome-dependent degradation. The Drosophila katanin regulatory subunit Kat80, which is required to stabilize Kat60 in cells, conversely reduces the proteasome-dependent degradation of Kat60. Second, the MIT domain and linker region of Kat60 augment its microtubule-disassembly activity by enhancing its association with microtubules. On the basis of our data, we propose that the non-catalytic domains of Drosophila katanin serve as the principal sites of integration of regulatory inputs, thereby controlling its ability to sever and disassemble microtubules. PMID:25886649

  12. First insight into catalytic activity of anionic iron porphyrins immobilized on exfoliated layered double hydroxides.

    PubMed

    Nakagaki, Shirley; Halma, Matilte; Bail, Alesandro; Arízaga, Gregório Guadalupe Carbajal; Wypych, Fernando

    2005-01-15

    Mg-Al layered double hydroxide (LDH) intercalated with glycinate anions was synthesized through co-precipitation and exfoliated in formamide and the single-layer suspension was reacted with aqueous iron porphyrin solutions (Fe(TDFSPP) and Fe(TCFSPP)). The obtained materials were characterized by X-ray powder diffraction, UV-vis, and electron paramagnetic resonance and investigated in the oxidation reaction of cyclooctene and cyclohexane using iodosylbenzene as oxidant. The iron porphyrin seems to be immobilized at the surface of the glycinate intercalated LDH. The catalytic activities obtained in heterogeneous media for iron porphyrin, Fe(TDFSPP), was superior to the results obtained under homogeneous conditions, but the opposite effect was observed on the Fe(TCFSPP), indicating that, instead of the structural similarity of both iron porphyrins (second-generation porphyrins), the immobilization of each one produced different catalysts. The best catalytic activity of the Fe(TDFSPP)/Gly-LDH, compared to Fe(TCFSPP)/Gly-LDH, can be explained by the easy access of the oxidant and the substrate to the catalytic sites in the former, probably located at the surface of the layered double hydroxide pillared with glycinate anions. A model for the immobilization and a mechanism for the oxidation reaction will be discussed. PMID:15571697

  13. Synthesis and catalytic activity of heteroatom doped metal-free single-wall carbon nanohorns.

    PubMed

    Wu, Xiaohui; Cui, Longbin; Tang, Pei; Hu, Ziqi; Ma, Ding; Shi, Zujin

    2016-04-01

    Boron-, phosphorus-, nitrogen-doped and co-doped single-wall carbon nanohorns were produced using an arc-vaporization method. These as-prepared doped materials consist of uniform isolated nanohorns and exhibit greatly enhanced catalytic capabilities in the reduction reaction of nitrobenzene and a volcano-shape trend between their activities with a B dopant content is found. Moreover, the B-C3 and P-C3 species in doped nanohorns might act as the acidic and basic sites to promote this reaction. PMID:27006980

  14. Antibacterial and catalytic activities of green synthesized silver nanoparticles

    NASA Astrophysics Data System (ADS)

    Bindhu, M. R.; Umadevi, M.

    2015-01-01

    The aqueous beetroot extract was used as reducing agent for silver nanoparticles synthesis. The synthesized nanoparticles were characterized using UV-visible spectroscopy, X-ray diffraction (XRD) and transmission electron microscopy (TEM). The surface plasmon resonance peak of synthesized nanoparticles was observed at 438 nm. As the concentration of beetroot extract increases, absorption spectra shows blue shift with decreasing particle size. The prepared silver nanoparticles were well dispersed, spherical in shape with the average particle size of 15 nm. The prepared silver nanoparticles are effective in inhibiting the growth of both gram positive and gram negative bacteria. The prepared silver nanoparticles reveal faster catalytic activity. This natural method for synthesis of silver nanoparticles offers a valuable contribution in the area of green synthesis and nanotechnology avoiding the presence of hazardous and toxic solvents and waste.

  15. Support nanostructure boosts oxygen transfer to catalytically active platinum nanoparticles.

    PubMed

    Vayssilov, Georgi N; Lykhach, Yaroslava; Migani, Annapaola; Staudt, Thorsten; Petrova, Galina P; Tsud, Nataliya; Skála, Tomáš; Bruix, Albert; Illas, Francesc; Prince, Kevin C; Matolín, Vladimír; Neyman, Konstantin M; Libuda, Jörg

    2011-04-01

    Interactions of metal particles with oxide supports can radically enhance the performance of supported catalysts. At the microscopic level, the details of such metal-oxide interactions usually remain obscure. This study identifies two types of oxidative metal-oxide interaction on well-defined models of technologically important Pt-ceria catalysts: (1) electron transfer from the Pt nanoparticle to the support, and (2) oxygen transfer from ceria to Pt. The electron transfer is favourable on ceria supports, irrespective of their morphology. Remarkably, the oxygen transfer is shown to require the presence of nanostructured ceria in close contact with Pt and, thus, is inherently a nanoscale effect. Our findings enable us to detail the formation mechanism of the catalytically indispensable Pt-O species on ceria and to elucidate the extraordinary structure-activity dependence of ceria-based catalysts in general. PMID:21423188

  16. Support nanostructure boosts oxygen transfer to catalytically active platinum nanoparticles

    NASA Astrophysics Data System (ADS)

    Vayssilov, Georgi N.; Lykhach, Yaroslava; Migani, Annapaola; Staudt, Thorsten; Petrova, Galina P.; Tsud, Nataliya; Skála, Tomáš; Bruix, Albert; Illas, Francesc; Prince, Kevin C.; MatolíN, VladimíR.; Neyman, Konstantin M.; Libuda, Jörg

    2011-04-01

    Interactions of metal particles with oxide supports can radically enhance the performance of supported catalysts. At the microscopic level, the details of such metal-oxide interactions usually remain obscure. This study identifies two types of oxidative metal-oxide interaction on well-defined models of technologically important Pt-ceria catalysts: (1) electron transfer from the Pt nanoparticle to the support, and (2) oxygen transfer from ceria to Pt. The electron transfer is favourable on ceria supports, irrespective of their morphology. Remarkably, the oxygen transfer is shown to require the presence of nanostructured ceria in close contact with Pt and, thus, is inherently a nanoscale effect. Our findings enable us to detail the formation mechanism of the catalytically indispensable Pt-O species on ceria and to elucidate the extraordinary structure-activity dependence of ceria-based catalysts in general.

  17. [Effect Of Polyelectrolytes on Catalytic Activity of Alcohol Dehydrogenase].

    PubMed

    Dubrovsky, A V; Musina, E V; Kim, A L; Tikhonenko, S A

    2016-01-01

    Fluorescent and optical spectroscopy were used to study the interaction of alcohol dehydrogenase (ADH) with negatively charged polystyrene sulfonate (PSS) and dextran sulfate (DS), as well as positively charged poly(diallyldimethylammonium) (PDADMA). As found, DS and PDADMA did not affect the structural and catalytic enzyme properties. In contrast, PSS slightly decreased the protein self-fluorescence over 1 h of incubation, which is associated with partial destruction of its quaternary (globular) structure. Investigation of the ADH activity with and without PSS showed its dependency on the incubation time and the PSS presence. Sodium chloride (2.0 M and 0.2 M) or ammonium sulfate (0.1 M) added to the reaction mixture did not completely protect the enzyme quaternary structure from the PSS action. However ammonium sulfate or 0.2 M sodium chloride stabilized the enzyme and partially inhibited the negative PSS effect. PMID:27266256

  18. Acceleration of catalytic activity of calcium oxide for biodiesel production.

    PubMed

    Kawashima, Ayato; Matsubara, Koh; Honda, Katsuhisa

    2009-01-01

    This research was aimed at studying the acceleration of the catalytic activity of calcium oxide (CaO) for developing an effective heterogeneous catalyst for biodiesel production by the transesterification of plant oil with methanol. CaO was activated by pretreatment with methanol and was used for the transesterification reaction. The activation and transesterification reaction conditions were examined. The obtained optimal reaction conditions were 0.1-g CaO, 3.9-g methanol, 15-g rapeseed oil, and 1.5-h activation time at room temperature that provided methyl ester in approximately 90% yield within a reaction time of 3h at 60 degrees C. The activation mechanism was also investigated, and the proposed mechanism is as follows. By pretreatment with methanol, a small amount of CaO gets converted into Ca(OCH(3))(2) that acts as an initiating reagent for the transesterification reaction and produces glycerin as a by-product. Subsequently, a calcium-glycerin complex, formed due to the reaction of CaO with glycerin, functions as the main catalyst and accelerates the transesterification reaction. PMID:18684617

  19. Imaging Isolated Gold Atom Catalytic Sites in Zeolite NaY

    SciTech Connect

    Lu, Jing; Aydin, C.; Browning, Nigel D.; Gates, Bruce C.

    2012-06-11

    Gold, the most stable metallic element, attracted wide attention as a catalyst only after the discovery that gold nanoclusters on oxide supports are highly active and selective for reactions including numerous oxidation,[1–8] hydrogenation,[9–11] hydroamination,[12, 13] ring expansion,[14, 15] and coupling[16, 17] reactions. The catalytic properties of supported gold strongly dependent on the gold–support interactions and the size of the active species, which must be small—typically clusters with diameters of the order of 1 nm.[18–20] Frequent discoveries of new gold-catalyzed reactions are leading the science; understanding has been slow to emerge.[21] Major challenges are to identify the catalytically active species and to characterize gold–support interactions.

  20. Structural changes induced by catalytic turnover at the molybdenum site of arabidopsis nitrate reductase

    SciTech Connect

    George, G.N.; Mertens, J.A.; Campbell, W.H.

    1999-10-20

    Assimilatory nitrate reductases catalyze the reduction of nitrate to nitrite, which is the first and rate-limiting step of nitrogen assimilation in algae, fungi, and higher plants. The nitrate reductase from the thale cress, Arabidopsis thaliana, is a dimer, with each of the {approximately} 103,000 molecular weight monomers containing one molybdenum associated with a single pterin dithiolene cofactor, a flavin adenine dinucleotide cofactor, and a cytochrome b-type heme. During the catalytic cycle, reducing equivalents in the form of NADH enter the enzyme at the flavin site and are subsequently transferred by intramolecular electron transfer via the heme to the molybdenum center, where the two-electron reduction of nitrate takes place. In this paper the authors present the Mo K-edge EXAFS of Arabidopsis nitrate reductase in three different forms: oxidized as-isolated, reduced, and oxidized after catalytic turnover of excess nitrate (nitrate-oxidized).

  1. The alpha subunit of nitrile hydratase is sufficient for catalytic activity and post-translational modification.

    PubMed

    Nelp, Micah T; Astashkin, Andrei V; Breci, Linda A; McCarty, Reid M; Bandarian, Vahe

    2014-06-24

    Nitrile hydratases (NHases) possess a mononuclear iron or cobalt cofactor whose coordination environment includes rare post-translationally oxidized cysteine sulfenic and sulfinic acid ligands. This cofactor is located in the α-subunit at the interfacial active site of the heterodimeric enzyme. Unlike canonical NHases, toyocamycin nitrile hydratase (TNHase) from Streptomyces rimosus is a unique three-subunit member of this family involved in the biosynthesis of pyrrolopyrimidine antibiotics. The subunits of TNHase are homologous to the α- and β-subunits of prototypical NHases. Herein we report the expression, purification, and characterization of the α-subunit of TNHase. The UV-visible, EPR, and mass spectra of the α-subunit TNHase provide evidence that this subunit alone is capable of synthesizing the active site complex with full post-translational modifications. Remarkably, the isolated post-translationally modified α-subunit is also catalytically active with the natural substrate, toyocamycin, as well as the niacin precursor 3-cyanopyridine. Comparisons of the steady state kinetic parameters of the single subunit variant to the heterotrimeric protein clearly show that the additional subunits impart substrate specificity and catalytic efficiency. We conclude that the α-subunit is the minimal sequence needed for nitrile hydration providing a simplified scaffold to study the mechanism and post-translational modification of this important class of catalysts. PMID:24914472

  2. Extensive site-directed mutagenesis reveals interconnected functional units in the alkaline phosphatase active site.

    PubMed

    Sunden, Fanny; Peck, Ariana; Salzman, Julia; Ressl, Susanne; Herschlag, Daniel

    2015-01-01

    Enzymes enable life by accelerating reaction rates to biological timescales. Conventional studies have focused on identifying the residues that have a direct involvement in an enzymatic reaction, but these so-called 'catalytic residues' are embedded in extensive interaction networks. Although fundamental to our understanding of enzyme function, evolution, and engineering, the properties of these networks have yet to be quantitatively and systematically explored. We dissected an interaction network of five residues in the active site of Escherichia coli alkaline phosphatase. Analysis of the complex catalytic interdependence of specific residues identified three energetically independent but structurally interconnected functional units with distinct modes of cooperativity. From an evolutionary perspective, this network is orders of magnitude more probable to arise than a fully cooperative network. From a functional perspective, new catalytic insights emerge. Further, such comprehensive energetic characterization will be necessary to benchmark the algorithms required to rationally engineer highly efficient enzymes. PMID:25902402

  3. Development of novel catalytically active polymer-metal-nanocomposites based on activated foams and textile fibers

    PubMed Central

    2013-01-01

    In this paper, we report the intermatrix synthesis of Ag nanoparticles in different polymeric matrices such as polyurethane foams and polyacrylonitrile or polyamide fibers. To apply this technique, the polymer must bear functional groups able to bind and retain the nanoparticle ion precursors while ions should diffuse through the matrix. Taking into account the nature of some of the chosen matrices, it was essential to try to activate the support material to obtain an acceptable value of ion exchange capacity. To evaluate the catalytic activity of the developed nanocomposites, a model catalytic reaction was carried out in batch experiments: the reduction of p-nitrophenol by sodium borohydride. PMID:23680063

  4. Development of novel catalytically active polymer-metal-nanocomposites based on activated foams and textile fibers

    NASA Astrophysics Data System (ADS)

    Domènech, Berta; Ziegler, Kharla K.; Carrillo, Fernando; Muñoz, Maria; Muraviev, Dimitri N.; Macanás, Jorge

    2013-05-01

    In this paper, we report the intermatrix synthesis of Ag nanoparticles in different polymeric matrices such as polyurethane foams and polyacrylonitrile or polyamide fibers. To apply this technique, the polymer must bear functional groups able to bind and retain the nanoparticle ion precursors while ions should diffuse through the matrix. Taking into account the nature of some of the chosen matrices, it was essential to try to activate the support material to obtain an acceptable value of ion exchange capacity. To evaluate the catalytic activity of the developed nanocomposites, a model catalytic reaction was carried out in batch experiments: the reduction of p-nitrophenol by sodium borohydride.

  5. Catalytic activity of bimetallic catalysts highly sensitive to the atomic composition and phase structure at the nanoscale

    NASA Astrophysics Data System (ADS)

    Shan, Shiyao; Petkov, Valeri; Prasai, Binay; Wu, Jinfang; Joseph, Pharrah; Skeete, Zakiya; Kim, Eunjoo; Mott, Derrick; Malis, Oana; Luo, Jin; Zhong, Chuan-Jian

    2015-11-01

    The ability to determine the atomic arrangement in nanoalloy catalysts and reveal the detailed structural features responsible for the catalytically active sites is essential for understanding the correlation between the atomic structure and catalytic properties, enabling the preparation of efficient nanoalloy catalysts by design. Herein we describe a study of CO oxidation over PdCu nanoalloy catalysts focusing on gaining insights into the correlation between the atomic structures and catalytic activity of nanoalloys. PdCu nanoalloys of different bimetallic compositions are synthesized as a model system and are activated by a controlled thermochemical treatment for assessing their catalytic activity. The results show that the catalytic synergy of Pd and Cu species evolves with both the bimetallic nanoalloy composition and temperature of the thermochemical treatment reaching a maximum at a Pd : Cu ratio close to 50 : 50. The nanoalloys are characterized structurally by ex situ and in situ synchrotron X-ray diffraction, including atomic pair distribution function analysis. The structural data show that, depending on the bimetallic composition and treatment temperature, PdCu nanoalloys adopt two different structure types. One features a chemically ordered, body centered cubic (B2) type alloy consisting of two interpenetrating simple cubic lattices, each occupied with Pd or Cu species alone, and the other structure type features a chemically disordered, face-centered cubic (fcc) type of alloy wherein Pd and Cu species are intermixed at random. The catalytic activity for CO oxidation is strongly influenced by the structural features. In particular, it is revealed that the prevalence of chemical disorder in nanoalloys with a Pd : Cu ratio close to 50 : 50 makes them superior catalysts for CO oxidation in comparison with the same nanoalloys of other bimetallic compositions. However, the catalytic synergy can be diminished if the Pd50Cu50 nanoalloys undergo phase

  6. Bacillus pumilus Cyanide Dihydratase Mutants with Higher Catalytic Activity.

    PubMed

    Crum, Mary A; Sewell, B Trevor; Benedik, Michael J

    2016-01-01

    Cyanide degrading nitrilases are noted for their potential to detoxify industrial wastewater contaminated with cyanide. However, such application would benefit from an improvement to characteristics such as their catalytic activity and stability. Following error-prone PCR for random mutagenesis, several cyanide dihydratase mutants from Bacillus pumilus were isolated based on improved catalysis. Four point mutations, K93R, D172N, A202T, and E327K were characterized and their effects on kinetics, thermostability and pH tolerance were studied. K93R and D172N increased the enzyme's thermostability whereas E327K mutation had a less pronounced effect on stability. The D172N mutation also increased the affinity of the enzyme for its substrate at pH 7.7 but lowered its k cat. However, the A202T mutation, located in the dimerization or the A surface, destabilized the protein and abolished its activity. No significant effect on activity at alkaline pH was observed for any of the purified mutants. These mutations help confirm the model of CynD and are discussed in the context of the protein-protein interfaces leading to the protein quaternary structure. PMID:27570524

  7. Catalytic Growth of Macroscopic Carbon Nanofibers Bodies with Activated Carbon

    SciTech Connect

    Abdullah, N.; Muhammad, I. S.; Hamid, S. B. Abd.; Rinaldi, A.; Su, D. S.; Schlogl, R.

    2009-06-01

    Carbon-carbon composite of activated carbon and carbon nanofibers have been synthesized by growing Carbon nanofiber (CNF) on Palm shell-based Activated carbon (AC) with Ni catalyst. The composites are in an agglomerated shape due to the entanglement of the defective CNF between the AC particles forming a macroscopic body. The macroscopic size will allow the composite to be used as a stabile catalyst support and liquid adsorbent. The preparation of CNT/AC nanocarbon was initiated by pre-treating the activated carbon with nitric acid, followed by impregnation of 1 wt% loading of nickel (II) nitrate solutions in acetone. The catalyst precursor was calcined and reduced at 300 deg. C for an hour in each step. The catalytic growth of nanocarbon in C{sub 2}H{sub 4}/H{sub 2} was carried out at temperature of 550 deg. C for 2 hrs with different rotating angle in the fluidization system. SEM and N{sub 2} isotherms show the level of agglomeration which is a function of growth density and fluidization of the system. The effect of fluidization by rotating the reactor during growth with different speed give a significant impact on the agglomeration of the final CNF/AC composite and thus the amount of CNFs produced. The macrostructure body produced in this work of CNF/AC composite will have advantages in the adsorbent and catalyst support application, due to the mechanical and chemical properties of the material.

  8. Bacillus pumilus Cyanide Dihydratase Mutants with Higher Catalytic Activity

    PubMed Central

    Crum, Mary A.; Sewell, B. Trevor; Benedik, Michael J.

    2016-01-01

    Cyanide degrading nitrilases are noted for their potential to detoxify industrial wastewater contaminated with cyanide. However, such application would benefit from an improvement to characteristics such as their catalytic activity and stability. Following error-prone PCR for random mutagenesis, several cyanide dihydratase mutants from Bacillus pumilus were isolated based on improved catalysis. Four point mutations, K93R, D172N, A202T, and E327K were characterized and their effects on kinetics, thermostability and pH tolerance were studied. K93R and D172N increased the enzyme’s thermostability whereas E327K mutation had a less pronounced effect on stability. The D172N mutation also increased the affinity of the enzyme for its substrate at pH 7.7 but lowered its kcat. However, the A202T mutation, located in the dimerization or the A surface, destabilized the protein and abolished its activity. No significant effect on activity at alkaline pH was observed for any of the purified mutants. These mutations help confirm the model of CynD and are discussed in the context of the protein–protein interfaces leading to the protein quaternary structure. PMID:27570524

  9. Human airway epithelia express catalytically active NEU3 sialidase

    PubMed Central

    Hyun, Sang Won; Feng, Chiguang; Zhang, Lei; Liu, Anguo; Guang, Wei; Nguyen, Chinh; Sun, Wenji; Luzina, Irina G.; Webb, Tonya J.; Atamas, Sergei P.; Passaniti, Antonino; Twaddell, William S.; Puché, Adam C.; Wang, Lai-Xi; Cross, Alan S.; Goldblum, Simeon E.

    2014-01-01

    Sialic acids on glycoconjugates play a pivotal role in many biological processes. In the airways, sialylated glycoproteins and glycolipids are strategically positioned on the plasma membranes of epithelia to regulate receptor-ligand, cell-cell, and host-pathogen interactions at the molecular level. We now demonstrate, for the first time, sialidase activity for ganglioside substrates in human airway epithelia. Of the four known mammalian sialidases, NEU3 has a substrate preference for gangliosides and is expressed at mRNA and protein levels at comparable abundance in epithelia derived from human trachea, bronchi, small airways, and alveoli. In small airway and alveolar epithelia, NEU3 protein was immunolocalized to the plasma membrane, cytosolic, and nuclear subcellular fractions. Small interfering RNA-induced silencing of NEU3 expression diminished sialidase activity for a ganglioside substrate by >70%. NEU3 immunostaining of intact human lung tissue could be localized to the superficial epithelia, including the ciliated brush border, as well as to nuclei. However, NEU3 was reduced in subepithelial tissues. These results indicate that human airway epithelia express catalytically active NEU3 sialidase. PMID:24658138

  10. Site-specific growth of Au-Pd alloy horns on Au nanorods: a platform for highly sensitive monitoring of catalytic reactions by surface enhancement Raman spectroscopy.

    PubMed

    Huang, Jianfeng; Zhu, Yihan; Lin, Ming; Wang, Qingxiao; Zhao, Lan; Yang, Yang; Yao, Ke Xin; Han, Yu

    2013-06-12

    Surface-enhanced Raman scattering (SERS) is a highly sensitive probe for molecular detection. The aim of this study was to develop an efficient platform for investigating the kinetics of catalytic reactions with SERS. To achieve this, we synthesized a novel Au-Pd bimetallic nanostructure (HIF-AuNR@AuPd) through site-specific epitaxial growth of Au-Pd alloy horns as catalytic sites at the ends of Au nanorods. Using high-resolution electron microscopy and tomography, we successfully reconstructed the complex three-dimensional morphology of HIF-AuNR@AuPd and identified that the horns are bound with high-index {11l} (0.25 < l < 0.43) facets. With an electron beam probe, we visualized the distribution of surface plasmon over the HIF-AuNR@AuPd nanorods, finding that strong longitudinal surface plasmon resonance concentrated at the rod ends. This unique crystal morphology led to the coupling of high catalytic activity with a strong SERS effect at the rod ends, making HIF-AuNR@AuPd an excellent bifunctional platform for in situ monitoring of surface catalytic reactions. Using the hydrogenation of 4-nitrothiophenol as a model reaction, we demonstrated that its first-order reaction kinetics could be accurately determined from this platform. Moreover, we clearly identified the superior catalytic activity of the rod ends relative to that of the rod bodies, owing to the different SERS activities at the two positions. In comparison with other reported Au-Pd bimetallic nanostructures, HIF-AuNR@AuPd offered both higher catalytic activity and greater detection sensitivity. PMID:23675958

  11. Catalytic activities of platinum nanotubes: a density functional study

    NASA Astrophysics Data System (ADS)

    Mukherjee, Prajna; Gupta, Bikash C.; Jena, Puru

    2015-10-01

    In this work we investigate the catalytic properties of platinum nanotubes using density functional theory based calculations. In particular, we study the dissociation of hydrogen and oxygen molecules as well as oxidation of CO molecules. The results indicate that platinum nanotubes have good catalytic properties and can be effectively used in converting CO molecule to CO2.

  12. Isolation of an Active Catalytic Core of Streptococcus downei MFe28 GTF-I Glucosyltransferase

    PubMed Central

    Monchois, Vincent; Arguello-Morales, Martha; Russell, Roy R. B.

    1999-01-01

    Truncated variants of GTF-I from Streptococcus downei MFe28 were purified by means of a histidine tag. Sequential deletions showed that the C-terminal domain was not directly involved in the catalytic process but was required for primer activation. A fully active catalytic core of only 100 kDa was isolated. PMID:10094712

  13. Effects of biomineralization peptide topology on the structure and catalytic activity of Pd nanomaterials.

    PubMed

    Janairo, Jose Isagani B; Sakaguchi, Tatsuya; Hara, Kenji; Fukuoka, Atsushi; Sakaguchi, Kazuyasu

    2014-08-25

    Highly branched, coral-like Pd nanostructures were formed using a biomineralization peptide conjugated to an oligomeric peptide that simultaneously controls the spatial orientation, arrangement and valency. The Pd nanocoral showed very high catalytic activity in the reduction of nitrophenol. The results highlight the importance of topological arrangement in nanostructure formation and catalytic activity. PMID:24963622

  14. Alternative catalytic anions differentially modulate human alpha-amylase activity and specificity.

    PubMed

    Maurus, Robert; Begum, Anjuman; Williams, Leslie K; Fredriksen, Jason R; Zhang, Ran; Withers, Stephen G; Brayer, Gary D

    2008-03-18

    A mechanistic study of the essential allosteric activation of human pancreatic alpha-amylase by chloride ion has been conducted by exploring a wide range of anion substitutions through kinetic and structural experiments. Surprisingly, kinetic studies indicate that the majority of these alternative anions can induce some level of enzymatic activity despite very different atomic geometries, sizes, and polyatomic natures. These data and subsequent structural studies attest to the remarkable plasticity of the chloride binding site, even though earlier structural studies of wild-type human pancreatic alpha-amylase suggested this site would likely be restricted to chloride binding. Notably, no apparent relationship is observed between anion binding affinity and relative activity, emphasizing the complexity of the relationship between chloride binding parameters and the activation mechanism that facilitates catalysis. Of the anions studied, particularly intriguing in terms of observed trends in substrate kinetics and their novel atomic compositions were the nitrite, nitrate, and azide anions, the latter of which was found to enhance the relative activity of human pancreatic alpha-amylase by nearly 5-fold. Structural studies have provided considerable insight into the nature of the interactions formed in the chloride binding site by the nitrite and nitrate anions. To probe the role such interactions play in allosteric activation, further structural analyses were conducted in the presence of acarbose, which served as a sensitive reporter molecule of the catalytic ability of these modified enzymes to carry out its expected rearrangement by human pancreatic alpha-amylase. These studies show that the largest anion of this group, nitrate, can comfortably fit in the chloride binding pocket, making all the necessary hydrogen bonds. Further, this anion has nearly the same ability to activate human pancreatic alpha-amylase and leads to the production of the same acarbose product

  15. Computational Design of Enone-Binding Proteins with Catalytic Activity for the Morita-Baylis-Hillman Reaction

    PubMed Central

    Bjelic, Sinisa; Nivon, Lucas G.; Çelebi-Ölçüm, Nihan; Kiss, Gert; Rosewall, Carolyn F.; Lovick, Helena M.; Ingalls, Erica L.; Gallaher, Jasmine Lynn; Seetharaman, Jayaraman; Lew, Scott; Montelione, Gaetano Thomas; Hunt, John Francis; Michael, Forrest Edwin; Houk, K. N.; Baker, David

    2013-01-01

    The Morita-Baylis-Hillman reaction forms a carbon-carbon bond between the alpha carbon of a conjugated carbonyl compound and a carbon electrophile. The reaction mechanism involves Michael addition of a nucleophile catalyst at the carbonyl beta carbon, followed by bond formation with the electrophile and catalyst disassociation to release the product. We used Rosetta to design 48 proteins containing active sites predicted to carry out this mechanism, of which two show catalytic activity by mass spectrometry (MS). Substrate labeling measured by MS and site-directed mutagenesis experiments show that the designed active-site residues are responsible for activity, although rate acceleration over background is modest. To characterize the designed proteins, we developed a fluorescence-based screen for intermediate formation in cell lysates, carried out microsecond molecular dynamics simulations, and solved X-ray crystal structures. These data indicate a partially formed active site, and suggest several clear avenues for designing more active catalysts. PMID:23330600

  16. Inhibiting caspase-6 activation and catalytic activity for neurodegenerative diseases.

    PubMed

    Flygare, John A; Arkin, Michelle R

    2014-01-01

    Partnerships between industry and academia are becoming increasingly complex and relevant in the drive to discover innovative new medicines. We describe the structure of the collaboration between the University of California - San Francisco - Small Molecule Discovery Center (UCSF-SMDC) and Genentech to develop chemical matter that inhibits the activity of caspase-6. We focus on the scientific basis for the partnership and how the orientation- and transaction-related barriers were overcome. We describe the division of labor that allowed two groups to operate as a unified team to generate multiple chemical series with distinct mechanisms of action. The successful structure of the agreement serves as a model for future collaborations at both institutions. PMID:24283214

  17. Design of activated serine-containing catalytic triads with atomic level accuracy

    PubMed Central

    Rajagopalan, Sridharan; Wang, Chu; Yu, Kai; Kuzin, Alexandre P.; Richter, Florian; Lew, Scott; Miklos, Aleksandr E.; Matthews, Megan L.; Seetharaman, Jayaraman; Su, Min; Hunt, John. F.; Cravatt, Benjamin F.; Baker, David

    2014-01-01

    A challenge in the computational design of enzymes is that multiple properties must be simultaneously optimized -- substrate-binding, transition state stabilization, and product release -- and this has limited the absolute activity of successful designs. Here, we focus on a single critical property of many enzymes: the nucleophilicity of an active site residue that initiates catalysis. We design proteins with idealized serine-containing catalytic triads, and assess their nucleophilicity directly in native biological systems using activity-based organophosphate probes. Crystal structures of the most successful designs show unprecedented agreement with computational models, including extensive hydrogen bonding networks between the catalytic triad (or quartet) residues, and mutagenesis experiments demonstrate that these networks are critical for serine activation and organophosphate-reactivity. Following optimization by yeast-display, the designs react with organophosphate probes at rates comparable to natural serine hydrolases. Co-crystal structures with diisopropyl fluorophosphate bound to the serine nucleophile suggest the designs could provide the basis for a new class of organophosphate captures agents. PMID:24705591

  18. The catalytic triad of the influenza C virus glycoprotein HEF esterase: characterization by site-directed mutagenesis and functional analysis.

    PubMed

    Pleschka, S; Klenk, H D; Herrler, G

    1995-10-01

    Influenza C virus is able to inactivate its own cellular receptors by virtue of a sialate 9-O-acetylesterase that releases the acetyl residue at position C-9 of N-acetyl-9-O-acetylneuraminic acid (Neu5,9Ac2). The receptor-destroying enzyme activity is a function of the surface glycoprotein HEF and this esterase belongs to the class of serine hydrolases. In their active site, these enzymes contain a catalytic triad made up of a serine, a histidine and an aspartic acid residue. Sequence comparison with other serine esterases has indicated that, in addition to serine-71 (S71), the amino acids histidine-368 or -369 (H368/369) and aspartic acid 261 (D261) are the most likely candidates to form the catalytic triad of the influenza C virus glycoprotein. By site-directed mutagenesis, mutants were generated in which alanine substituted for either of these amino acids. Using a phagemid expression vector, pSP1D-HEF the HEF gene was expressed in both COS 7 and MDCK I cells. The glycoprotein was obtained in a functional form only in the latter cells, as indicated by its transport to the cell surface and measurable enzyme activity. The low level of expression could be increased by stimulating the NF-KB-binding activity of the cytomegalovirus immediate-early promoter/enhancer element of the vector. The esterase activity of the mutant proteins was compared with that of the wild-type glycoprotein. With Neu5,9Ac2 as the substrate, the esterase specific activities of the S71/A mutant and the H368,369/A mutant were reduced by more than 90%. In the case of the D261/A mutant the specific activity was reduced by 64%. From this data we conclude that S71, H368/369 and D261 are likely to represent the catalytic triad of the influenza C virus glycoprotein HEF. In addition, N280 is proposed to stabilize the oxyanion of the presumptive transition state intermediate formed by the enzyme-substrate complex. PMID:7595356

  19. Enhanced thermostability of mesophilic endoglucanase Z with a high catalytic activity at active temperatures.

    PubMed

    Kim, Su Jung; Joo, Ji Eun; Jeon, Sang Duck; Hyeon, Jeong Eun; Kim, Seung Wook; Um, Young Soon; Han, Sung Ok

    2016-05-01

    This is the first study for therrmostable mutants of mesophilic endoglucanase EngZ from Clostridium cellulovorans using by site-directed mutagenesis. K94R, S365P and their double mutant K94R/S365P had a wide range of active temperatures (30-60°C). In addition, the optimal temperature of K94R/S365P was increased by 7.5°C. K94R/S365P retained 78.3% relative activity at 70°C, while the wild type retained only 5.8%. Especially, K94R/S365P remained 45.1-fold higher activity than the wild type at 70°C. In addition, K94R/S365P was 3.1-fold higher activity than the wild type at 42.5°C, which is the optimal temperature of the wild type. K94R/S365P showed also stimulated in 2.5-fold lower concentration of CaCl2 and delayed aggregation temperature in the presence of CaCl2 compared to the wild type. In pH stability, K94R/S365P was not influenced, but the optimum pH was transferred from pH 7 to pH 6. In long-term hydrolysis, K94R/S365P reduced the newly released reducing sugar yields after 12h reaction; however, the yields consistently increased until 72h. Finally, the total reducing sugar of K94R/S365P was 5.0-fold higher than the wild type at 50°C, pH6. EngZ (K94R/S365P) can support information to develop thermostability of GH9 endoglucanase with a high catalytic efficiency as the potential industrial bioprocess candidate. PMID:26808019

  20. Synthesis and catalytic activity of polysaccharide templated nanocrystalline sulfated zirconia

    SciTech Connect

    Sherly, K. B.; Rakesh, K.

    2014-01-28

    Nanoscaled materials are of great interest due to their unique enhanced optical, electrical and magnetic properties. Sulfate-promoted zirconia has been shown to exhibit super acidic behavior and high activity for acid catalyzed reactions. Nanocrystalline zirconia was prepared in the presence of polysaccharide template by interaction between ZrOCl{sub 2}⋅8H{sub 2}O and chitosan template. The interaction was carried out in aqueous phase, followed by the removal of templates by calcination at optimum temperature and sulfation. The structural and textural features were characterized by powder XRD, TG, SEM and TEM. XRD patterns showed the peaks of the diffractogram were in agreement with the theoretical data of zirconia with the catalytically active tetragonal phase and average crystalline size of the particles was found to be 9 nm, which was confirmed by TEM. TPD using ammonia as probe, FTIR and BET surface area analysis were used for analyzing surface features like acidity and porosity. The BET surface area analysis showed the sample had moderately high surface area. FTIR was used to find the type species attached to the surface of zirconia. UV-DRS found the band gap of the zirconia was found to be 2.8 eV. The benzylation of o-xylene was carried out batchwise in atmospheric pressure and 433K temperature using sulfated zirconia as catalyst.

  1. Synthesis and catalytic activity of polysaccharide templated nanocrystalline sulfated zirconia

    NASA Astrophysics Data System (ADS)

    Sherly, K. B.; Rakesh, K.

    2014-01-01

    Nanoscaled materials are of great interest due to their unique enhanced optical, electrical and magnetic properties. Sulfate-promoted zirconia has been shown to exhibit super acidic behavior and high activity for acid catalyzed reactions. Nanocrystalline zirconia was prepared in the presence of polysaccharide template by interaction between ZrOCl2ṡ8H2O and chitosan template. The interaction was carried out in aqueous phase, followed by the removal of templates by calcination at optimum temperature and sulfation. The structural and textural features were characterized by powder XRD, TG, SEM and TEM. XRD patterns showed the peaks of the diffractogram were in agreement with the theoretical data of zirconia with the catalytically active tetragonal phase and average crystalline size of the particles was found to be 9 nm, which was confirmed by TEM. TPD using ammonia as probe, FTIR and BET surface area analysis were used for analyzing surface features like acidity and porosity. The BET surface area analysis showed the sample had moderately high surface area. FTIR was used to find the type species attached to the surface of zirconia. UV-DRS found the band gap of the zirconia was found to be 2.8 eV. The benzylation of o-xylene was carried out batchwise in atmospheric pressure and 433K temperature using sulfated zirconia as catalyst.

  2. Adventitious Arsenate Reductase Activity of the Catalytic Domain of the Human Cdc25B and Cdc25C Phosphatases†

    PubMed Central

    Bhattacharjee, Hiranmoy; Sheng, Ju; Ajees, A. Abdul; Mukhopadhyay, Rita; Rosen, Barry P.

    2013-01-01

    A number of eukaryotic enzymes that function as arsenate reductases are homologues of the catalytic domain of the human Cdc25 phosphatase. For example, the Leishmania major enzyme LmACR2 is both a phosphatase and an arsenate reductase, and its structure bears similarity to the structure of the catalytic domain of human Cdc25 phosphatase. These reductases contain an active site C-X5-R signature motif, where C is the catalytic cysteine, the five X residues form a phosphate binding loop, and R is a highly conserved arginine, which is also present in human Cdc25 phosphatases. We therefore investigated the possibility that the three human Cdc25 isoforms might have adventitious arsenate reductase activity. The sequences for the catalytic domains of Cdc25A, -B, and -C were cloned individually into a prokaryotic expression vector, and their gene products were purified from a bacterial host using nickel affinity chromatography. While each of the three Cdc25 catalytic domains exhibited phosphatase activity, arsenate reductase activity was observed only with Cdc25B and -C. These two enzymes reduced inorganic arsenate but not methylated pentavalent arsenicals. Alteration of either the cysteine and arginine residues of the Cys-X5-Arg motif led to the loss of both reductase and phosphatase activities. Our observations suggest that Cdc25B and -C may adventitiously reduce arsenate to the more toxic arsenite and may also provide a framework for identifying other human protein tyrosine phosphatases containing the active site Cys-X5-Arg loop that might moonlight as arsenate reductases. PMID:20025242

  3. Correlations between surface structure and catalytic activity/selectivity. Progress report, January 1, 1992--December 31, 1992

    SciTech Connect

    Goodman, D.W.

    1992-10-01

    Objective is to address the keys to understanding the relation between surface structure and catalytic activity/selectivity. Of concern are questions related to enhanced catalytic properties of mixed-metal catalysts and critical active site requirements for molecular synthesis and rearrangement. The experimental approach utilizes a microcatalytic reactor contiguous to a surface analysis system, an arrangement which allows in vacuo transfer of the catalyst from one chamber to the other. Surface techniques being used include Auger (AES), UV and X-ray photoemission spectroscopy (UPS and XPS), temperature programmed desorption (TPD), low energy electron diffraction (LEED), high resolution electron energy loss spectroscopy (HREELS) and infrared reflection-absorption spectroscopy (IRAS). Our research program builds upon our previous experience relating the results of single crystal kinetic measurements with the results obtained with supported analogs. As well we are exploiting our recent work on the preparation, the characterization, and the determination of the catalytic properties of ultra-thin metal and metal oxide films. The program is proceeding toward the study of the unique catalytic properties of ultrathin metal films; the investigation of the critical ensemble size requirements for principal catalytic reaction types; and the modelling of supported catalysts using ultra-thin planar oxide surfaces.

  4. Enhanced Activity of Nanocrystalline Zeolites for Selective Catalytic Reduction of NOx

    SciTech Connect

    Sarah C. Larson; Vicki H. Grassian

    2006-12-31

    Nanocrystalline zeolites with discrete crystal sizes of less than 100 nm have different properties relative to zeolites with larger crystal sizes. Nanocrystalline zeolites have improved mass transfer properties and very large internal and external surface areas that can be exploited for many different applications. The additional external surface active sites and the improved mass transfer properties of nanocrystalline zeolites offer significant advantages for selective catalytic reduction (SCR) catalysis with ammonia as a reductant in coal-fired power plants relative to current zeolite based SCR catalysts. Nanocrystalline NaY was synthesized with a crystal size of 15-20 nm and was thoroughly characterized using x-ray diffraction, electron paramagnetic resonance spectroscopy, nitrogen adsorption isotherms and Fourier Transform Infrared (FT-IR) spectroscopy. Copper ions were exchanged into nanocrystalline NaY to increase the catalytic activity. The reactions of nitrogen dioxides (NO{sub x}) and ammonia (NH{sub 3}) on nanocrystalline NaY and CuY were investigated using FT-IR spectroscopy. Significant conversion of NO{sub 2} was observed at room temperature in the presence of NH{sub 3} as monitored by FT-IR spectroscopy. Copper-exchanged nanocrystalline NaY was more active for NO{sub 2} reduction with NH{sub 3} relative to nanocrystalline NaY.

  5. CO oxidation over ruthenium: identification of the catalytically active phases at near-atmospheric pressures

    SciTech Connect

    Gao, Feng; Goodman, Wayne D.

    2012-05-21

    CO oxidation was carried out over Ru(0001) and RuO2(110) thin film grown on Ru(0001) at various O2/CO ratios near atmospheric pressures. Reaction kinetics, coupled with in situ polarization modulation infrared reflection absorption spectroscopy (PM-IRAS) and post-reaction Auger electron spectroscopy (AES) measurements were used to identify the catalytically relevant phases at different reaction conditions. Under stoichiometric and reducing conditions at all reaction temperatures, as well as net-oxidizing reaction conditions below {approx}475 K, a reduced metallic phase with chemisorbed oxygen is the thermodynamically stable and catalytically active phase. On this surface CO oxidation occurs at surface defect sites, for example step edges. Only at net-oxidizing reaction conditions and above {approx}475 K is the RuO2 thin film grown on metallic Ru stable and active. However, RuO2 is not active itself without the existence of the metal substrate, suggesting the importance of a strong metal-substrate interaction (SMSI).

  6. Role of Arginine 293 and Glutamine 288 in Communication between Catalytic and Allosteric Sites in Yeast Ribonucleotide Reductase

    SciTech Connect

    Ahmad, Md. Faiz; Kaushal, Prem Singh; Wan, Qun; Wijerathna, Sanath R.; An, Xiuxiang; Huang, Mingxia; Dealwis, Chris Godfrey

    2012-11-01

    Ribonucleotide reductases (RRs) catalyze the rate-limiting step of de novo deoxynucleotide (dNTP) synthesis. Eukaryotic RRs consist of two proteins, RR1 ({alpha}) that contains the catalytic site and RR2 ({beta}) that houses a diferric-tyrosyl radical essential for ribonucleoside diphosphate reduction. Biochemical analysis has been combined with isothermal titration calorimetry (ITC), X-ray crystallography and yeast genetics to elucidate the roles of two loop 2 mutations R293A and Q288A in Saccharomyces cerevisiae RR1 (ScRR1). These mutations, R293A and Q288A, cause lethality and severe S phase defects, respectively, in cells that use ScRR1 as the sole source of RR1 activity. Compared to the wild-type enzyme activity, R293A and Q288A mutants show 4% and 15%, respectively, for ADP reduction, whereas they are 20% and 23%, respectively, for CDP reduction. ITC data showed that R293A ScRR1 is unable to bind ADP and binds CDP with 2-fold lower affinity compared to wild-type ScRR1. With the Q288A ScRR1 mutant, there is a 6-fold loss of affinity for ADP binding and a 2-fold loss of affinity for CDP compared to the wild type. X-ray structures of R293A ScRR1 complexed with dGTP and AMPPNP-CDP [AMPPNP, adenosine 5-({beta},{gamma}-imido)triphosphate tetralithium salt] reveal that ADP is not bound at the catalytic site, and CDP binds farther from the catalytic site compared to wild type. Our in vivo functional analyses demonstrated that R293A cannot support mitotic growth, whereas Q288A can, albeit with a severe S phase defect. Taken together, our structure, activity, ITC and in vivo data reveal that the arginine 293 and glutamine 288 residues of ScRR1 are crucial in facilitating ADP and CDP substrate selection.

  7. Salt site performance assessment activities

    SciTech Connect

    Kircher, J.F.; Gupta, S.K.

    1983-01-01

    During this year the first selection of the tools (codes) for performance assessments of potential salt sites have been tentatively selected and documented; the emphasis has shifted from code development to applications. During this period prior to detailed characterization of a salt site, the focus is on bounding calculations, sensitivity and with the data available. The development and application of improved methods for sensitivity and uncertainty analysis is a focus for the coming years activities and the subject of a following paper in these proceedings. Although the assessments to date are preliminary and based on admittedly scant data, the results indicate that suitable salt sites can be identified and repository subsystems designed which will meet the established criteria for protecting the health and safety of the public. 36 references, 5 figures, 2 tables.

  8. Catalytic activity of allamanda mediated phytosynthesized anisotropic gold nanoparticles

    NASA Astrophysics Data System (ADS)

    Gangwar, Rajesh K.; Dhumale, Vinayak A.; Gosavi, S. W.; Sharma, Rishi B.; Datar, Suwarna S.

    2013-12-01

    A simple and eco-friendly method has been developed for the synthesis of gold nanoparticles using allamanda flower extract. In this green synthesis method, chloroauric acid (HAuCl4) solution was reduced with the help of allamanda flower extract. The synthesized gold nanoparticles were characterized by atomic force microscopy (AFM), transmission electron microscopy (TEM) and x-ray diffraction technique for their morphological and structural analysis. The size of the spherical and triangular gold nanoparticles was found to be in the range of 5-40 and 20-70 nm, respectively. The x-ray diffraction analysis revealed that the crystallite size of face-centered cubic (FCC) gold nanoparticles was ˜ 11 nm. These synthesized gold nanoparticles exhibit good catalytic activity towards the reduction of H2O2. The fabricated sensor exhibits good sensitivity of 21.33 μA mM-1 cm-2 with linear relationship (R2 = 0.996) in the range from 2 to 10 mM of H2O2 concentration. This work can be extended further for potential applications such as antimicrobial studies, bio-imaging and drug-delivery owing to the known properties of the allamanda flower extract.

  9. Amino- and Sulfo-Bifunctionalized Metal-Organic Frameworks: One-Pot Tandem Catalysis and the Catalytic Sites.

    PubMed

    Liu, Hui; Xi, Fu-Gui; Sun, Wei; Yang, Ning-Ning; Gao, En-Qing

    2016-06-20

    New MIL-101 metal-organic frameworks (MOFs) dually functionalized with amino and sulfo groups were fabricated by postsynthetic modification and used to catalyze one-pot deacetalization-Knoevenagel condensation. We proved that the MOFs take the zwitterionic form, with the catalytic acid site being the ammonium group rather than the sulfo one. The acid and base concentrations in the materials are correlated, and the ratio can be readily tuned to achieve optimal catalytic performance. PMID:27254287

  10. High viscosity to highly dispersed PtPd bimetallic nanocrystals for enhanced catalytic activity and stability.

    PubMed

    Ying, Jie; Hu, Zhi-Yi; Yang, Xiao-Yu; Wei, Hao; Xiao, Yu-Xuan; Janiak, Christoph; Mu, Shi-Chun; Tian, Ge; Pan, Mu; Van Tendeloo, Gustaaf; Su, Bao-Lian

    2016-07-01

    A facile high-viscosity-solvent method is presented to synthesize PtPd bimetallic nanocrystals highly dispersed in different mesostructures (2D and 3D structures), porosities (large and small pore sizes), and compositions (silica and carbon). Further, highly catalytic activity, stability and durability of the nanometals have been proven in different catalytic reactions. PMID:27222099

  11. UNIVERSITY OF WISCONSIN - PHOTO ELECTRO CATALYTIC DEGRADATION AND REMOVAL OFORGANIC AND INORGANIC CONTAMINANTS IN GROUND WATERS: SITE DOC

    EPA Science Inventory

    SITE DOC NRMRL-CIN-1338 Gallardo*, V. University of Wisconsin - Photo Electro Catalytic Degradation and Removal of Organic and Inorganic Contaminants in Ground Waters. 2001. EPA/540/R-01/502, http://www.epa.gov/ORD/SITE. 02/22/2001 Photocatalytic oxidation offers a means of...

  12. The Origin of the Catalytic Activity of a Metal Hydride in CO2 Reduction.

    PubMed

    Kato, Shunsuke; Matam, Santhosh Kumar; Kerger, Philipp; Bernard, Laetitia; Battaglia, Corsin; Vogel, Dirk; Rohwerder, Michael; Züttel, Andreas

    2016-05-10

    Atomic hydrogen on the surface of a metal with high hydrogen solubility is of particular interest for the hydrogenation of carbon dioxide. In a mixture of hydrogen and carbon dioxide, methane was markedly formed on the metal hydride ZrCoHx in the course of the hydrogen desorption and not on the pristine intermetallic. The surface analysis was performed by means of time-of-flight secondary ion mass spectroscopy and near-ambient pressure X-ray photoelectron spectroscopy, for the in situ analysis. The aim was to elucidate the origin of the catalytic activity of the metal hydride. Since at the initial stage the dissociation of impinging hydrogen molecules is hindered by a high activation barrier of the oxidised surface, the atomic hydrogen flux from the metal hydride is crucial for the reduction of carbon dioxide and surface oxides at interfacial sites. PMID:27061237

  13. Pt3Co concave nanocubes: synthesis, formation understanding, and enhanced catalytic activity toward hydrogenation of styrene.

    PubMed

    Wang, Chenyu; Lin, Cuikun; Zhang, Lihua; Quan, Zewei; Sun, Kai; Zhao, Bo; Wang, Feng; Porter, Nathan; Wang, Yuxuan; Fang, Jiye

    2014-02-01

    We report a facile synthesis route to prepare high-quality Pt3Co nanocubes with a concave structure, and further demonstrate that these concave Pt3Co nanocubes are terminated with high-index crystal facets. The success of this preparation is highly dependent on an appropriate nucleation process with a successively anisotropic overgrowth and a preservation of the resultant high-index planes by control binding of oleyl-amine/oleic acid with a fine-tuned composition. Using a hydrogenation of styrene as a model reaction, these Pt3Co concave nanocubes as a new class of nanocatalysts with more open structure and active atomic sites located on their high-index crystallographic planes exhibit an enhanced catalytic activity in comparison with low-indexed surface terminated Pt3Co nanocubes in similar size. PMID:24382713

  14. Preparation and Acid Catalytic Activity of TiO2 Grafted Silica MCM-41 with Sulfate Treatment

    NASA Astrophysics Data System (ADS)

    Guo, Dai-shi; Ma, Zi-feng; Yin, Chun-sheng; Jiang, Qi-zhong

    2008-02-01

    TiO2 grafted silica MCM-41 catalyst with and without sulfate treatment were prepared. The structural and acid properties of these materials were investigated by XRD, N2 adsorption-desorption, element analysis, thermal analysis, Raman and FTIR measurements. Their acid-catalytic activities were evaluated using the cyclization reaction of pseudoionone. It was found that the obtained materials possess well-ordered mesostructure, and the grafted TiO2 components were in highly dispersed amorphous form. T/MCM41 without sulfation contained only Lewis acid sites, while Brønsted and Lewis acidities were remarkably improved for the sulfated materials ST/MCM41 and d-ST/MCM41. T/MCM-41 was not active for the cyclization reaction of pseudoionone, but ST/MCM-41 and d-ST/MCM-41 possessed favorable catalytic activities. The catalytic performance of ST/MCM-41 was comparable with that of the commercial solid acid catalyst of Amberlyst-15, and better than that of d-ST/MCM-41, although the latter underwent a second TiO2 grafting process and accordingly had higher Ti and S content. The specific surface structure of Si-O-Ti-O-S=O in ST/MCM-41 and the bilateral induction effect of Si and S=O on Si-O-Ti bonds were speculated to account for its higher acid catalytic activity.

  15. Fabrication of catalytically active Au/Pt/Pd trimetallic nanoparticles by rapid injection of NaBH{sub 4}

    SciTech Connect

    Zhang, Haijun; Lu, Lilin; Cao, Yingnan; Du, Shuang; Cheng, Zhong; Zhang, Shaowei

    2014-01-01

    Graphical abstract: The synthesis and characterization of 2.0 nm-diameter Au/Pt/Pd nanoparticles are reported. The catalytic activity for glucose oxidation of the nanoparticles is several times higher than that of Au nanoparticles with nearly same size. - Highlights: • PVP-protected Au/Pt/Pd trimetallic nanoparticles (TNPs) of 2.0 nm in diameter were prepared. • The catalytic activity of TNPs is several times higher than that of Au nanoparticles. • Negatively charged Au atoms in the TNPs were confirmed by DFT calculation. - Abstract: Au/Pt/Pd trimetallic nanoparticles (TNPs) with an alloyed structure and an average diameter of about 2.0 nm were prepared via reducing the corresponding ions with rapidly injected NaBH{sub 4}, and characterized by UV–vis, TEM and HR-TEM. The catalytic activity of as-prepared TNPs for the aerobic glucose oxidation is several times higher than that of Au monometallic nanoparticles with about the same average size, which could be attributed to the catalytically active sites provided by the negatively charged Au atoms as a result of the electron donation from the neighboring Pd atoms. This was well supported by the electron density calculations based on the density functional theory.

  16. Principles of water oxidation and O2-based hydrocarbon transformation by multinuclear catalytic sites

    SciTech Connect

    Musaev, Djamaladdin G; Hill, Craig L; Morokuma, Keiji

    2014-10-28

    Abstract The central thrust of this integrated experimental and computational research program was to obtain an atomistic-level understanding of the structural and dynamic factors underlying the design of catalysts for water oxidation and selective reductant-free O2-based transformations. The focus was on oxidatively robust polyoxometalate (POM) complexes in which a catalytic active site interacts with proximal metal centers in a synergistic manner. Thirty five publications in high-impact journals arose from this grant. I. Developing an oxidatively and hydrolytically stable and fast water oxidation catalyst (WOC), a central need in the production of green fuels using water as a reductant, has proven particularly challenging. During this grant period we have designed and investigated several carbon-free, molecular (homogenous), oxidatively and hydrolytically stable WOCs, including the Rb8K2[{Ru4O4(OH)2(H2O)4}(γ-SiW10O36)2]·25H2O (1) and [Co4(H2O)2(α-PW9O34)2]10- (2). Although complex 1 is fast, oxidatively and hydrolytically stable WOC, Ru is neither abundant nor inexpensive. Therefore, development of a stable and fast carbon-free homogenous WOC, based on earth-abundant elements became our highest priority. In 2010, we reported the first such catalyst, complex 2. This complex is substantially faster than 1 and stable under homogeneous conditions. Recently, we have extended our efforts and reported a V2-analog of the complex 2, i.e. [Co4(H2O)2(α-VW9O34)2]10- (3), which shows an even greater stability and reactivity. We succeeded in: (a) immobilizing catalysts 1 and 2 on the surface of various electrodes, and (b) elucidating the mechanism of O2 formation and release from complex 1, as well as the Mn4O4L6 “cubane” cluster. We have shown that the direct O-O bond formation is the most likely pathway for O2 formation during water oxidation catalyzed by 1. II. Oxo transfer catalysts that contain two proximal and synergistically interacting redox active metal

  17. Rat intestinal trehalase. Studies of the active site.

    PubMed

    Chen, C C; Guo, W J; Isselbacher, K J

    1987-11-01

    Rat intestinal trehalase was solubilized, purified and reconstituted into proteoliposomes. With octyl glucoside as the solubilizing detergent, the purified protein appeared as a single band on SDS/polyacrylamide-gel electrophoresis with an apparent molecular mass of 67 kDa. Kinetic studies indicated that the active site of this enzyme can be functionally divided into two adjacent regions, namely a binding site (with pKa 4.8) and a catalytic site (with pKa 7.2). Other findings suggested that the catalytic site contains a functional thiol group, which is sensitive to inhibition by N-ethylmaleimide, Hg2+ and iodoacetate. Substrate protection and iodoacetate labelling of the thiol group demonstrated that only a protein of 67 kDa was labelled. Furthermore, sucrose and phlorizin protected the thiol group, but Tris-like inhibitors did not. Structure-inhibition analysis of Tris-like inhibitors, the pH effect of Tris inhibition and Tris protection of 1-(3-dimethylaminopropyl)-3-ethylcarbodi-imide inactivation permitted characterization and location of a separate site containing a carboxy group for Tris binding, which may also be the binding region. On the basis of these findings, a possible structure for the active site of trehalase is proposed. PMID:3426558

  18. Support Morphology-Dependent Catalytic Activity of Pd/CeO₂ for Formaldehyde Oxidation.

    PubMed

    Tan, Hongyi; Wang, Jin; Yu, Shuzhen; Zhou, Kebin

    2015-07-21

    To eliminate indoor formaldehyde (HCHO) pollution, Pd/CeO2 catalysts with different morphologies of ceria support were employed. The palladium nanoparticles loaded on {100}-faceted CeO2 nanocubes exhibited much higher activity than those loaded on {111}-faceted ceria nanooctahedrons and nanorods (enclosed by {100} and {111} facets). The HCHO could be fully converted into CO2 over the Pd/CeO2 nanocubes at a GHSV of 10,000 h(-1) and a HCHO inlet concentration of 600 ppm at ambient temperature. The prepared catalysts were characterized by a series of techniques. The HRTEM, ICP-MS and XRD results confirmed the exposed facets of the ceria and the sizes (1-2 nm) of the palladium nanoparticles with loading amounts close to 1%. According to the Pd 3d XPS and H2-TPR results, the status of the Pd-species was dependent on the morphologies of the supports. The {100} facets of ceria could maintain the metallic Pd species rather than the {111} facets, which promoted HCHO catalytic combustion. The Raman and O 1s XPS results revealed that the nanorods with more defect sites and oxygen vacancies were responsible for the easy oxidation of the Pd-species and low catalytic activity. PMID:26120873

  19. 3-Nitropropionic Acid is a Suicide Inhibitor of MitochondrialRespiration that, Upon Oxidation by Complex II, Forms a Covalent AdductWith a Catalytic Base Arginine in the Active Site of the Enzyme

    SciTech Connect

    Huang, Li-shar; Sun, Gang; Cobessi, David; Wang, Andy C.; Shen,John T.; Tung, Eric Y.; Anderson, Vernon E.; Berry, Edward A.

    2005-12-01

    We report three new structures of mitochondrial respiratory Complex II (succinate ubiquinone oxidoreductase, E.C. 1.3.5.1) at up to 2.1 {angstrom} resolution, with various inhibitors. The structures define the conformation of the bound inhibitors and suggest the residues involved in substrate binding and catalysis at the dicarboxylate site. In particular they support the role of Arg297 as a general base catalyst accepting a proton in the dehydrogenation of succinate. The dicarboxylate ligand in oxaloacetate-containing crystals appears to be the same as that reported for Shewanella flavocytochrome c treated with fumarate. The plant and fungal toxin 3-nitropropionic acid, an irreversible inactivator of succinate dehydrogenase, forms a covalent adduct with the side chain of Arg297. The modification eliminates a trypsin cleavage site in the flavoprotein, and tandem mass spectroscopic analysis of the new fragment shows the mass of Arg 297 to be increased by 83 Da and to have potential of losing 44 Da, consistent with decarboxylation, during fragmentation.

  20. Catalytic site inhibition of insulin-degrading enzyme by a small molecule induces glucose intolerance in mice

    DOE PAGESBeta

    Deprez-Poulain, Rebecca; Hennuyer, Nathalie; Bosc, Damien; Liang, Wenguang G.; Enée, Emmanuelle; Marechal, Xavier; Charton, Julie; Totobenazara, Jane; Berte, Gonzague; Jahklal, Jouda; et al

    2015-09-23

    Insulin-degrading enzyme (IDE) is a protease that cleaves insulin and other bioactive peptides such as amyloid-β. Knockout and genetic studies have linked IDE to Alzheimer’s disease and type-2 diabetes. As the major insulin-degrading protease, IDE is a candidate drug target in diabetes. Here we have used kinetic target-guided synthesis to design the first catalytic site inhibitor of IDE suitable for in vivo studies (BDM44768). Crystallographic and small angle X-ray scattering analyses show that it locks IDE in a closed conformation. Among a panel of metalloproteases, BDM44768 selectively inhibits IDE. Acute treatment of mice with BDM44768 increases insulin signalling and surprisinglymore » impairs glucose tolerance in an IDE-dependent manner. These results confirm that IDE is involved in pathways that modulate short-term glucose homeostasis, but casts doubt on the general usefulness of the inhibition of IDE catalytic activity to treat diabetes.« less

  1. Optical activity of catalytic elements of hetero-metallic nanostructures

    NASA Astrophysics Data System (ADS)

    Antosiewicz, Tomasz J.; Apell, S. Peter; Wadell, Carl; Langhammer, Christoph

    2015-05-01

    Interaction of light with metals in the form of surface plasmons is used in a wide range of applications in which the scattering decay channel is important. The absorption channel is usually thought of as unwanted and detrimental to the efficiency of the device. This is true in many applications, however, recent studies have shown that maximization of the decay channel of surface plasmons has potentially significant uses. One of these is the creation of electron-hole pairs or hot electrons which can be used for e.g. catalysis. Here, we study the optical properties of hetero-metallic nanostructures that enhance light interaction with the catalytic elements of the nanostructures. A hybridized LSPR that matches the spectral characteristic of the light source is excited. This LSPR through coupling between the plasmonic elements maximizes light absorption in the catalytic part of the nanostructure. Numerically calculated visible light absorption in the catalytic nanoparticles is enhanced 12-fold for large catalytic disks and by more 30 for small nanoparticles on the order of 5 nm. In experiments we measure a sizable increase in the absorption cross section when small palladium nanoparticles are coupled to a large silver resonator. These observations suggest that heterometallic nanostructures can enhance catalytic reaction rates.

  2. Tuning the catalytic activity of graphene nanosheets for oxygen reduction reaction via size and thickness reduction.

    PubMed

    Benson, John; Xu, Qian; Wang, Peng; Shen, Yuting; Sun, Litao; Wang, Tanyuan; Li, Meixian; Papakonstantinou, Pagona

    2014-11-26

    Currently, the fundamental factors that control the oxygen reduction reaction (ORR) activity of graphene itself, in particular, the dependence of the ORR activity on the number of exposed edge sites remain elusive, mainly due to limited synthesis routes of achieving small size graphene. In this work, the synthesis of low oxygen content (<2.5±0.2 at. %), few layer graphene nanosheets with lateral dimensions smaller than a few hundred nanometers were achieved using a combination of ionic liquid assisted grinding of high purity graphite coupled with sequential centrifugation. We show for the first time that the graphene nanosheets possessing a plethora of edges exhibited considerably higher electron transfer numbers compared to the thicker graphene nanoplatelets. This enhanced ORR activity was accomplished by successfully exploiting the plethora of edges of the nanosized graphene as well as the efficient electron communication between the active edge sites and the electrode substrate. The graphene nanosheets were characterized by an onset potential of -0.13 V vs Ag/AgCl and a current density of -3.85 mA/cm2 at -1 V, which represent the best ORR performance ever achieved from an undoped carbon based catalyst. This work demonstrates how low oxygen content nanosized graphene synthesized by a simple route can considerably impact the ORR catalytic activity and hence it is of significance in designing and optimizing advanced metal-free ORR electrocatalysts. PMID:25334050

  3. Catalytic dehydrogenation of isobutane in the presence of hydrogen over Cs-modified Ni2P supported on active carbon

    NASA Astrophysics Data System (ADS)

    Xu, Yanli; Sang, Huanxin; Wang, Kang; Wang, Xitao

    2014-10-01

    In this article, an environmentally friendly non-noble-metal class of Cs-Ni2P/active carbon (AC) catalyst was prepared and demonstrated to exhibit enhanced catalytic performance in isobutane dehydrogenation. The results of activity tests reveal that Ni/AC catalyst was highly active for isobutane cracking, which led to the formation of abundant methane and coke. After the introduction of phosphorus through impregnation with ammonium di-hydrogen phosphate and H2-temperature programmed reduction, undesired cracking reactions were effectively inhibited, and the selectivity to isobutene and stability of catalyst increased remarkably. The characterization results indicate that, after the addition of phosphorous, the improvement of dehydrogenation selectivity is ascribed to the partial positive charges carried on Ni surface in Ni2P particles, which decreases the strength of Nisbnd C bond between Ni and carbonium-ion intermediates and the possibility of excessive dehydrogenation. In addition, Cs-modified Ni2P/AC catalysts display much higher catalytic performance as compared to Ni2P/AC catalyst. Cs-Ni2P-6.5 catalyst has the highest catalytic performance, and the selectivity to isobutene higher than 93% can be obtained even after 4 h reaction. The enhancement in catalytic performance of the Cs-modified catalysts is mainly attributed to the function of Cs to improve the dispersion of Ni2P particles, transfer electron from Cs to Ni, and decrease acid site number and strength.

  4. Active sites for NO reduction over Fe-ZSM-5 catalysts.

    PubMed

    Schwidder, M; Santhosh Kumar, M; Brückner, A; Grünert, W

    2005-02-14

    A study of Fe-ZSM-5 catalysts with variable amounts of isolated, oligomeric and heavily aggregated Fe3+ oxo sites (as evidenced by UV-Vis and EPR spectroscopic data) and their catalytic properties in the selective catalytic reduction of NO by isobutane or by NH3 is presented, which allows development of a unified concept of the active Fe sites in these reactions, according to which isolated Fe sites catalyse both SCR reactions while oligomeric sites, though also involved in the selective reduction path, limit the catalyst performance by causing the total oxidation of the reductant. PMID:15685345

  5. Activities of human RRP6 and structure of the human RRP6 catalytic domain

    SciTech Connect

    Januszyk, Kurt; Liu, Quansheng; Lima, Christopher D.

    2011-08-29

    The eukaryotic RNA exosome is a highly conserved multi-subunit complex that catalyzes degradation and processing of coding and noncoding RNA. A noncatalytic nine-subunit exosome core interacts with Rrp44 and Rrp6, two subunits that possess processive and distributive 3'-to-5' exoribonuclease activity, respectively. While both Rrp6 and Rrp44 are responsible for RNA processing in budding yeast, Rrp6 may play a more prominent role in processing, as it has been demonstrated to be inhibited by stable RNA secondary structure in vitro and because the null allele in budding yeast leads to the buildup of specific structured RNA substrates. Human RRP6, otherwise known as PM/SCL-100 or EXOSC10, shares sequence similarity to budding yeast Rrp6 and is proposed to catalyze 3'-to-5' exoribonuclease activity on a variety of nuclear transcripts including ribosomal RNA subunits, RNA that has been poly-adenylated by TRAMP, as well as other nuclear RNA transcripts destined for processing and/or destruction. To characterize human RRP6, we expressed the full-length enzyme as well as truncation mutants that retain catalytic activity, compared their activities to analogous constructs for Saccharomyces cerevisiae Rrp6, and determined the X-ray structure of a human construct containing the exoribonuclease and HRDC domains that retains catalytic activity. Structural data show that the human active site is more exposed when compared to the yeast structure, and biochemical data suggest that this feature may play a role in the ability of human RRP6 to productively engage and degrade structured RNA substrates more effectively than the analogous budding yeast enzyme.

  6. Extending Thymidine Kinase Activity to the Catalytic Repertoire of Human Deoxycytidine Kinase

    SciTech Connect

    Hazra, Saugata; Sabini, Eliszbetta; Ort, Stephan; Konrad, Manfred; Lavie, Arnon

    2009-03-04

    Salvage of nucleosides in the cytosol of human cells is carried out by deoxycytidine kinase (dCK) and thymidine kinase 1 (TK1). Whereas TK1 is only responsible for thymidine phosphorylation, dCK is capable of converting dC, dA, and dG into their monophosphate forms. Using structural data on dCK, we predicted that select mutations at the active site would, in addition to making the enzyme faster, expand the catalytic repertoire of dCK to include thymidine. Specifically, we hypothesized that steric repulsion between the methyl group of the thymine base and Arg104 is the main factor preventing the phosphorylation of thymidine by wild-type dCK. Here we present kinetic data on several dCK variants where Arg104 has been replaced by select residues, all performed in combination with the mutation of Asp133 to an alanine. We show that several hydrophobic residues at position 104 endow dCK with thymidine kinase activity. Depending on the exact nature of the mutations, the enzyme's substrate preference is modified. The R104M-D133A double mutant is a pyrimidine-specific enzyme due to large K{sub m} values with purines. The crystal structure of the double mutant R104M-D133A in complex with the L-form of thymidine supplies a structural explanation for the ability of this variant to phosphorylate thymidine and thymidine analogs. The replacement of Arg104 by a smaller residue allows L-dT to bind deeper into the active site, making space for the C5-methyl group of the thymine base. The unique catalytic properties of several of the mutants make them good candidates for suicide-gene/protein-therapy applications.

  7. Structure of the Pseudokinase VRK3 Reveals a Degraded Catalytic Site, a Highly Conserved Kinase Fold, and a Putative Regulatory Binding Site

    PubMed Central

    Scheeff, Eric D.; Eswaran, Jeyanthy; Bunkoczi, Gabor; Knapp, Stefan; Manning, Gerard

    2009-01-01

    Summary About 10% of all protein kinases are predicted to be enzymatically inactive pseudokinases, but the structural details of kinase inactivation have remained unclear. We present the first structure of a pseudokinase, VRK3, and that of its closest active relative, VRK2. Profound changes to the active site region underlie the loss of catalytic activity, and VRK3 cannot bind ATP because of residue substitutions in the binding pocket. However, VRK3 still shares striking structural similarity with VRK2, and appears to be locked in a pseudoactive conformation. VRK3 also conserves residue interactions that are surprising in the absence of enzymatic function; these appear to play important architectural roles required for the residual functions of VRK3. Remarkably, VRK3 has an “inverted” pattern of sequence conservation: although the active site is poorly conserved, portions of the molecular surface show very high conservation, suggesting that they form key interactions that explain the evolutionary retention of VRK3. PMID:19141289

  8. DEVELOPMENT OF HIGH ACTIVITY, CATALYTIC SYSTEMS FOR NOx REDUCTION

    SciTech Connect

    Unknown

    2001-12-01

    This project was directed at an investigation of catalytic NO{sub x} reduction on carbonaceous supports at low temperatures. The experimental work was conducted primarily in a packed bed reactor/gas flow system that was constructed for this work. The analytical techniques employed were mass spectrometry, NO{sub x} chemiluminescence, and gas chromatography. The experimental plan was focused on steady-state reactivity experiments, followed by temperature programmed desorption (TPD) of surface intermediates, and also selected temperature-programmed reaction (TPR) experiments. Both uncatalyzed and catalyzed (potassium-promoted) phenolic resin char, were investigated as well as the catalytic effect of additional CO in the gas phase.

  9. Mutations in the Catalytic Loop HRD Motif Alter the Activity and Function of Drosophila Src64

    PubMed Central

    Strong, Taylor C.; Kaur, Gurvinder; Thomas, Jeffrey H.

    2011-01-01

    The catalytic loop HRD motif is found in most protein kinases and these amino acids are predicted to perform functions in catalysis, transition to, and stabilization of the active conformation of the kinase domain. We have identified mutations in a Drosophila src gene, src64, that alter the three HRD amino acids. We have analyzed the mutants for both biochemical activity and biological function during development. Mutation of the aspartate to asparagine eliminates biological function in cytoskeletal processes and severely reduces fertility, supporting the amino acid's critical role in enzymatic activity. The arginine to cysteine mutation has little to no effect on kinase activity or cytoskeletal reorganization, suggesting that the HRD arginine may not be critical for coordinating phosphotyrosine in the active conformation. The histidine to leucine mutant retains some kinase activity and biological function, suggesting that this amino acid may have a biochemical function in the active kinase that is independent of its side chain hydrogen bonding interactions in the active site. We also describe the phenotypic effects of other mutations in the SH2 and tyrosine kinase domains of src64, and we compare them to the phenotypic effects of the src64 null allele. PMID:22132220

  10. Establishing wild-type levels of catalytic activity on natural and artificial (βα)8-barrel protein scaffolds

    PubMed Central

    Claren, Jörg; Malisi, Christoph; Höcker, Birte; Sterner, Reinhard

    2009-01-01

    The generation of high levels of new catalytic activities on natural and artificial protein scaffolds is a major goal of enzyme engineering. Here, we used random mutagenesis and selection in vivo to establish a sugar isomerisation reaction on both a natural (βα)8-barrel enzyme and a catalytically inert chimeric (βα)8-barrel scaffold, which was generated by the recombination of 2 (βα)4-half barrels. The best evolved variants show turnover numbers and substrate affinities that are similar to those of wild-type enzymes catalyzing the same reaction. The determination of the crystal structure of the most proficient variant allowed us to model the substrate sugar in the novel active site and to elucidate the mechanistic basis of the newly established activity. The results demonstrate that natural and inert artificial protein scaffolds can be converted into highly proficient enzymes in the laboratory, and provide insights into the mechanisms of enzyme evolution. PMID:19237570

  11. Catalytic site of human protein-glucosylgalactosylhydroxylysine glucosidase: Three crucial carboxyl residues were determined by cloning and site-directed mutagenesis.

    PubMed

    Hamazaki, Hideaki; Hamazaki, Michiko Horikawa

    2016-01-15

    Protein-glucosylgalactosylhydroxylysine glucosidase (PGGHG; EC3.2.1.107) cleaves glucose from disaccharide unit (Glc-α1,2-Gal) linked to hydroxylysine residues of collagen. In the present paper we first show that PGGHG is the product of ATHL1 gene as follows. (1) PGGHG was purified from chick embryos and digested with trypsin. LC-MS/MS analysis suggested the tryptic-peptides were from the ATHL1 gene product. (2) Chick embryo ATHL1 cDNA was cloned to a cloning and expression vector and two plasmid clones with different ATHL1 CDS insert were obtained. (3) Each plasmid DNA was transformed into Escherichia coli cells for expression and two isoforms of chicken PGGHG were obtained. (4) Both isoforms effectively released glucose from type IV collagen. Next, we searched for carboxyl residues crucial for catalytic activity as follows; human ATHL1 cDNA was cloned into a cloning and expression vector and 18 mutants were obtained by site-directed mutagenesis for 15 carboxyl residues conserved in ATHL1 of jawed vertebrates. The expression analysis indicated that substitutions of Asp301, Glu430 and Glu574 with sterically conservative (D301N, E430Q, E574Q) or functionally conservative (D301E, E430D, E574D) residues led to the complete elimination of enzyme activity. These findings lead us to the conclusion that PGGHG is encoded by ATHL1 and three carboxyl residues (corresponding to Asp301, Glu430 and Glu574 of human PGGHG) might be involved in the catalytic site of PGGHG. PMID:26682924

  12. Cytochrome c oxidase loses catalytic activity and structural integrity during the aging process in Drosophila melanogaster

    SciTech Connect

    Ren, Jian-Ching; Rebrin, Igor; Klichko, Vladimir; Orr, William C.; Sohal, Rajindar S.

    2010-10-08

    Research highlights: {yields} Cytochrome c oxidase loses catalytic activity during the aging process. {yields} Abundance of seven nuclear-encoded subunits of cytochrome c oxidase decreased with age in Drosophila. {yields} Cytochrome c oxidase is specific intra-mitochondrial site of age-related deterioration. -- Abstract: The hypothesis, that structural deterioration of cytochrome c oxidase (CcO) is a causal factor in the age-related decline in mitochondrial respiratory activity and an increase in H{sub 2}O{sub 2} generation, was tested in Drosophila melanogaster. CcO activity and the levels of seven different nuclear DNA-encoded CcO subunits were determined at three different stages of adult life, namely, young-, middle-, and old-age. CcO activity declined progressively with age by 33%. Western blot analysis, using antibodies specific to Drosophila CcO subunits IV, Va, Vb, VIb, VIc, VIIc, and VIII, indicated that the abundance these polypeptides decreased, ranging from 11% to 40%, during aging. These and previous results suggest that CcO is a specific intra-mitochondrial site of age-related deterioration, which may have a broad impact on mitochondrial physiology.

  13. Energetic basis of catalytic activity of layered nanophase calcium manganese oxides for water oxidation

    PubMed Central

    Birkner, Nancy; Nayeri, Sara; Pashaei, Babak; Najafpour, Mohammad Mahdi; Casey, William H.; Navrotsky, Alexandra

    2013-01-01

    Previous measurements show that calcium manganese oxide nanoparticles are better water oxidation catalysts than binary manganese oxides (Mn3O4, Mn2O3, and MnO2). The probable reasons for such enhancement involve a combination of factors: The calcium manganese oxide materials have a layered structure with considerable thermodynamic stability and a high surface area, their low surface energy suggests relatively loose binding of H2O on the internal and external surfaces, and they possess mixed-valent manganese with internal oxidation enthalpy independent of the Mn3+/Mn4+ ratio and much smaller in magnitude than the Mn2O3-MnO2 couple. These factors enhance catalytic ability by providing easy access for solutes and water to active sites and facile electron transfer between manganese in different oxidation states. PMID:23667149

  14. Role of lattice defects in catalytic activities of graphene clusters for fuel cells.

    PubMed

    Zhang, Lipeng; Xu, Quan; Niu, Jianbing; Xia, Zhenhai

    2015-07-14

    Defects are common but important in graphene, which could significantly tailor the electronic structures and physical and chemical properties. In this study, the density functional theory (DFT) method was applied to study the electronic structure and catalytic properties of graphene clusters containing various point and line defects. The electron transfer processes in oxygen reduction reaction (ORR) on perfect and defective graphene clusters in fuel cells was simulated, and the free energy and reaction energy barrier of the elementary reactions were calculated to determine the reaction pathways. It was found that the graphene cluster with the point defect having pentagon rings at the zigzag edge, or line defects (grain boundaries) consisting of pentagon-pentagon-octagon or pentagon-heptagon chains also at the edges, shows the electrocatalytic capability for ORR. Four-electron and two-electron transfer processes could occur simultaneously on graphene clusters with certain types of defects. The energy barriers of the reactions are comparable to that of platinum(111). The catalytic active sites were determined on the defective graphene. PMID:26033301

  15. Site-specific cleavage by metal ion cofactors and inhibitors of M1 RNA, the catalytic subunit of RNase P from Escherichia coli.

    PubMed Central

    Kazakov, S; Altman, S

    1991-01-01

    The location of phosphate residues involved in specific centers for binding of metal ions in M1 RNA, the catalytic RNA subunit of RNase P from Escherichia coli, was determined by analysis of induction of cleavage of RNA by metal ions. At pH 9.5, Mg2+ catalyzes cleavage of M1 RNA at five principal sites. Under certain conditions, Mn2+ and Ca2+ can each replace Mg2+ as the cofactor in the processing of precursor tRNAs by M1 RNA and P RNA, the RNA subunit of RNase P from Bacillus subtilis. These cations, as well as various metal ion inhibitors of the catalytic activity of M1 RNA, also promote cleavage of M1 RNA in a specific manner. Certain conditions that affect the catalytic activity of M1 RNA also alter the rate of metal ion-induced cleavage at the various sites. From these results and a comparison of cleavage of M1 RNA with that of a deletion mutant of M1 RNA and of P RNA, we have identified two different centers for binding of metal ions in M1 RNA that are important for the processing of the precursor to tRNA(Tyr) from E. coli. There is also a center for the binding of metal ions in the substrate, close to the site of cleavage by M1 RNA. Images PMID:1718000

  16. Catalytic surface radical in dye-decolorizing peroxidase: a computational, spectroscopic and site-directed mutagenesis study

    PubMed Central

    Linde, Dolores; Pogni, Rebecca; Cañellas, Marina; Lucas, Fátima; Guallar, Victor; Baratto, Maria Camilla; Sinicropi, Adalgisa; Sáez-Jiménez, Verónica; Coscolín, Cristina; Romero, Antonio; Medrano, Francisco Javier; Ruiz-Dueñas, Francisco J.; Martínez, Angel T.

    2014-01-01

    Dye-decolorizing peroxidase (DyP) of Auricularia auricula-judae has been expressed in Escherichia coli as a representative of a new DyP family, and subjected to mutagenic, spectroscopic, crystallographic and computational studies. The crystal structure of DyP shows a buried haem cofactor, and surface tryptophan and tyrosine residues potentially involved in long-range electron transfer from bulky dyes. Simulations using PELE (Protein Energy Landscape Exploration) software provided several binding-energy optima for the anthraquinone-type RB19 (Reactive Blue 19) near the above aromatic residues and the haem access-channel. Subsequent QM/MM (quantum mechanics/molecular mechanics) calculations showed a higher tendency of Trp-377 than other exposed haem-neighbouring residues to harbour a catalytic protein radical, and identified the electron-transfer pathway. The existence of such a radical in H2O2-activated DyP was shown by low-temperature EPR, being identified as a mixed tryptophanyl/tyrosyl radical in multifrequency experiments. The signal was dominated by the Trp-377 neutral radical contribution, which disappeared in the W377S variant, and included a tyrosyl contribution assigned to Tyr-337 after analysing the W377S spectra. Kinetics of substrate oxidation by DyP suggests the existence of high- and low-turnover sites. The high-turnover site for oxidation of RB19 (kcat> 200 s−1) and other DyP substrates was assigned to Trp-377 since it was absent from the W377S variant. The low-turnover site/s (RB19 kcat ~20 s−1) could correspond to the haem access-channel, since activity was decreased when the haem channel was occluded by the G169L mutation. If a tyrosine residue is also involved, it will be different from Tyr-337 since all activities are largely unaffected in the Y337S variant. PMID:25495127

  17. Physicochemical properties and catalytic activity of metal tetraphenyl porphins in the oxidation of alkylaromatic hydrocarbons

    NASA Astrophysics Data System (ADS)

    Kobotaeva, N. S.; Skorokhodova, T. S.; Kokova, D. A.

    2013-06-01

    We consider the effect of complexing metal in a tetraphenylporphin molecule on its catalytic activity in oxidizing alkylaromatic hydrocarbons by molecular oxygen. The catalytic activity of metal porphyrins (Co, Cu, Zn, Mn, and In TPP) is found to depend on their oxidation potentials and the distribution of electron density in the molecule. The electron-donating compound imidazole is shown to affect the oxidation rate.

  18. Carbon Nanotube Materials for Substrate Enhanced Control of Catalytic Activity

    SciTech Connect

    Heben, M.; Dillon, A. C.; Engtrakul, C.; Lee, S.-H.; Kelley, R. D.; Kini, A. M.

    2007-05-01

    Carbon SWNTs are attractive materials for supporting electrocatalysts. The properties of SWNTs are highly tunable and controlled by the nanotube's circumferential periodicity and their surface chemistry. These unique characteristics suggest that architectures constructed from these types of carbon support materials would exhibit interesting and useful properties. Here, we expect that the structure of the carbon nanotube support will play a major role in stabilizing metal electrocatalysts under extreme operating conditions and suppress both catalyst and support degradation. Furthermore, the chemical modification of the carbon nanotube surfaces can be expected to alter the interface between the catalyst and support, thus, enhancing the activity and utilization of the electrocatalysts. We plan to incorporate discrete reaction sites into the carbon nanotube lattice to create intimate electrical contacts with the catalyst particles to increase the metal catalyst activity and utilization. The work involves materials synthesis, design of electrode architectures on the nanoscale, control of the electronic, ionic, and mass fluxes, and use of advanced optical spectroscopy techniques.

  19. Aminoalcohols as Probes of the Two-subsite Active Site of Beta-D-xylosidase from Selenomonas ruminantium

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Catalysis and inhibitor binding by the GH43 beta-xylosidase are governed by the protonation state of catalytic base (D14, pKa 5.0) and catalytic acid (E186, pKa 7.2) which reside in subsite -1 of the two-subsite active site. Cationic aminoalcohols are shown to bind exclusively to subsite -1 of the ...

  20. Active-Site-Accessible, Porphyrinic Metal;#8722;Organic Framework Materials

    SciTech Connect

    Farha, Omar K.; Shultz, Abraham M.; Sarjeant, Amy A.; Nguyen, SonBinh T.; Hupp, Joseph T.

    2012-02-06

    On account of their structural similarity to cofactors found in many metallo-enzymes, metalloporphyrins are obvious potential building blocks for catalytically active, metal-organic framework (MOF) materials. While numerous porphyrin-based MOFs have already been described, versions featuring highly accessible active sites and permanent microporosity are remarkably scarce. Indeed, of the more than 70 previously reported porphyrinic MOFs, only one has been shown to be both permanently microporous and contain internally accessible active sites for chemical catalysis. Attempts to generalize the design approach used in this single successful case have failed. Reported here, however, is the synthesis of an extended family of MOFs that directly incorporate a variety of metalloporphyrins (specifically Al{sup 3+}, Zn{sup 2+}, Pd{sup 2+}, Mn{sup 3+}, and Fe{sup 3+} complexes). These robust porphyrinic materials (RPMs) feature large channels and readily accessible active sites. As an illustrative example, one of the manganese-containing RPMs is shown to be catalytically competent for the oxidation of alkenes and alkanes.

  1. Copper metal-organic framework nanocrystal for plane effect nonenzymatic electro-catalytic activity of glucose

    NASA Astrophysics Data System (ADS)

    Liu, Yuanying; Zhang, Youjuan; Chen, Jing; Pang, Huan

    2014-09-01

    This work describes the first demonstration of nanocrystal plane dependent nonenzymatic electro-catalytic glucose activity of [Cu3(btc)2] nanocrystals with different shapes (nanocube, truncated cube, cuboctahedron, and octahedron). From electrochemical results, the obtained [Cu3(btc)2] nanocube modified electrode shows the best nonenzymatic electro-catalytic glucose activity. Interestingly, decreasing the {100} crystal planes from cubes to octahedra, changes the nonenzymatic electro-catalytic activity from highly sensitive to general.This work describes the first demonstration of nanocrystal plane dependent nonenzymatic electro-catalytic glucose activity of [Cu3(btc)2] nanocrystals with different shapes (nanocube, truncated cube, cuboctahedron, and octahedron). From electrochemical results, the obtained [Cu3(btc)2] nanocube modified electrode shows the best nonenzymatic electro-catalytic glucose activity. Interestingly, decreasing the {100} crystal planes from cubes to octahedra, changes the nonenzymatic electro-catalytic activity from highly sensitive to general. Electronic supplementary information (ESI) available. See DOI: 10.1039/c4nr03396e

  2. A small ribozyme with dual-site kinase activity

    PubMed Central

    Biondi, Elisa; Maxwell, Adam W.R.; Burke, Donald H.

    2012-01-01

    Phosphoryl transfer onto backbone hydroxyls is a recognized catalytic activity of nucleic acids. We find that kinase ribozyme K28 possesses an unusually complex active site that promotes (thio)phosphorylation of two residues widely separated in primary sequence. After allowing the ribozyme to radiolabel itself by phosphoryl transfer from [γ-32P]GTP, DNAzyme-mediated cleavage yielded two radiolabeled cleavage fragments, indicating phosphorylation sites within each of the two cleavage fragments. These sites were mapped by alkaline digestion and primer extension pausing. Enzymatic digestion and mutational analysis identified nucleotides important for activity and established the active structure as being a constrained pseudoknot with unusual connectivity that may juxtapose the two reactive sites. Nuclease sensitivities for nucleotides near the pseudoknot core were altered in the presence of GTPγS, indicating donor-induced folding. The 5′ target site was more strongly favored in full-length ribozyme K28 (128 nt) than in truncated RNAs (58 nt). Electrophoretic mobilities of self-thiophosphorylated products on organomercurial gels are distinct from the 5′ mono-thiophosphorylated product produced by reaction with polynucleotide kinase, potentially indicating simultaneous labeling of both sites within individual RNA strands. Our evidence supports a single, compact structure with local dynamics, rather than global rearrangement, as being responsible for dual-site phosphorylation. PMID:22618879

  3. Catalytic activity of bimetallic catalysts highly sensitive to the atomic composition and phase structure at the nanoscale.

    PubMed

    Shan, Shiyao; Petkov, Valeri; Prasai, Binay; Wu, Jinfang; Joseph, Pharrah; Skeete, Zakiya; Kim, Eunjoo; Mott, Derrick; Malis, Oana; Luo, Jin; Zhong, Chuan-Jian

    2015-12-01

    The ability to determine the atomic arrangement in nanoalloy catalysts and reveal the detailed structural features responsible for the catalytically active sites is essential for understanding the correlation between the atomic structure and catalytic properties, enabling the preparation of efficient nanoalloy catalysts by design. Herein we describe a study of CO oxidation over PdCu nanoalloy catalysts focusing on gaining insights into the correlation between the atomic structures and catalytic activity of nanoalloys. PdCu nanoalloys of different bimetallic compositions are synthesized as a model system and are activated by a controlled thermochemical treatment for assessing their catalytic activity. The results show that the catalytic synergy of Pd and Cu species evolves with both the bimetallic nanoalloy composition and temperature of the thermochemical treatment reaching a maximum at a Pd : Cu ratio close to 50 : 50. The nanoalloys are characterized structurally by ex situ and in situ synchrotron X-ray diffraction, including atomic pair distribution function analysis. The structural data show that, depending on the bimetallic composition and treatment temperature, PdCu nanoalloys adopt two different structure types. One features a chemically ordered, body centered cubic (B2) type alloy consisting of two interpenetrating simple cubic lattices, each occupied with Pd or Cu species alone, and the other structure type features a chemically disordered, face-centered cubic (fcc) type of alloy wherein Pd and Cu species are intermixed at random. The catalytic activity for CO oxidation is strongly influenced by the structural features. In particular, it is revealed that the prevalence of chemical disorder in nanoalloys with a Pd : Cu ratio close to 50 : 50 makes them superior catalysts for CO oxidation in comparison with the same nanoalloys of other bimetallic compositions. However, the catalytic synergy can be diminished if the Pd50Cu50 nanoalloys undergo

  4. Simultaneous realization of high catalytic activity and stability for catalytic cracking of n-heptane on highly exposed (010) crystal planes of nanosheet ZSM-5 zeolite.

    PubMed

    Xiao, Xia; Zhang, Yaoyuan; Jiang, Guiyuan; Liu, Jia; Han, Shanlei; Zhao, Zhen; Wang, Ruipu; Li, Cong; Xu, Chunming; Duan, Aijun; Wang, Yajun; Liu, Jian; Wei, Yuechang

    2016-08-01

    Nanosheet ZSM-5 zeolite with highly exposed (010) crystal planes demonstrates high reactivity and good anti-coking stability for the catalytic cracking of n-heptane, which is attributed to the synergy of high external surface area and acid sites, fully accessible channel intersection acid sites, and hierarchical porosity caused by the unique morphology. PMID:27458616

  5. The role of short-range Cys171-Cys178 disulfide bond in maintaining cutinase active site integrity: A molecular dynamics simulation

    SciTech Connect

    Matak, Mehdi Youssefi; Moghaddam, Majid Erfani

    2009-12-11

    Understanding structural determinants in enzyme active site integrity can provide a good knowledge to design efficient novel catalytic machineries. Fusarium solani pisi cutinase with classic triad Ser-His-Asp is a promising enzyme to scrutinize these structural determinants. We performed two MD simulations: one, with the native structure, and the other with the broken Cys171-Cys178 disulfide bond. This disulfide bond stabilizes a turn in active site on which catalytic Asp175 is located. Functionally important H-bonds and atomic fluctuations in catalytic pocket have been changed. We proposed that this disulfide bond within active site can be considered as an important determinant of cutinase active site structural integrity.

  6. Phosphorylation of Ser-204 and Tyr-405 in human malonyl-CoA decarboxylase expressed in silkworm Bombyx mori regulates catalytic decarboxylase activity.

    PubMed

    Hwang, In-Wook; Makishima, Yu; Suzuki, Tomohiro; Kato, Tatsuya; Park, Sungjo; Terzic, Andre; Chung, Shin-Kyo; Park, Enoch Y

    2015-11-01

    Decarboxylation of malonyl-CoA to acetyl-CoA by malonyl-CoA decarboxylase (MCD; EC 4.1.1.9) is a vital catalytic reaction of lipid metabolism. While it is established that phosphorylation of MCD modulates the enzymatic activity, the specific phosphorylation sites associated with the catalytic function have not been documented due to lack of sufficient production of MCD with proper post-translational modifications. Here, we used the silkworm-based Bombyx mori nucleopolyhedrovirus (BmNPV) bacmid system to express human MCD (hMCD) and mapped phosphorylation effects on enzymatic function. Purified MCD from silkworm displayed post-translational phosphorylation and demonstrated coherent enzymatic activity with high yield (-200 μg/silkworm). Point mutations in putative phosphorylation sites, Ser-204 or Tyr-405 of hMCD, identified by bioinformatics and proteomics analyses reduced the catalytic activity, underscoring the functional significance of phosphorylation in modulating decarboxylase-based catalysis. Identified phosphorylated residues are distinct from the decarboxylation catalytic site, implicating a phosphorylation-induced global conformational change of MCD as responsible in altering catalytic function. We conclude that phosphorylation of Ser-204 and Tyr-405 regulates the decarboxylase function of hMCD leveraging the silkworm-based BmNPV bacmid expression system that offers a fail-safe eukaryotic production platform implementing proper post-translational modification such as phosphorylation. PMID:26004805

  7. Determinants of ligand binding and catalytic activity in the myelin enzyme 2′,3′-cyclic nucleotide 3′-phosphodiesterase

    PubMed Central

    Raasakka, Arne; Myllykoski, Matti; Laulumaa, Saara; Lehtimäki, Mari; Härtlein, Michael; Moulin, Martine; Kursula, Inari; Kursula, Petri

    2015-01-01

    2′,3′-cyclic nucleotide 3′-phosphodiesterase (CNPase) is an enzyme highly abundant in the central nervous system myelin of terrestrial vertebrates. The catalytic domain of CNPase belongs to the 2H phosphoesterase superfamily and catalyzes the hydrolysis of nucleoside 2′,3′-cyclic monophosphates to nucleoside 2′-monophosphates. The detailed reaction mechanism and the essential catalytic amino acids involved have been described earlier, but the roles of many amino acids in the vicinity of the active site have remained unknown. Here, several CNPase catalytic domain mutants were studied using enzyme kinetics assays, thermal stability experiments, and X-ray crystallography. Additionally, the crystal structure of a perdeuterated CNPase catalytic domain was refined at atomic resolution to obtain a detailed view of the active site and the catalytic mechanism. The results specify determinants of ligand binding and novel essential residues required for CNPase catalysis. For example, the aromatic side chains of Phe235 and Tyr168 are crucial for substrate binding, and Arg307 may affect active site electrostatics and regulate loop dynamics. The β5-α7 loop, unique for CNPase in the 2H phosphoesterase family, appears to have various functions in the CNPase reaction mechanism, from coordinating the nucleophilic water molecule to providing a binding pocket for the product and being involved in product release. PMID:26563764

  8. Temporal separation of catalytic activities allows anti-Markovnikov reductive functionalization of terminal alkynes

    NASA Astrophysics Data System (ADS)

    Li, Le; Herzon, Seth B.

    2014-01-01

    There is currently great interest in the development of multistep catalytic processes in which one or several catalysts act sequentially to rapidly build complex molecular structures. Many enzymes—often the inspiration for new synthetic transformations—are capable of processing a single substrate through a chain of discrete, mechanistically distinct catalytic steps. Here, we describe an approach to emulate the efficiency of these natural reaction cascades within a synthetic catalyst by the temporal separation of catalytic activities. In this approach, a single catalyst exhibits multiple catalytic activities sequentially, allowing for the efficient processing of a substrate through a cascade pathway. Application of this design strategy has led to the development of a method to effect the anti-Markovnikov (linear-selective) reductive functionalization of terminal alkynes. The strategy of temporal separation may facilitate the development of other efficient synthetic reaction cascades.

  9. Toward efficient nanoporous catalysts: controlling site-isolation and concentration of grafted catalytic sites on nanoporous materials with solvents and colorimetric elucidation of their site-isolation.

    PubMed

    Sharma, Krishna K; Anan, Abhishek; Buckley, Robert P; Ouellette, Wayne; Asefa, Tewodros

    2008-01-01

    We report that the polarity and dielectric constants of solvents used for grafting organosilanes on mesoporous materials strongly affect the concentration of grafted organic groups, the degree of their site-isolation, and the catalytic properties of the resulting materials. Polar and nonpolar organosilanes as well as polar-protic, dipolar-aprotic, and nonpolar solvents were investigated. Polar-protic solvents, which have high dielectric constants, resulted in smaller concentrations ( approximately 1-2 mmol/g) of polar organic groups such as 3-aminopropyl groups, higher surface area materials, site-isolated organic groups, and more efficient catalytic properties toward the Henry reaction of p-hydroxybenzaldehyde with nitromethane. On the other hand, dipolar-aprotic and nonpolar solvents resulted in larger concentrations ( approximately 2-3 mmol/g) of grafted polar functional groups, lower-to-higher surface area materials, more densely populated catalytic groups, and poor-to-efficient catalytic properties toward the Henry reaction. Both the polar-protic and dipolar-aprotic solvents resulted in significantly lower concentration of grafted groups for nonpolar organosilanes such as (3-mercaptopropyl)trimethoxysilane compared to corresponding grafting of the polar amino-organosilanes. The relationship between the solvent properties and the percentage and degree of site-isolation of the grafted functional groups was attributed to differences in solvation of the organosilanes and silanols in various solvents and possible hydrogen-bonding between the organsilanes and the solvents. The degree of site-isolation of the amine groups, which affect the material's catalytic properties, was elucidated by a new colorimetric method involving probing of the absorption maxima (lambdamax) on the d-d electronic spectrum of Cu2+ complexes with the amine-functionalized materials and the colors of the samples. The absorption lambdamax and the colors of the materials were found to be

  10. Direct photoaffinity labeling by nucleotides of the apparent catalytic site on the heavy chains of smooth muscle and Acanthamoeba myosins

    SciTech Connect

    Maruta, H.; Korn, E.D.

    1981-01-10

    The heavy chains of Acanthamoeba myosins, IA, IB and II, turkey gizzard myosin, and rabbit skeletal muscle myosin subfragment-1 were specifically labeled by radioactive ATP, ADP, and UTP, each of which is a substrate or product of myosin ATPase activity, when irradiated with uv light at 0/sup 0/C. With UTP, as much as 0.45 mol/mol of Acanthamoeba myosin IA heavy chain and 1 mol/mol of turkey gizzard myosin heavy chain was incorporated. Evidence that the ligands were associated with the catalytic site included the observations that reaction occurred only with nucleotides that are substrates or products of the ATPase activity; that the reaction was blocked by pyrophosphate which is an inhibitor of the ATPase activity; that ATP was bound as ADP; and that label was probably restricted to a single peptide following limited subtilisin proteolysis of labeled Acanthamoeba myosin IA heavy chain and extensive cleavage with CNBr and trypsin of labeled turkey gizzard myosin heavy chain.

  11. Thermal activation of catalytic microjets in blood samples using microfluidic chips†

    PubMed Central

    Soler, Lluís; Martínez-Cisneros, Cynthia; Swiersy, Anka; Sánchez, Samuel; Schmidt, Oliver G.

    2014-01-01

    We demonstrate that catalytic microjet engines can out-swim high complex media composed of red blood cells and serum. Despite the challenge presented by the high viscosity of the solution at room temperature, the catalytic microjets can be activated at physiological temperature and, consequently, self-propel in diluted solutions of blood samples. We prove that these microjets self-propel in 10× diluted blood samples using microfluidic chips. PMID:24089195

  12. Asymmetric Intramolecular Alkylation of Chiral Aromatic Imines via Catalytic C-H Bond Activation

    SciTech Connect

    Watzke, Anja; Wilson, Rebecca; O'Malley, Steven; Bergman, Robert; Ellman, Jonathan

    2007-04-16

    The asymmetric intramolecular alkylation of chiral aromatic aldimines, in which differentially substituted alkenes are tethered meta to the imine, was investigated. High enantioselectivities were obtained for imines prepared from aminoindane derivatives, which function as directing groups for the rhodium-catalyzed C-H bond activation. Initial demonstration of catalytic asymmetric intramolecular alkylation also was achieved by employing a sterically hindered achiral imine substrate and catalytic amounts of a chiral amine.

  13. Cold catalytic recovery of loaded activated carbon using iron oxide-based nanoparticles.

    PubMed

    Bach, Altai; Zelmanov, Grigory; Semiat, Raphael

    2008-01-01

    A novel approach for the recovery of spent activated carbon by an advanced oxidation process using iron oxide-based nanocatalysts was proposed and investigated. Model organic contaminants, such as ethylene glycol and phenol, were chosen for this study as water pollutants. It was shown that there are several advantages in using catalytic oxidation recovery of activated carbon with iron oxide-based nanocatalysts: low temperature reactivity of catalytic recovery without heating; and a relatively large number of adsorption-recovery cycles, without a reduction in the adsorptive properties of the virgin activated carbon or without a performance decrease from the first adsorption-recovery cycle of the new modified adsorptive properties of the activated carbon. The catalytic recovery takes place without ultraviolet light or any visible radiation sources. Results show a high efficiency of catalytic recovery of spent activated carbon using iron oxide-based nanocatalysts. A 97-99% efficiency of spent activated carbon catalytic regeneration was achieved under chosen conditions after 15-20 min of reaction. The process may be also considered as cold in situ recovery of active carbon. PMID:17826818

  14. Chemical Engineering of Enzymes: Altered Catalytic Activity, Predictable Selectivity and Exceptional Stability of the Semisynthetic Peroxidase Seleno-Subtilisin

    NASA Astrophysics Data System (ADS)

    Häring, Dietmar; Schreier, Peter

    The increasing demand for enzymes as highly selective, mild, and environmentally benign catalysts is often limited by the lack of an enzyme with the desired catalytic activity or substrate selectivity and by their instability in biotechnological processes. The previous answers to these problems comprised genetically engineered enzymes and several classes of enzyme mimics. Here we describe the potential of chemical enzyme engineering: native enzymes can be modified by merely chemical means and basic equipment yielding so-called semisynthetic enzymes. Thus, the high substrate selectivity of the enzymatic peptide framework is combined with the catalytic versatility of a synthetic active site. We illustrate the potential of chemically engineered enzymes with the conception of the semisynthetic peroxidase seleno-subtilisin. First, the serine endoprotease subtilisin was crystallized and cross-linked with glutaraldehyde to give cross-linked enzyme crystals which were found to be insoluble in water or organic solvents and highly stable. Second, serine 221 in the active site (Enz-OH) was chemically converted into an oxidized derivative of selenocystein (Enz-SeO2H). As a consequence, the former proteolytic enzyme gained peroxidase activity and catalyzed the selective reduction of hydroperoxides. Due to the identical binding sites of the semisynthetic peroxidase and the protease, the substrate selectivity of seleno-subtilisin was predictable in view of the well-known selectivity of subtilisin.

  15. Reactivity and Catalytic Activity of Hydrogen Atom Chemisorbed Silver Clusters.

    PubMed

    Manzoor, Dar; Pal, Sourav

    2015-06-18

    Metal clusters of silver have attracted recent interest of researchers as a result of their potential in different catalytic applications and low cost. However, due to the completely filled d orbital and very high first ionization potential of the silver atom, the silver-based catalysts interact very weakly with the reacting molecules. In the current work, density functional theory calculations were carried out to investigate the effect of hydrogen atom chemisorption on the reactivity and catalytic properties of inert silver clusters. Our results affirm that the hydrogen atom chemisorption leads to enhancement in the binding energy of the adsorbed O2 molecule on the inert silver clusters. The increase in the binding energy is also characterized by the decrease in the Ag-O and increase in the O-O bond lengths in the case of the AgnH silver clusters. Pertinent to the increase in the O-O bond length, a significant red shift in the O-O stretching frequency is also noted in the case of the AgnH silver clusters. Moreover, the hydrogen atom chemisorbed silver clusters show low reaction barriers and high heat of formation of the final products for the environmentally important CO oxidation reaction as compared to the parent catalytically inactive clusters. The obtained results were compared with those of the corresponding gold and hydrogen atom chemisorbed gold clusters obtained at the same level of theory. It is expected the current computational study will provide key insights for future advances in the design of efficient nanosilver-based catalysts through the adsorption of a small atom or a ligand. PMID:25988294

  16. Directed evolution of Tau class glutathione transferases reveals a site that regulates catalytic efficiency and masks co-operativity.

    PubMed

    Axarli, Irine; Muleta, Abdi W; Vlachakis, Dimitrios; Kossida, Sophia; Kotzia, Georgia; Maltezos, Anastasios; Dhavala, Prathusha; Papageorgiou, Anastassios C; Labrou, Nikolaos E

    2016-03-01

    A library of Tau class GSTs (glutathione transferases) was constructed by DNA shuffling using the DNA encoding the Glycine max GSTs GmGSTU2-2, GmGSTU4-4 and GmGSTU10-10. The parental GSTs are >88% identical at the sequence level; however, their specificity varies towards different substrates. The DNA library contained chimaeric structures of alternated segments of the parental sequences and point mutations. Chimaeric GST sequences were expressed in Escherichia coli and their enzymatic activities towards CDNB (1-chloro-2,4-dinitrobenzene) and the herbicide fluorodifen (4-nitrophenyl α,α,α-trifluoro-2-nitro-p-tolyl ether) were determined. A chimaeric clone (Sh14) with enhanced CDNB- and fluorodifen-detoxifying activities, and unusual co-operative kinetics towards CDNB and fluorodifen, but not towards GSH, was identified. The structure of Sh14 was determined at 1.75 Å (1 Å=0.1 nm) resolution in complex with S-(p-nitrobenzyl)-glutathione. Analysis of the Sh14 structure showed that a W114C point mutation is responsible for the altered kinetic properties. This was confirmed by the kinetic properties of the Sh14 C114W mutant. It is suggested that the replacement of the bulky tryptophan residue by a smaller amino acid (cysteine) results in conformational changes of the active-site cavity, leading to enhanced catalytic activity of Sh14. Moreover, the structural changes allow the strengthening of the two salt bridges between Glu(66) and Lys(104) at the dimer interface that triggers an allosteric effect and the communication between the hydrophobic sites. PMID:26637269

  17. Development of catalytically active and highly stable catalyst supports for polymer electrolyte membrane fuel cells

    NASA Astrophysics Data System (ADS)

    Kim, Taekeun; Xie, Tianyuan; Jung, Wonsuk; Gadala-Maria, Francis; Ganesan, Prabhu; Popov, Branko N.

    2015-01-01

    Novel procedures are developed for the synthesis of highly stable carbon composite catalyst supports (CCCS-800 °C and CCCS-1100 °C) and an activated carbon composite catalyst support (A-CCCS). These supports are synthesized through: (i) surface modification with acids and inclusion of oxygen groups, (ii) metal-catalyzed pyrolysis, and (iii) chemical leaching to remove excess metal used to dope the support. The procedure results in increasing carbon graphitization and inclusion of non-metallic active sites on the support surface. Catalytic activity of CCCS indicates an onset potential of 0.86 V for the oxygen reduction reaction (ORR) with well-defined kinetic and mass-transfer regions and ∼2.5% H2O2 production in rotating ring disk electrode (RRDE) studies. Support stability studies at 1.2 V constant potential holding for 400 h indicate high stability for the 30% Pt/A-CCCS catalyst with a cell potential loss of 27 mV at 800 mA cm-2 under H2-air, 32% mass activity loss, and 30% ECSA loss. Performance evaluation in polymer electrolyte membrane (PEM) fuel cell shows power densities (rated) of 0.18 and 0.23 gPt kW-1 for the 30% Pt/A-CCCS and 30% Pt/CCCS-800 °C catalysts, respectively. The stabilities of various supports developed in this study are compared with those of a commercial Pt/C catalyst.

  18. The Influence of Elastic Strain on Catalytic Activity in the Hydrogen Evolution Reaction.

    PubMed

    Yan, Kai; Maark, Tuhina Adit; Khorshidi, Alireza; Sethuraman, Vijay A; Peterson, Andrew A; Guduru, Pradeep R

    2016-05-17

    Understanding the role of elastic strain in modifying catalytic reaction rates is crucial for catalyst design, but experimentally, this effect is often coupled with a ligand effect. To isolate the strain effect, we have investigated the influence of externally applied elastic strain on the catalytic activity of metal films in the hydrogen evolution reaction (HER). We show that elastic strain tunes the catalytic activity in a controlled and predictable way. Both theory and experiment show strain controls reactivity in a controlled manner consistent with the qualitative predictions of the HER volcano plot and the d-band theory: Ni and Pt's activities were accelerated by compression, while Cu's activity was accelerated by tension. By isolating the elastic strain effect from the ligand effect, this study provides a greater insight into the role of elastic strain in controlling electrocatalytic activity. PMID:27079940

  19. Marine Rhodobacteraceae L-haloacid dehalogenase contains a novel His/Glu dyad that could activate the catalytic water.

    PubMed

    Novak, Halina R; Sayer, Christopher; Isupov, Michail N; Paszkiewicz, Konrad; Gotz, Dorothee; Spragg, Andrew Mearns; Littlechild, Jennifer A

    2013-04-01

    The putative L-haloacid dehalogenase gene (DehRhb) from a marine Rhodobacteraceae family was cloned and overexpressed in Escherichia coli. The DehRhb protein was shown to be an L-haloacid dehalogenase with highest activity towards brominated substrates with short carbon chains (≤ C3). The optimal temperature for enzyme activity was 55 °C, and the Vmax and Km were 1.75 μm·min(-1) ·mg(-1) of protein and 6.72 mm, respectively, when using monobromoacetic acid as a substrate. DehRhb showed moderate thermal stability, with a melting temperature of 67 °C. The enzyme demonstrated high tolerance to solvents, as shown by thermal shift experiments and solvent incubation assays. The DehRhb protein was crystallized and structures of the native, reaction intermediate and substrate-bound forms were determined. The active site of DehRhb had significant differences from previously studied L-haloacid dehalogenases. The asparagine and arginine residues shown to be essential for catalytic activity in other L-haloacid dehalogenases are not present in DehRhb. The histidine residue which replaces the asparagine residue in DehRhb was coordinated by a conformationally strained glutamate residue that replaces a conserved glycine. The His/Glu dyad is positioned for deprotonation of the catalytic water which attacks the ester bond in the reaction intermediate. The catalytic water in DehRhb is shifted by ~ 1.5 Å from its position in other L-haloacid dehalogenases. A similar His/Glu or Asp dyad is known to activate the catalytic water in haloalkane dehalogenases. The DehRhb enzyme represents a novel member within the L-haloacid dehalogenase family and it has potential to be used as a commercial biocatalyst. PMID:23384397

  20. Encapsulating Metal Clusters and Acid Sites within Small Voids: Synthetic Strategies and Catalytic Consequences

    NASA Astrophysics Data System (ADS)

    Goel, Sarika

    active sites. We have demonstrated the selectivity of the encapsulation processes by combining transmission electron microscopy and chemisorptive titrations with rigorous catalytic assessments of the ability of these materials to catalyze reactions of small molecules, which can access the intracrystalline voids, but not of larger molecules that cannot access the metal clusters within such voids. The selective confinement of clusters also prevented their contact with sulfur compounds (e.g., thiophene and H2S), thus allowing reactions to occur at conditions that otherwise render unconfined clusters unreactive. We have also developed synthetic protocols and guiding principles, inspired by mechanistic considerations, for the synthesis of zeolites via interzeolite transformations without the use of organic structure-directing agents (OSDA). More specifically, we have synthesized high-silica MFI (ZSM-5), CHA (chabazite), STF (SSZ-35) and MTW (ZSM-12) zeolites from FAU (faujasite) or BEA (beta) parent materials. Structures with lower framework densities (FAU or BEA) were successfully transformed into thermodynamically-favored, more stable structures with higher framework densities (MFI, CHA, STF, and MTW); to date, target materials with higher Si/Al ratios (Si/Al >10) have not been synthesized via interzeolite transformations without the aid of the OSDA species used to discover these zeolite structures and deemed essential up until now for their successful synthesis. Overcoming kinetic hurdles in such transformations required either the presence of common composite building units (CBU) between parent and target structures or, in their absence, the introduction of small amount of seeds of the daughter structures. The NaOH/SiO2 ratio, H2O/SiO2 ratio and Al content in reagents are used to enforce synchronization between the swelling and local restructuring within parent zeolite domains with the spalling of fragments or building units from seeds of the target structure. The

  1. A study on the morphology and catalytic activity of gold nanoparticles by the kinetic Monte Carlo simulation

    NASA Astrophysics Data System (ADS)

    He, Xiang; Chen, Zhao-Xu

    2016-05-01

    We studied the thermal-stability of supported Au nanoparticles on the substrates of different binding strength to gold by Monte Carlo simulations. It has been revealed that the stable Au morphology is determined by the temperature and the binding strength. When heated on the strongly-binding substrates, the Au nanoparticles would wet the substrate completely and form monolayer. The stable Au layered structure of few layers can be formed by the incomplete wetting of clusters on the intermediate-binding substrates. The simulation results are in good agreement with pertinent experimental and theoretical results. Based on the simulation results and experimental observations, we find the strong linkage between the top edge sites and the activity TOF of low-temperature CO oxidation. We conclude that the top edges sites of Au layered structures are possible reactive sites. This study may provide new perspective for controlling morphology and understanding catalytic activity of supported metallic clusters.

  2. Site-specific growth and density control of carbon nanotubes by direct deposition of catalytic nanoparticles generated by spark discharge

    PubMed Central

    2013-01-01

    Catalytic iron nanoparticles generated by spark discharge were used to site-selectively grow carbon nanotubes (CNTs) and control their density. The generated aerosol nanoparticles were deposited on a cooled substrate by thermophoresis. The shadow mask on top of the cooled substrate enabled patterning of the catalytic nanoparticles and, thereby, patterning of CNTs synthesized by chemical vapor deposition. The density of CNTs could be controlled by varying the catalytic nanoparticle deposition time. It was also demonstrated that the density could be adjusted by changing the gap between the shadow mask and the substrate, taking advantage of the blurring effect of the deposited nanoparticles, for an identical deposition time. As all the processing steps for the patterned growth and density control of CNTs can be performed under dry conditions, we also demonstrated the integration of CNTs on fully processed, movable silicon microelectromechanical system (MEMS) structures. PMID:24090218

  3. Hybrid [FeFe]-hydrogenases with modified active sites show remarkable residual enzymatic activity.

    PubMed

    Siebel, Judith F; Adamska-Venkatesh, Agnieszka; Weber, Katharina; Rumpel, Sigrun; Reijerse, Edward; Lubitz, Wolfgang

    2015-02-24

    [FeFe]-hydrogenases are to date the only enzymes for which it has been demonstrated that the native inorganic binuclear cofactor of the active site Fe2(adt)(CO)3(CN)2 (adt = azadithiolate = [S-CH2-NH-CH2-S](2-)) can be synthesized on the laboratory bench and subsequently inserted into the unmaturated enzyme to yield fully functional holo-enzyme (Berggren, G. et al. (2013) Nature 499, 66-70; Esselborn, J. et al. (2013) Nat. Chem. Biol. 9, 607-610). In the current study, we exploit this procedure to introduce non-native cofactors into the enzyme. Mimics of the binuclear subcluster with a modified bridging dithiolate ligand (thiodithiolate, N-methylazadithiolate, dimethyl-azadithiolate) and three variants containing only one CN(-) ligand were inserted into the active site of the enzyme. We investigated the activity of these variants for hydrogen oxidation as well as proton reduction and their structural accommodation within the active site was analyzed using Fourier transform infrared spectroscopy. Interestingly, the monocyanide variant with the azadithiolate bridge showed ∼50% of the native enzyme activity. This would suggest that the CN(-) ligands are not essential for catalytic activity, but rather serve to anchor the binuclear subsite inside the protein pocket through hydrogen bonding. The inserted artificial cofactors with a propanedithiolate and an N-methylazadithiolate bridge as well as their monocyanide variants also showed residual activity. However, these activities were less than 1% of the native enzyme. Our findings indicate that even small changes in the dithiolate bridge of the binuclear subsite lead to a rather strong decrease of the catalytic activity. We conclude that both the Brønsted base function and the conformational flexibility of the native azadithiolate amine moiety are essential for the high catalytic activity of the native enzyme. PMID:25633077

  4. A Lamellar Coordination Polymer with Remarkable Catalytic Activity.

    PubMed

    Mendes, Ricardo F; Antunes, Margarida M; Silva, Patrícia; Barbosa, Paula; Figueiredo, Filipe; Linden, Anthony; Rocha, João; Valente, Anabela A; Almeida Paz, Filipe A

    2016-09-01

    A positively charged lamellar coordination polymer based on a flexible triphosphonic acid linker is reported. [Gd(H4 nmp)(H2 O)2 ]Cl⋅2 H2 O (1) [H6 nmp=nitrilotris(methylenephosphonic acid)] was obtained by a one-pot approach by using water as a green solvent and by forcing the inclusion of additional acid sites by employing HCl in the synthesis. Compound 1 acts as a versatile heterogeneous acid catalyst with outstanding activity in organic reactions such as alcoholysis of styrene oxide, acetalization of benzaldehyde and cyclohexanaldehyde and ketalization of cyclohexanone. For all reaction systems, very high conversions were reached (92-97 %) in only 15-30 min under mild conditions (35 °C, atmospheric pressure). The coordination polymer exhibits a protonic conductivity of 1.23×10(-5)  S cm(-1) at 98 % relative humidity and 40 °C. PMID:27505712

  5. Polysugar-stabilized Pd nanoparticles exhibiting high catalytic activities for hydrodechlorination of environmentally deleterious trichloroethylene.

    PubMed

    Liu, Juncheng; He, Feng; Durham, Ed; Zhao, Dongye; Roberts, Christopher B

    2008-01-01

    In this paper, we present a straightforward and environmentally friendly aqueous-phase synthesis of small Pd nanoparticles (approximately 2.4 nm under the best stabilization) by employing a "green", inexpensive, and biodegradable/biocompatible polysugar, sodium carboxymethylcellulose (CMC), as a capping agent. The Pd nanoparticles exhibited rather high catalytic activity (observed pseudo-first-order reaction kinetic rate constant, k(obs), is up to 828 L g(-1) min(-1)) for the hydrodechlorination of environmentally deleterious trichloroethene (TCE) in water. Fourier transform IR (FT-IR) spectra indicate that CMC molecules interact with the Pd nanoparticles via both carboxyl (-COO-) and hydroxyl (-OH) groups, thereby functioning to passivate the surface and suppress the growth of the Pd nanoparticles. Hydrodechlorination of TCE using differently sized CMC-capped Pd nanoparticles as catalyst was systematically investigated in this work. Both the catalytic activity (k(obs)) and the surface catalytic activity (turnover frequency, TOF) of these CMC-capped Pd nanoparticles for TCE degradation are highly size-dependent. This point was further verified by a comparison of the catalytic activities and surface catalytic activities of CMC-capped Pd nanoparticles with those of beta-D-glucose-capped Pd and neat Pd nanoparticles for TCE degradation. PMID:18044944

  6. Structural and adsorption characteristics and catalytic activity of titania and titania-containing nanomaterials.

    PubMed

    Gun'ko, V M; Blitz, J P; Zarko, V I; Turov, V V; Pakhlov, E M; Oranska, O I; Goncharuk, E V; Gornikov, Y I; Sergeev, V S; Kulik, T V; Palyanytsya, B B; Samala, R K

    2009-02-01

    Morphological, structural, adsorption, and catalytic properties of highly disperse titania prepared using sulfate and pyrogenic methods, and fumed titania-containing mixed oxides, were studied using XRD, TG/DTA, nitrogen adsorption, (1)H NMR, FTIR, microcalorimetry on immersion of oxides in water and decane, thermally stimulated depolarization current (TSDC) and catalytic photodecomposition of methylene blue (MB). Phase composition and aggregation characteristics of nanoparticles (pore size distribution) of sulfate and pyrogenically prepared titania are very different; temperature dependent structural properties are thus very different. Catalytic activity for the photodecomposition of MB is greatest (per gram of TiO(2) for the pure oxide materials) for non-treated ultrafine titania PC-500, which has the largest S(BET) value and smallest particle size of the materials studied. However, this activity calculated per m(2) is higher for PC-105, possessing a much smaller S(BET) value than PC-500. The activity per unit surface area of titania is greatest for the fumed silica-titania mixed oxide ST20. Calcination of PC-500 at 650 degrees C leads to enhancement of anatase content and catalytic activity, but heating at 800 and 900 degrees C lowers the anatase content (since rutile appears) and diminishes catalytic activity, as well as the specific surface area because of nanoparticle sintering. PMID:18996539

  7. Selective Catalytic Oxidation of Hydrogen Sulfide on Activated Carbons Impregnated with Sodium Hydroxide

    SciTech Connect

    Schwartz, Viviane; Baskova, Svetlana; Armstrong, Timothy R.

    2009-01-01

    Two activated carbons of different origin were impregnated with the solution of sodium hydroxide (NaOH) of various concentrations up to 10 wt %, and the effect of impregnation on the catalytic performance of the carbons was evaluated. The catalytic activity was analyzed in terms of the capacity of carbons for hydrogen sulfide (H2S) conversion and removal from hydrogen-rich fuel streams and the emission times of H2S and the products of its oxidation [e.g., sulfur dioxide (SO2) and carbonyl sulfide (COS)]. The results of impregnation showed a significant improvement in the catalytic activity of both carbons proportional to the amount of NaOH introduced. NaOH introduces hydroxyl groups (OH-) on the surface of the activated carbon that increase its surface reactivity and its interaction with sulfur-containing compounds.

  8. Molecular Imprint of Enzyme Active Site by Camel Nanobodies

    PubMed Central

    Li, Jiang-Wei; Xia, Lijie; Su, Youhong; Liu, Hongchun; Xia, Xueqing; Lu, Qinxia; Yang, Chunjin; Reheman, Kalbinur

    2012-01-01

    Screening of inhibitory Ab1 antibodies is a critical step for producing catalytic antibodies in the anti-idiotypic approach. However, the incompatible surface of the active site of the enzyme and the antigen-binding site of heterotetrameric conventional antibodies become the limiting step. Because camelid-derived nanobodies possess the potential to preferentially bind to the active site of enzymes due to their small size and long CDR3, we have developed a novel approach to produce antibodies with alliinase activities by exploiting the molecular mimicry of camel nanobodies. By screening the camelid-derived variable region of the heavy chain cDNA phage display library with alliinase, we obtained an inhibitory nanobody VHHA4 that recognizes the active site. Further screening with VHHA4 from the same variable domain of the heavy chain of a heavy-chain antibody library led to a higher incidence of anti-idiotypic Ab2 abzymes with alliinase activities. One of the abzymes, VHHC10, showed the highest activity that can be inhibited by Ab1 VHHA4 and alliinase competitive inhibitor penicillamine and significantly suppressed the B16 tumor cell growth in the presence of alliin in vitro. The results highlight the feasibility of producing abzymes via anti-idiotypic nanobody approach. PMID:22374998

  9. Use of Solvatochromism to Assay Preferential Solvation of a Prototypic Catalytic Site

    SciTech Connect

    Schwenzer, Birgit; Cosimbescu, Lelia; Glezakou, Vassiliki Alexandra; Karkamkar, Abhijeet J.; Wang, Zheming; Weber, Robert S.

    2015-04-01

    The composition of the reaction medium near photoactive catalytic sites can be inferred from the solvatochromism of the absorption and emission spectra of the wetted sites, which depend on the polarizability of the fluid. In brief, solvatochromism measures the interaction of the dipole moments of the ground and excited states with the electric field imposed by the solvent shell: a field, which does not relax on the time scale of the absorption or emission events. As a first step in establishing the utility of the technique for inorganic catalysts that operate in complex reaction media, such as encountered in the upgrading of biogenic fuels, we have measured the solvatochromism of a common, structural feature of metal oxide catalysts. In toluene, cyclohexene, chloroform and tetrahydrofuran, POSS-ligated oxometalates exhibit strong ligand-to-metal charge-transfer bands in their UV-visible absorption and emission spectra. The magnitudes of the solvatochromic effects agreed well with the calculated changes in dipole moments that accompany the electronic transitions. From the solvatochromism of the chromophores dissolved in toluene-chloroform mixtures we inferred an unexpectedly strong, preferential solvation of the chromophore even when all three components (oxometalate and the two solvents) were highly miscible. This research was supported in part by the Laboratory Directed Research & Development program at Pacific Northwest National Laboratory. PNNL is operated by Battelle for the US Department of Energy under contract DE-AC05-76RL01830. A portion of the research was performed at EMSL, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at PNNL.

  10. Effects of Particle Size on the Gas Sensitivity and Catalytic Activity of In2O3

    NASA Astrophysics Data System (ADS)

    Zhang, Xiaoshui; Gu, Ruiqin; Zhao, Jinling; Jin, Guixin; Zhao, Mengke; Xue, Yongliang

    2015-10-01

    Nanosized In2O3 powders with different particle sizes were prepared by the microemulsion synthetic method. The effects of particle size on the gas-sensing and catalytic properties of the as-prepared In2O3 were investigated. Reductions in particle size to nanometer levels improved the sensitivity and catalytic activity of In2O3 to i-C4H10 and C2H5OH. The sensitivity of nanosized In2O3 (<42 nm) sensors to i-C4H10, H2 and C2H5OH was 2-4 times higher than that of chemically precipitated In2O3 (130 nm) sensor. A nearly linear relationship was observed between the catalytic activity and specific surface area of In2O3 for the oxidation of i-C4H10 and C2H5OH at 275 °C. The relationship between gas sensitivity and catalytic activity was further discussed. The results of this work reveal that catalytic activity plays a key role in enhancing the sensitivity of gas-sensing materials.

  11. Greatly Enhancing Catalytic Activity of Graphene by Doping the Underlying Metal Substrate.

    PubMed

    Guo, Na; Xi, Yongjie; Liu, Shuanglong; Zhang, Chun

    2015-01-01

    Graphene-based solid-state catalysis represents a new direction in applications of graphene and has attracted a lot of interests recently. However, the difficulty in fine control and large-scale production of previously proposed graphene catalysts greatly limits their industrial applications. Here we present a novel way to enhance the catalytic activity of graphene, which is highly efficient yet easy to fabricate and control. By first-principles calculations, we show that when the underlying metal substrate is doped with impurities, the catalytic activity of the supported graphene can be drastically enhanced. Graphene supported on a Fe/Ni(111) surface is chosen as a model catalyst, and the chemical reaction of CO oxidation is used to probe the catalytic activity of graphene. When the underlying Fe/Ni(111) substrate is impurity free, the graphene is catalytically inactive. When a Zn atom is doped into the substrate, the catalytic activity of the supported graphene is greatly enhanced, and the reaction barrier of the catalyzed CO oxidation is reduced to less than 0.5 eV. Intriguing reaction mechanism of catalyzed CO oxidation is revealed. These studies suggest a new class of graphene-based catalysts and pave the way for future applications of graphene in solid-state catalysis. PMID:26156332

  12. Synthesis, Characterization, and Catalytic Properties of Novel Single-Site and Nanosized Platinum Catalysts

    SciTech Connect

    Bonati, Matteo L.M.; Douglas, Thomas M.; Gaemers, Sander; Guo, Neng

    2013-01-10

    Novel single-site platinum catalysts have been synthesized by reacting platinum(II) organometallics with partially dehydroxylated silica. The resulting materials have been characterized by various methods such as IR, MAS NMR, and EXAFS. Further, the single-site platinum catalysts were calcined in air to remove the ligand and produce nanosized platinum particles, that were characterized by TEM and H{sub 2} chemisorption. All catalysts were tested for the hydrogenation of toluene. The single-site platinum catalysts were less active than a commercial Pt/SiO{sub 2} catalyst with comparable platinum loading, and this has been ascribed to ligand effects. Conversely, the nanosized platinum catalysts were more active than the commercial Pt/SiO{sub 2} catalyst due to their high dispersion and small particle sizes.

  13. Active sites in char gasification: Final technical report

    SciTech Connect

    Wojtowicz, M.; Lilly, W.D.; Perkins, M.T.; Hradil, G.; Calo, J.M.; Suuberg, E.M.

    1987-09-01

    Among the key variables in the design of gasifiers and combustors is the reactivity of the chars which must be gasified or combusted. Significant loss of unburned char is unacceptable in virtually any process; the provision of sufficient residence time for complete conversion is essential. A very wide range of reactivities are observed, depending upon the nature of the char in a process. The current work focuses on furthering the understanding of gasification reactivities of chars. It has been well established that the reactivity of char to gasification generally depends upon three principal factors: (1) the concentration of ''active sites'' in the char; (2) mass transfer within the char; and (3) the type and concentration of catalytic impurities in the char. The present study primarily addresses the first factor. The subject of this research is the origin, nature, and fate of active sites in chars derived from parent hydrocarbons with coal-like structure. The nature and number of the active sites and their reactivity towards oxygen are examined in ''model'' chars derived from phenol-formaldehyde type resins. How the active sites are lost by the process of thermal annealing during heat treatment of chars are studied, and actual rate for the annealing process is derived. Since intrinsic char reactivities are of primary interest in the present study, a fair amount of attention was given to the model char synthesis and handling so that the effect of catalytic impurities and oxygen-containing functional groups in the chemical structure of the material were minimized, if not completely eliminated. The project would not be considered complete without comparing characteristic features of synthetic chars with kinetic behavior exhibited by natural chars, including coal chars.

  14. Copper on responsive polymer microgels: a recyclable catalyst exhibiting tunable catalytic activity.

    PubMed

    Wu, Qingshi; Cheng, Han; Chang, Aiping; Bai, Xue; Lu, Fan; Wu, Weitai

    2014-11-25

    Copper has been immobilized on a chitosan-based responsive polymer microgel by simply stirring the microgel dispersion with copper sulfate. The ensuing catalyst is highly active for a model azide-alkyne [3+2]-cycloaddition reaction, and can be recycled at least 5 times; the catalytic activity can be tuned via swelling-deswelling transitions of the polymer gels. PMID:25283806

  15. An Active Site Water Network in the Plasminogen Activator Pla from Yersinia pestis

    SciTech Connect

    Eren, Elif; Murphy, Megan; Goguen, Jon; van den Berg, Bert

    2010-08-13

    The plasminogen activator Pla from Yersinia pestis is an outer membrane protease (omptin) that is important for the virulence of plague. Here, we present the high-resolution crystal structure of wild-type, enzymatically active Pla at 1.9 {angstrom}. The structure shows a water molecule located between active site residues D84 and H208, which likely corresponds to the nucleophilic water. A number of other water molecules are present in the active site, linking residues important for enzymatic activity. The R211 sidechain in loop L4 is close to the nucleophilic water and possibly involved in the stabilization of the oxyanion intermediate. Subtle conformational changes of H208 result from the binding of lipopolysaccharide to the outside of the barrel, explaining the unusual dependence of omptins on lipopolysaccharide for activity. The Pla structure suggests a model for the interaction with plasminogen substrate and provides a more detailed understanding of the catalytic mechanism of omptin proteases.

  16. Mixed Inhibition of cPEPCK by Genistein, Using an Extended Binding Site Located Adjacent to Its Catalytic Cleft

    PubMed Central

    Dhanjal, Jaspreet Kaur; Sundar, Durai

    2015-01-01

    Cytosolic phosphoenolpyruvate carboxykinase (cPEPCK) is a critical enzyme involved in gluconeogenesis, glyceroneogenesis and cataplerosis. cPEPCK converts oxaloacetic acid (OAA) into phosphoenol pyruvate (PEP) in the presence of GTP. cPEPCK is known to be associated with type 2 diabetes. Genistein is an isoflavone compound that shows anti-diabetic and anti-obesitic properties. Experimental studies have shown a decrease in the blood glucose level in the presence of genistein by lowering the functional activity of cPEPCK, an enzyme of gluconeogenesis. Using computational techniques such as molecular modeling, molecular docking, molecular dynamics simulation and binding free energy calculations, we identified cPEPCK as a direct target of genistein. We studied the molecular interactions of genistein with three possible conformations of cPEPCK—unbound cPEPCK (u_cPEPCK), GTP bound cPEPCK (GTP_cPEPCK) and GDP bound cPEPCK (GDP_cPEPCK). Binding of genistein was also compared with an already known cPEPCK inhibitor. We analyzed the interactions of genistein with cPEPCK enzyme and compared them with its natural substrate (OAA), product (PEP) and known inhibitor (3-MPA). Our results demonstrate that genistein uses the mechanism of mixed inhibition to block the functional activity of cPEPCK and thus can serve as a potential anti-diabetic and anti-obesity drug candidate. We also identified an extended binding site in the catalytic cleft of cPEPCK which is used by 3-MPA to inhibit cPEPCK non-competitively. We demonstrate that extended binding site of cPEPCK can further be exploited for designing new drugs against cPEPCK. PMID:26528723

  17. Comparison of Two Preparation Methods on Catalytic Activity and Selectivity of Ru-Mo/HZSM5 for Methane Dehydroaromatization

    DOE PAGESBeta

    Petkovic, Lucia M.; Ginosar, Daniel M.

    2014-01-01

    Catalytic performance of Mo/HZSM5 and Ru-Mo/HZSM5 catalysts prepared by vaporization-deposition of molybdenum trioxide and impregnation with ammonium heptamolybdate was analyzed in terms of catalyst activity and selectivity, nitrogen physisorption analyses, temperature-programmed oxidation of carbonaceous residues, and temperature-programmed reduction. Vaporization-deposition rendered the catalyst more selective to ethylene and coke than the catalyst prepared by impregnation. This result was assigned to lower interaction of molybdenum carbide with the zeolite acidic sites.

  18. Iridium ultrasmall nanoparticles, worm-like chain nanowires, and porous nanodendrites: One-pot solvothermal synthesis and catalytic CO oxidation activity

    NASA Astrophysics Data System (ADS)

    Zhang, Tao; Li, Shuai-Chen; Zhu, Wei; Ke, Jun; Yu, Jing-Wen; Zhang, Zhi-Ping; Dai, Lin-Xiu; Gu, Jun; Zhang, Ya-Wen

    2016-06-01

    We report a facile one-pot solvothermal synthesis of monodisperse iridium (Ir) ultrasmall (1.5-2.5 nm in diameter) nanoparticles (NPs), worm-like chain nanowires (NWs), and porous nanodendrites (NDs), for which CO oxidation reaction has been employed as a probe reaction to investigate the effects of nanoparticle size and surface-capping organics on the catalytic activities. Time-dependent experiments revealed that an oriented attachment mechanism induced by the strong adsorption of halide anions (Br- and I-) on specific facet of Ir nanoclusters or by decreasing the reduction rate of Ir precursors with changing their concentrations during the synthesis was responsible for the formation of Ir NWs and NDs. Annealing tests indicated that an O2-H2 atmosphere treatment turned out to be an effective measure to clean up the surface-capping organics of Ir NPs supported on commercial SiO2. Catalytic CO oxidation reaction illustrated that a significant improvement in the catalytic activity of CO oxidation reaction was achieved together with the changing of activation energies after such atmosphere treatment for the supported catalysts of the ultrasmall Ir NPs. It is noteworthy that this enhancement in catalytic activity could be ascribed to the changes in the surface status (including populations of Ir species in metallic and oxidized states, removal of surface capping organics, the variety of active sites, and total effective active site number) for the supported nanocatalysts during the atmosphere treatment.

  19. Redox tuning of the catalytic activity of soluble fumarate reductases from Shewanella.

    PubMed

    Paquete, Catarina M; Saraiva, Ivo H; Louro, Ricardo O

    2014-06-01

    Many enzymes involved in bioenergetic processes contain chains of redox centers that link the protein surface, where interaction with electron donors or acceptors occurs, to a secluded catalytic site. In numerous cases these redox centers can transfer only single electrons even when they are associated to catalytic sites that perform two-electron chemistry. These chains provide no obvious contribution to enhance chemiosmotic energy conservation, and often have more redox centers than those necessary to hold sufficient electrons to sustain one catalytic turnover of the enzyme. To investigate the role of such a redox chain we analyzed the transient kinetics of fumarate reduction by two flavocytochromes c3 of Shewanella species while these enzymes were being reduced by sodium dithionite. These soluble monomeric proteins contain a chain of four hemes that interact with a flavin adenine dinucleotide (FAD) catalytic center that performs the obligatory two electron-two proton reduction of fumarate to succinate. Our results enabled us to parse the kinetic contribution of each heme towards electron uptake and conduction to the catalytic center, and to determine that the rate of fumarate reduction is modulated by the redox stage of the enzyme, which is defined by the number of reduced centers. In both enzymes the catalytically most competent redox stages are those least prevalent in a quasi-stationary condition of turnover. Furthermore, the electron distribution among the redox centers during turnover suggested how these enzymes can play a role in the switch between respiration of solid and soluble terminal electron acceptors in the anaerobic bioenergetic metabolism of Shewanella. PMID:24530355

  20. The Role of Organic Capping Layers of Platinum Nanoparticles in Catalytic Activity of CO Oxidation

    SciTech Connect

    Park, Jeong Y.; Aliaga, Cesar; Renzas, J. Russell; Lee, Hyunjoo; Somorjai, Gabor A.

    2008-12-17

    We report the catalytic activity of colloid platinum nanoparticles synthesized with different organic capping layers. On the molecular scale, the porous organic layers have open spaces that permit the reactant and product molecules to reach the metal surface. We carried out CO oxidation on several platinum nanoparticle systems capped with various organic molecules to investigate the role of the capping agent on catalytic activity. Platinum colloid nanoparticles with four types of capping layer have been used: TTAB (Tetradecyltrimethylammonium Bromide), HDA (hexadecylamine), HDT (hexadecylthiol), and PVP (poly(vinylpyrrolidone)). The reactivity of the Pt nanoparticles varied by 30%, with higher activity on TTAB coated nanoparticles and lower activity on HDT, while the activation energy remained between 27-28 kcal/mol. In separate experiments, the organic capping layers were partially removed using ultraviolet light-ozone generation techniques, which resulted in increased catalytic activity due to the removal of some of the organic layers. These results indicate that the nature of chemical bonding between organic capping layers and nanoparticle surfaces plays a role in determining the catalytic activity of platinum colloid nanoparticles for carbon monoxide oxidation.

  1. Catalytic activity of lime for N{sub 2}O decomposition under coal combustion conditions

    SciTech Connect

    Sasaoka, Eiji; Sada, Norimasa; Hara, Kenichi; Uddin, M.A.; Sakata, Yusaku

    1999-04-01

    To understand the contribution of lime to the abatement of N{sub 2}O emission from fluidized coal combustor, the catalytic activity of the lime for the decomposition of N{sub 2}O under coal combustion conditions was studied. Lime was active for the catalytic decomposition of N{sub 2}O, and its activity was stable in the simulated coal combustion flue gas in the absence of SO{sub 2} at 800 C. The catalytic activity of lime was depressed by the presence of CO{sub 2}, H{sub 2}O, and SO{sub 2}. The affect of the presence of SO{sub 2} seemed to be most important: the catalytic activity of the lime gradually decreased as the degree of sulfation increased, and the specific surface area decreased with the progression of sulfation. From N{sub 2}O pretreatment and temperature-programmed desorption studies on the used lime, it was found that two oxygen species and one species of No desorbed. A surface character change due to sulfation is expected from these gas desorptions. From the relation of the activity to the surface area or the desorption of the gases or both, it was concluded that a decrease in the surface area contributed to the decay of the activity more effectively than the surface character change caused by the sulfation.

  2. Catalytic activity in lithium-treated core–shell MoOx/MoS2 nanowires

    DOE PAGESBeta

    Cummins, Dustin R.; Martinez, Ulises; Kappera, Rajesh; Voiry, Damien; Martinez-Garcia, Alejandro; Jasinski, Jacek; Kelly, Dan; Chhowalla, Manish; Mohite, Aditya D.; Sunkara, Mahendra K.; et al

    2015-09-22

    Significant interest has grown in the development of earth-abundant and efficient catalytic materials for hydrogen generation. Layered transition metal dichalcogenides present opportunities for efficient electrocatalytic systems. Here, we report the modification of 1D MoOx/MoS2 core–shell nanostructures by lithium intercalation and the corresponding changes in morphology, structure, and mechanism of H2 evolution. The 1D nanowires exhibit significant improvement in H2 evolution properties after lithiation, reducing the hydrogen evolution reaction (HER) onset potential by ~50 mV and increasing the generated current density by ~600%. The high electrochemical activity in the nanowires results from disruption of MoS2 layers in the outer shell, leadingmore » to increased activity and concentration of defect sites. This is in contrast to the typical mechanism of improved catalysis following lithium exfoliation, i.e., crystal phase transformation. As a result, these structural changes are verified by a combination of Raman and X-ray photoelectron spectroscopy (XPS).« less

  3. Catalytic activities of Werner protein are affected by adduction with 4-hydroxy-2-nonenal

    PubMed Central

    Czerwińska, Jolanta; Poznański, Jarosław; Dębski, Janusz; Bukowy, Zuzanna; Bohr, Vilhelm A.; Tudek, Barbara; Speina, Elżbieta

    2014-01-01

    4-Hydroxy-2-nonenal (HNE) is a reactive α,β-unsaturated aldehyde generated during oxidative stress and subsequent peroxidation of polyunsaturated fatty acids. Here, Werner protein (WRN) was identified as a novel target for modification by HNE. Werner syndrome arises through mutations in the WRN gene that encodes the RecQ DNA helicase which is critical for maintaining genomic stability. This hereditary disease is associated with chromosomal instability, premature aging and cancer predisposition. WRN appears to participate in the cellular response to oxidative stress and cells devoid of WRN display elevated levels of oxidative DNA damage. We demonstrated that helicase/ATPase and exonuclease activities of HNE-modified WRN protein were inhibited both in vitro and in immunocomplexes purified from the cell extracts. Sites of HNE adduction in human WRN were identified at Lys577, Cys727, His1290, Cys1367, Lys1371 and Lys1389. We applied in silico modeling of the helicase and RQC domains of WRN protein with HNE adducted to Lys577 and Cys727 and provided a potential mechanism of the observed deregulation of the protein catalytic activities. In light of the obtained results, we postulate that HNE adduction to WRN is a post-translational modification, which may affect WRN conformational stability and function, contributing to features and diseases associated with premature senescence. PMID:25170083

  4. Ag–Fe2O3 nanocomposites with enhanced catalytic activity for reduction of 4-nitrophenol

    NASA Astrophysics Data System (ADS)

    Liu, Shiben; Chen, Yingjie; Dong, Lifeng

    2016-07-01

    Hybrid nanostructures can be multifunctional and even possess enhanced properties. Ag–Fe2O3 nanocomposites and Ag nanoparticles (NPs) were fabricated and applied to catalyze the reduction of 4-nitrophenol. Compared with Ag NPs, Ag–Fe2O3 nanocomposites demonstrated enhanced catalytic activities. Furthermore, due to their magnetic properties, Ag–Fe2O3 nanocomposites could be easily separated from the reaction mixture and recycled through an external magnetic field. These findings will help us design hybrid nanostructures with catalytic activity and explore other potential applications of magnetic nanocomposites.

  5. Hematite concave nanocubes and their superior catalytic activity for low temperature CO oxidation

    NASA Astrophysics Data System (ADS)

    Liang, Hanfeng; Jiang, Xinde; Qi, Zhengbing; Chen, Wei; Wu, Zhengtao; Xu, Binbin; Wang, Zhoucheng; Mi, Jinxiao; Li, Qingbiao

    2014-06-01

    Hematite (α-Fe2O3) concave nanocubes bound by high-index {134&cmb.macr;4} and {123&cmb.macr;8} facets were synthesized and their catalytic activity for CO oxidation were also investigated.Hematite (α-Fe2O3) concave nanocubes bound by high-index {134&cmb.macr;4} and {123&cmb.macr;8} facets were synthesized and their catalytic activity for CO oxidation were also investigated. Electronic supplementary information (ESI) available. See DOI: 10.1039/c4nr00552j

  6. Screening Outside the Catalytic Site: Inhibition of Macromolecular Inter-actions Through Structure-Based Virtual Ligand Screening Experiments

    PubMed Central

    Sperandio, Olivier; Miteva, Maria A; Segers, Kenneth; Nicolaes, Gerry A. F; Villoutreix, Bruno O

    2008-01-01

    During these last 15 years, drug discovery strategies have essentially focused on identifying small molecules able to inhibit catalytic sites. However, other mechanisms could be targeted. Protein-protein interactions play crucial roles in a number of biological processes, and, as such, their disruption or stabilization is becoming an area of intense activity. Along the same line, inhibition of protein-membrane could be of major importance in several disease indications. Despite the many challenges associated with the development of such classes of interaction modulators, there has been considerable success in the recent years. Importantly, through the existence of protein hot-spots and the presence of druggable pockets at the macromolecular interfaces or in their vicinities, it has been possible to find small molecule effectors using a variety of screening techniques, including combined virtual ligand-in vitro screening strategy. Indeed such in silico-in vitro protocols emerge as the method of choice to facilitate our quest of novel drug-like compounds or of mechanistic probes aiming at facilitating the understanding of molecular reactions involved in the Health and Disease process. In this review, we comment recent successes of combined in silico-in vitro screening methods applied to modulating macromolecular interactions with a special emphasis on protein-membrane interactions. PMID:18949072

  7. Triosephosphate Isomerase I170V Alters Catalytic Site, Enhances Stability and Induces Pathology in a Drosophila Model of TPI Deficiency

    PubMed Central

    Roland, Bartholomew P.; Amrich, Christopher G.; Kammerer, Charles J.; Stuchul, Kimberly A.; Larsen, Samantha B.; Rode, Sascha; Aslam, Anoshé A.; Heroux, Annie; Wetzel, Ronald; VanDemark, Andrew P.; Palladino, Michael J.

    2014-01-01

    Triosephosphate isomerase (TPI) is a glycolytic enzyme which homodimerizes for full catalytic activity. Mutations of the TPI gene elicit a disease known as TPI Deficiency, a glycolytic enzymopathy noted for its unique severity of neurological symptoms. Evidence suggests that TPI Deficiency pathogenesis may be due to conformational changes of the protein, likely affecting dimerization and protein stability. In this report, we genetically and physically characterize a human disease-associated TPI mutation caused by an I170V substitution. Human TPII170V elicits behavioral abnormalities in Drosophila. An examination of hTPII170V enzyme kinetics revealed this substitution reduced catalytic turnover, while assessments of thermal stability demonstrated an increase in enzyme stability. The crystal structure of the homodimeric I170V mutant reveals changes in the geometry of critical residues within the catalytic pocket. Collectively these data reveal new observations of the structural and kinetic determinants of TPI deficiency pathology, providing new insights into disease pathogenesis. PMID:25463631

  8. Wobble Pairs of the HDV Ribozyme Play Specific Roles in Stabilization of Active Site Dynamics

    PubMed Central

    Sripathi, Kamali N.; Banáš, Pavel; Reblova, Kamila; Šponer, Jiři; Otyepka, Michal

    2015-01-01

    The hepatitis delta virus (HDV) is the only known human pathogen whose genome contains a catalytic RNA motif (ribozyme). The overall architecture of the HDV ribozyme is that of a double-nested pseudoknot, with two GU pairs flanking the active site. Although extensive studies have shown that mutation of either wobble results in decreased catalytic activity, little work has focused on linking these mutations to specific structural effects on catalytic fitness. Here we use molecular dynamics simulations based on an activated structure to probe the active site dynamics as a result of wobble pair mutations. In both wild-type and mutant ribozymes, the in-line fitness of the active site (as a measure of catalytic proficiency) strongly depends on the presence of a C75(N3H3+)N1(O5′) hydrogen bond, which positions C75 as the general acid for the reaction. Our mutational analyses show that each GU wobble supports catalytically fit conformations in distinct ways; the reverse G25U20 wobble promotes high in-line fitness, high occupancy of the C75(N3H3+)G1(O5′) general-acid hydrogen bond and stabilization of the G1U37 wobble, while the G1U37 wobble acts more locally by stabilizing high in-line fitness and the C75(N3H3+)G1(O5′) hydrogen bond. We also find that stable type I A-minor and P1.1 hydrogen bonding above and below the active site, respectively, prevent local structural disorder from spreading and disrupting global conformation. Taken together, our results define specific, often redundant architectural roles for several structural motifs of the HDV ribozyme active site, expanding the known roles of these motifs within all HDV-like ribozymes and other structured RNAs. PMID:25631765

  9. Mimicking enzymatic active sites on surfaces for energy conversion chemistry.

    PubMed

    Gutzler, Rico; Stepanow, Sebastian; Grumelli, Doris; Lingenfelder, Magalí; Kern, Klaus

    2015-07-21

    Metal-organic supramolecular chemistry on surfaces has matured to a point where its underlying growth mechanisms are well understood and structures of defined coordination environments of metal atoms can be synthesized in a controlled and reproducible procedure. With surface-confined molecular self-assembly, scientists have a tool box at hand which can be used to prepare structures with desired properties, as for example a defined oxidation number and spin state of the transition metal atoms within the organic matrix. From a structural point of view, these coordination sites in the supramolecular structure resemble the catalytically active sites of metallo-enzymes, both characterized by metal centers coordinated to organic ligands. Several chemical reactions take place at these embedded metal ions in enzymes and the question arises whether these reactions also take place using metal-organic networks as catalysts. Mimicking the active site of metal atoms and organic ligands of enzymes in artificial systems is the key to understanding the selectivity and efficiency of enzymatic reactions. Their catalytic activity depends on various parameters including the charge and spin configuration in the metal ion, but also on the organic environment, which can stabilize intermediate reaction products, inhibits catalytic deactivation, and serves mostly as a transport channel for the reactants and products and therefore ensures the selectivity of the enzyme. Charge and spin on the transition metal in enzymes depend on the one hand on the specific metal element, and on the other hand on its organic coordination environment. These two parameters can carefully be adjusted in surface confined metal-organic networks, which can be synthesized by virtue of combinatorial mixing of building synthons. Different organic ligands with varying functional groups can be combined with several transition metals and spontaneously assemble into ordered networks. The catalytically active metal

  10. Evolution of a designed retro-aldolase leads to complete active site remodeling

    PubMed Central

    Giger, Lars; Caner, Sami; Obexer, Richard; Kast, Peter; Baker, David; Ban, Nenad; Hilvert, Donald

    2013-01-01

    Evolutionary advances are often fueled by unanticipated innovation. Directed evolution of a computationally designed enzyme suggests that dramatic molecular changes can also drive the optimization of primitive protein active sites. The specific activity of an artificial retro-aldolase was boosted >4,400 fold by random mutagenesis and screening, affording catalytic efficiencies approaching those of natural enzymes. However, structural and mechanistic studies reveal that the engineered catalytic apparatus, consisting of a reactive lysine and an ordered water molecule, was unexpectedly abandoned in favor of a new lysine residue in a substrate binding pocket created during the optimization process. Structures of the initial in silico design, a mechanistically promiscuous intermediate, and one of the most evolved variants highlight the importance of loop mobility and supporting functional groups in the emergence of the new catalytic center. Such internal competition between alternative reactive sites may have characterized the early evolution of many natural enzymes. PMID:23748672

  11. Extreme electric fields power catalysis in the active site of ketosteroid isomerase

    PubMed Central

    Fried, Stephen D.; Bagchi, Sayan; Boxer, Steven G.

    2015-01-01

    Enzymes use protein architecture to impose specific electrostatic fields onto their bound substrates, but the magnitude and catalytic effect of these electric fields have proven difficult to quantify with standard experimental approaches. Using vibrational Stark effect spectroscopy, we found that the active site of the enzyme ketosteroid isomerase (KSI) exerts an extremely large electric field onto the C=O chemical bond that undergoes a charge rearrangement in KSI’s rate-determining step. Moreover, we found that the magnitude of the electric field exerted by the active site strongly correlates with the enzyme’s catalytic rate enhancement, enabling us to quantify the fraction of the catalytic effect that is electrostatic in origin. The measurements described here may help explain the role of electrostatics in many other enzymes and biomolecular systems. PMID:25525245

  12. The importance of hinge sequence for loop function and catalytic activity in the reaction catalyzed by triosephosphate isomerase.

    PubMed

    Xiang, J; Sun, J; Sampson, N S

    2001-04-01

    We have determined the sequence requirements for the N-terminal protein hinge of the active-site lid of triosephosphate isomerase. The codons for the hinge (PVW) were replaced with a genetic library of all possible 8000 amino acid combinations. The most active of these 8000 mutants were selected using in vivo complementation of a triosephosphate isomerase-deficient strain of Escherichia coli, DF502. Approximately 0.3 % of the mutants complement DF502 with an activity that is between 10 and 70 % of wild-type activity. They all contain Pro at the first position. Furthermore, the sequences of these hinge mutants reveal that hydrophobic packing is very important for efficient formation of the enediol intermediate. However, the reduced catalytic activities observed are not due to increased rates of loop opening. To explore the relationship between the N-terminal and C-terminal hinges, three semi-active mutants from the N-terminal hinge selection experiment (PLH, PHS and PTF), and six active C-terminal hinge mutants from previous work (NSS, LWA, YSL, KTK, NPN, KVA) were combined to form 18 "double-hinge" mutants. The activities of these mutants suggest that the N-terminal and C-terminal hinge structures affect one another. It appears that specific side-chain interactions are important for forming a catalytically active enzyme, but not for preventing release of the unstable enediol intermediate from the active site of the enzyme. The independence of intermediate release on amino acid sequence is consistent with the absence of a "universal" hinge sequence in structurally related enzymes. PMID:11286559

  13. Energy-dependent dissociation of ATP from high affinity catalytic sites of beef heart mitochondrial adenosine triphosphatase

    SciTech Connect

    Penefsky, H.S.

    1985-11-05

    Incubation of (gamma-TSP)ATP with a molar excess of the membrane-bound form of mitochondrial ATPase (F1) results in binding of the bulk of the radioactive nucleotide in high affinity catalytic sites (Ka = 10(12) M-1). Subsequent initiation of respiration by addition of succinate or NADH is accompanied by a profound decrease in the affinity for ATP. About one-third of the bound radioactive ATP appears to dissociate, that is, the (gamma-TSP)ATP becomes accessible to hexokinase. The NADH-stimulated dissociation of (gamma-TSP)ATP is energy-dependent since the stimulation is inhibited by uncouplers of oxidative phosphorylation and is prevented by respiratory chain inhibitors. The rate of the energy-dependent dissociation of ATP that occurs in the presence of NADH, ADP, and Pi is commensurate with the measured initial rate of ATP synthesis in NADH-supported oxidative phosphorylation catalyzed by the same submitochondrial particles. Thus, the rate of dissociation of ATP from the high affinity catalytic site of submitochondrial particles meets the criterion of kinetic competency under the conditions of oxidative phosphorylation. These experiments provide evidence in support of the argument that energy conserved during the oxidation of substrates by the respiratory chain can be utilized to reduce the very tight binding of product ATP in high affinity catalytic sites and to promote dissociation of the nucleotide.

  14. Sulphate-activated phosphorylase b: the pH-dependence of catalytic activity.

    PubMed Central

    Zographos, S E; Oikonomakos, N G; Dixon, H B; Griffin, W G; Johnson, L N; Leonidas, D D

    1995-01-01

    The pH-dependence of sulphate-activated phosphorylase b has been studied in the direction of glycogen synthesis. The bell-shaped curve of the pH-dependence of the catalytic constant for the AMP-activated enzyme showed pK values of 6.1 and 7.3, but the curve for the enzyme activated by 0.9 M ammonium sulphate showed a drop of activity on the acid side at much higher pH values. Its bell was centred at pH 7.8 but it was too narrow to be characterized by only two pK values. The narrowness of the curve could be explained by positive co-operativity, but not its unusually steep acid side. We suggest that the fall on the acid side is due to more than one hydronation (addition of H+). The points can be fitted by a curve with two de-activating hydronations and a de-activating dehydronation having identical titration pK values of 7.5, and hence molecular values of 7.0, 7.5 and 8.0. If both 0.9 M ammonium sulphate and 5 mM AMP are added, the bell is as broad as with AMP alone, but is somewhat raised in pH optimum. The results are discussed in the light of new structural data from crystallographic studies on binary complexes of the enzyme. PMID:7654195

  15. Sulphate-activated phosphorylase b: the pH-dependence of catalytic activity.

    PubMed

    Zographos, S E; Oikonomakos, N G; Dixon, H B; Griffin, W G; Johnson, L N; Leonidas, D D

    1995-09-01

    The pH-dependence of sulphate-activated phosphorylase b has been studied in the direction of glycogen synthesis. The bell-shaped curve of the pH-dependence of the catalytic constant for the AMP-activated enzyme showed pK values of 6.1 and 7.3, but the curve for the enzyme activated by 0.9 M ammonium sulphate showed a drop of activity on the acid side at much higher pH values. Its bell was centred at pH 7.8 but it was too narrow to be characterized by only two pK values. The narrowness of the curve could be explained by positive co-operativity, but not its unusually steep acid side. We suggest that the fall on the acid side is due to more than one hydronation (addition of H+). The points can be fitted by a curve with two de-activating hydronations and a de-activating dehydronation having identical titration pK values of 7.5, and hence molecular values of 7.0, 7.5 and 8.0. If both 0.9 M ammonium sulphate and 5 mM AMP are added, the bell is as broad as with AMP alone, but is somewhat raised in pH optimum. The results are discussed in the light of new structural data from crystallographic studies on binary complexes of the enzyme. PMID:7654195

  16. Use of an Improved Matching Algorithm to Select Scaffolds for Enzyme Design Based on a Complex Active Site Model.

    PubMed

    Huang, Xiaoqiang; Xue, Jing; Lin, Min; Zhu, Yushan

    2016-01-01

    Active site preorganization helps native enzymes electrostatically stabilize the transition state better than the ground state for their primary substrates and achieve significant rate enhancement. In this report, we hypothesize that a complex active site model for active site preorganization modeling should help to create preorganized active site design and afford higher starting activities towards target reactions. Our matching algorithm ProdaMatch was improved by invoking effective pruning strategies and the native active sites for ten scaffolds in a benchmark test set were reproduced. The root-mean squared deviations between the matched transition states and those in the crystal structures were < 1.0 Å for the ten scaffolds, and the repacking calculation results showed that 91% of the hydrogen bonds within the active sites are recovered, indicating that the active sites can be preorganized based on the predicted positions of transition states. The application of the complex active site model for de novo enzyme design was evaluated by scaffold selection using a classic catalytic triad motif for the hydrolysis of p-nitrophenyl acetate. Eighty scaffolds were identified from a scaffold library with 1,491 proteins and four scaffolds were native esterase. Furthermore, enzyme design for complicated substrates was investigated for the hydrolysis of cephalexin using scaffold selection based on two different catalytic motifs. Only three scaffolds were identified from the scaffold library by virtue of the classic catalytic triad-based motif. In contrast, 40 scaffolds were identified using a more flexible, but still preorganized catalytic motif, where one scaffold corresponded to the α-amino acid ester hydrolase that catalyzes the hydrolysis and synthesis of cephalexin. Thus, the complex active site modeling approach for de novo enzyme design with the aid of the improved ProdaMatch program is a promising approach for the creation of active sites with high catalytic

  17. Use of an Improved Matching Algorithm to Select Scaffolds for Enzyme Design Based on a Complex Active Site Model

    PubMed Central

    Huang, Xiaoqiang; Xue, Jing; Lin, Min; Zhu, Yushan

    2016-01-01

    Active site preorganization helps native enzymes electrostatically stabilize the transition state better than the ground state for their primary substrates and achieve significant rate enhancement. In this report, we hypothesize that a complex active site model for active site preorganization modeling should help to create preorganized active site design and afford higher starting activities towards target reactions. Our matching algorithm ProdaMatch was improved by invoking effective pruning strategies and the native active sites for ten scaffolds in a benchmark test set were reproduced. The root-mean squared deviations between the matched transition states and those in the crystal structures were < 1.0 Å for the ten scaffolds, and the repacking calculation results showed that 91% of the hydrogen bonds within the active sites are recovered, indicating that the active sites can be preorganized based on the predicted positions of transition states. The application of the complex active site model for de novo enzyme design was evaluated by scaffold selection using a classic catalytic triad motif for the hydrolysis of p-nitrophenyl acetate. Eighty scaffolds were identified from a scaffold library with 1,491 proteins and four scaffolds were native esterase. Furthermore, enzyme design for complicated substrates was investigated for the hydrolysis of cephalexin using scaffold selection based on two different catalytic motifs. Only three scaffolds were identified from the scaffold library by virtue of the classic catalytic triad-based motif. In contrast, 40 scaffolds were identified using a more flexible, but still preorganized catalytic motif, where one scaffold corresponded to the α-amino acid ester hydrolase that catalyzes the hydrolysis and synthesis of cephalexin. Thus, the complex active site modeling approach for de novo enzyme design with the aid of the improved ProdaMatch program is a promising approach for the creation of active sites with high catalytic

  18. Active Sites Environmental Monitoring Program: Program plan

    SciTech Connect

    Ashwood, T.L.; Wickliff, D.S.; Morrissey, C.M.

    1990-10-01

    DOE Order 5820.2A requires that low-level waste (LLW) disposal sites active on or after September 1988 and all transuranic (TRU) waste storage sites be monitored periodically to assure that radioactive contamination does not escape from the waste sites and pose a threat to the public or to the environment. This plan describes such a monitoring program for the active LLW disposal sites in SWSA 6 and the TRU waste storage sites in SWSA 5 North. 14 refs., 8 figs.

  19. Catalytic deactivation of methane steam reforming catalysts. I. Activation

    SciTech Connect

    Agnelli, M.E.; Demicheli, M.C.; Ponzi, E.N.

    1987-08-01

    An alumina-supported catalyst was studied both in its original state and after activation and sintering. Chemical composition and textural properties were determined, and crystalline compounds were identified. Active-phase and support transformations occurring during activation were determined by differential thermoanalysis (DTA), temperature-programmed reduction (TPR), and X-ray diffraction. The catalyst activated by means of various procedures was characterized by measuring crystallite size.

  20. Preclinical Profile of BI 224436, a Novel HIV-1 Non-Catalytic-Site Integrase Inhibitor

    PubMed Central

    Amad, Ma'an; Bailey, Murray D.; Bethell, Richard; Bös, Michael; Bonneau, Pierre; Cordingley, Michael; Coulombe, René; Duan, Jianmin; Edwards, Paul; Faucher, Anne-Marie; Garneau, Michel; Jakalian, Araz; Kawai, Stephen; Lamorte, Louie; LaPlante, Steven; Luo, Laibin; Mason, Steve; Poupart, Marc-André; Rioux, Nathalie; Schroeder, Patricia; Simoneau, Bruno; Tremblay, Sonia; Tsantrizos, Youla; Witvrouw, Myriam; Yoakim, Christiane

    2014-01-01

    BI 224436 is an HIV-1 integrase inhibitor with effective antiviral activity that acts through a mechanism that is distinct from that of integrase strand transfer inhibitors (INSTIs). This 3-quinolineacetic acid derivative series was identified using an enzymatic integrase long terminal repeat (LTR) DNA 3′-processing assay. A combination of medicinal chemistry, parallel synthesis, and structure-guided drug design led to the identification of BI 224436 as a candidate for preclinical profiling. It has antiviral 50% effective concentrations (EC50s) of <15 nM against different HIV-1 laboratory strains and cellular cytotoxicity of >90 μM. BI 224436 also has a low, ∼2.1-fold decrease in antiviral potency in the presence of 50% human serum and, by virtue of a steep dose-response curve slope, exhibits serum-shifted EC95 values ranging between 22 and 75 nM. Passage of virus in the presence of inhibitor selected for either A128T, A128N, or L102F primary resistance substitutions, all mapping to a conserved allosteric pocket on the catalytic core of integrase. BI 224436 also retains full antiviral activity against recombinant viruses encoding INSTI resistance substitutions N155S, Q148H, and E92Q. In drug combination studies performed in cellular antiviral assays, BI 224436 displays an additive effect in combination with most approved antiretrovirals, including INSTIs. BI 224436 has drug-like in vitro absorption, distribution, metabolism, and excretion (ADME) properties, including Caco-2 cell permeability, solubility, and low cytochrome P450 inhibition. It exhibited excellent pharmacokinetic profiles in rat (clearance as a percentage of hepatic flow [CL], 0.7%; bioavailability [F], 54%), monkey (CL, 23%; F, 82%), and dog (CL, 8%; F, 81%). Based on the excellent biological and pharmacokinetic profile, BI 224436 was advanced into phase 1 clinical trials. PMID:24663024

  1. Active-site mobility revealed by the crystal structure of arylmalonate decarboxylase from Bordetella bronchiseptica.

    PubMed

    Kuettner, E Bartholomeus; Keim, Antje; Kircher, Markus; Rosmus, Susann; Sträter, Norbert

    2008-03-21

    Arylmalonate decarboxylase (AMDase) from Bordetella bronchiseptica catalyzes the enantioselective decarboxylation of arylmethylmalonates without the need for an organic cofactor or metal ion. The decarboxylation reaction is of interest for the synthesis of fine chemicals. As basis for an analysis of the catalytic mechanism of AMDase and for a rational enzyme design, we determined the X-ray structure of the enzyme up to 1.9 A resolution. Like the distantly related aspartate or glutamate racemases, AMDase has an aspartate transcarbamoylase fold consisting of two alpha/beta domains related by a pseudo dyad. However, the domain orientation of AMDase differs by about 30 degrees from that of the glutamate racemases, and also significant differences in active-site structures are observed. In the crystals, four independent subunits showing different conformations of active-site loops are present. This finding is likely to reflect the active-site mobility necessary for catalytic activity. PMID:18258259

  2. IFCC primary reference procedures for the measurement of catalytic activity concentrations of enzymes at 37 degrees C. Part 1. The concept of reference procedures for the measurement of catalytic activity concentrations of enzymes.

    PubMed

    Siekmann, Lothar; Bonora, Roberto; Burtis, Carl A; Ceriotti, Ferruccio; Clerc-Renaud, Pascale; Férard, Georges; Ferrero, Carlo A; Forest, Jean-Claude; Franck, Paul F H; Gella, F Javier; Hoelzel, Wieland; Jørgensen, Poul Jørgen; Kanno, Takashi; Kessner, Art; Klauke, Rainer; Kristiansen, Nina; Lessinger, Jean-Marc; Linsinger, Thomas P J; Misaki, Hideo; Mueller, Mathias M; Panteghini, Mauro; Pauwels, Jean; Schiele, Françoise; Schimmel, Heinz G; Vialle, Arlette; Weidemann, Gerhard; Schumann, Gerhard

    2002-06-01

    This paper is the first in a series dealing with reference procedures for the measurement of catalytic activity concentrations of enzymes at 37 degrees C and with the certification of reference preparations. Other parts deal with: Part 2. Reference Procedure for the Measurement of Catalytic Concentration of Creatine Kinase; Part 3. Reference Procedure for the Measurement of Catalytic Concentration of Lactate Dehydrogenase; Part 4. Reference Procedure for the Measurement of Catalytic Concentration of Alanine Aminotransferase; Part 5. Reference Procedure for the Measurement of Catalytic Concentration of Aspartate Aminotransferase; Part 6. Reference Procedure for the Measurement of Catalytic fication of Four Reference Materials for the Determination of Enzymatic Activity of y-Glutamyltransferase, Lactate Dehydrogenase, Alanine Aminotransferase and Creatine Kinase at 37 degrees C. A document describing the determination of preliminary reference values is also in preparation. PMID:12211661

  3. Changed membrane integration and catalytic site conformation are two mechanisms behind the increased Aβ42/Aβ40 ratio by presenilin 1 familial Alzheimer-linked mutations.

    PubMed

    Wanngren, Johanna; Lara, Patricia; Ojemalm, Karin; Maioli, Silvia; Moradi, Nasim; Chen, Lu; Tjernberg, Lars O; Lundkvist, Johan; Nilsson, IngMarie; Karlström, Helena

    2014-01-01

    The enzyme complex γ-secretase generates amyloid β-peptide (Aβ), a 37-43-residue peptide associated with Alzheimer disease (AD). Mutations in presenilin 1 (PS1), the catalytical subunit of γ-secretase, result in familial AD (FAD). A unifying theme among FAD mutations is an alteration in the ratio Aβ species produced (the Aβ42/Aβ40 ratio), but the molecular mechanisms responsible remain elusive. In this report we have studied the impact of several different PS1 FAD mutations on the integration of selected PS1 transmembrane domains and on PS1 active site conformation, and whether any effects translate to a particular amyloid precursor protein (APP) processing phenotype. Most mutations studied caused an increase in the Aβ42/Aβ40 ratio, but via different mechanisms. The mutations that caused a particular large increase in the Aβ42/Aβ40 ratio did also display an impaired APP intracellular domain (AICD) formation and a lower total Aβ production. Interestingly, seven mutations close to the catalytic site caused a severely impaired integration of proximal transmembrane/hydrophobic sequences into the membrane. This structural defect did not correlate to a particular APP processing phenotype. Six selected FAD mutations, all of which exhibited different APP processing profiles and impact on PS1 transmembrane domain integration, were found to display an altered active site conformation. Combined, our data suggest that FAD mutations affect the PS1 structure and active site differently, resulting in several complex APP processing phenotypes, where the most aggressive mutations in terms of increased Aβ42/Aβ40 ratio are associated with a decrease in total γ-secretase activity. PMID:24918054

  4. A catalytic role for threonine-12 of E. coli asparaginase II as established by site-directed mutagenesis.

    PubMed

    Harms, E; Wehner, A; Aung, H P; Röhm, K H

    1991-07-01

    A threonine-12 to alanine mutant of E. coli asparaginase II (EC 3.5.1.1) has less than 0.01% of the activity of wild-type enzyme. Both tertiary and quaternary structure of the enzyme are essentially unaffected by the mutation; thus the activity loss seems to be the result of a direct impairment of catalytic function. As aspartate is still bound by the mutant enzyme, Thr-12 appears not be involved in substrate binding. PMID:1906013

  5. Studies relevant to the catalytic activation of carbon monoxide

    SciTech Connect

    Ford, P.C.

    1992-06-04

    Research activity during the 1991--1992 funding period has been concerned with the following topics relevant to carbon monoxide activation. (1) Exploratory studies of water gas shift catalysts heterogenized on polystyrene based polymers. (2) Mechanistic investigation of the nucleophilic activation of CO in metal carbonyl clusters. (3) Application of fast reaction techniques to prepare and to investigate reactive organometallic intermediates relevant to the activation of hydrocarbons toward carbonylation and to the formation of carbon-carbon bonds via the migratory insertion of CO into metal alkyl bonds.

  6. Localization of the binding site of tissue-type plasminogen activator to fibrin.

    PubMed Central

    Ichinose, A; Takio, K; Fujikawa, K

    1986-01-01

    Functionally active A and B chains were separated from a two-chain form of recombinant tissue-type plasminogen activator after mild reduction and alkylation. The A chain was found to be responsible for the binding to lysine-Sepharose or fibrin and the B chain contained the catalytic activity of tissue-type plasminogen activator. An extensive reduction of two-chain tissue-type plasminogen activator, however, destroyed both the binding and catalytic activities. A thermolytic fragment, Fr. 1, of tissue-type plasminogen activator that contained a growth factor and two kringle segments retained its lysine binding activity. Additional thermolytic cleavages in the kringle-2 segment of Fr. 1 caused a total loss of the binding activity. These results indicated that the binding site of tissue-type plasminogen activator to fibrin was located in the kringle-2 segment. Images PMID:3088041

  7. Synthesis of concave gold nanocuboids with high-index facets and their enhanced catalytic activity.

    PubMed

    Li, Lidong; Peng, Yi; Yue, Yonghai; Hu, Ye; Liang, Xiu; Yin, Penggang; Guo, Lin

    2015-07-25

    Novel concave gold nanocuboids bounded by 24 high-index {611} facets are synthesized using the seed-mediated growth method via an overgrowth mechanism. The as-synthesized products demonstrated greatly enhanced catalytic activity for the electro-oxidation of glucose and the reduction of 4-nitrothiophenol (4-NTP) under a laser. PMID:26097908

  8. A reconstruction strategy to synthesize mesoporous SAPO molecular sieve single crystals with high MTO catalytic activity.

    PubMed

    Wang, Chan; Yang, Miao; Li, Mingrun; Xu, Shutao; Yang, Yue; Tian, Peng; Liu, Zhongmin

    2016-05-11

    Mesoporous SAPO-34 single crystals with tunable porosity and Si content have been fast synthesized within 4 hours by a reconstruction strategy, which show excellent hydrothermal stability and MTO catalytic activity. This new strategy is further proven to be applicable to prepare other mesoporous SAPO molecular sieve single crystals. PMID:27101359

  9. Enantioselective Synthesis of a PKC Inhibitor via Catalytic C-HBond Activation

    SciTech Connect

    Wilson, Rebecca M.; Thalji, Reema K.; Bergman, Robert G.; Ellman,Jonathan A.

    2006-02-26

    The syntheses of two biologically active molecules possessing dihydropyrroloindole cores (1 and 2) were completed using rhodium-catalyzed imine-directed C-H bond functionalization, with the second of these molecules containing a stereocenter that can be set with 90% ee during cyclization using chiral nonracemic phosphoramidite ligands. Catalytic decarbonylation and direct indole/maleimide coupling provide efficient access to 2.

  10. A highly sensitive technique for detecting catalytically active nanoparticles against a background of general workplace aerosols

    NASA Astrophysics Data System (ADS)

    Neubauer, N.; Weis, F.; Binder, A.; Seipenbusch, M.; Kasper, G.

    2011-07-01

    A new measurement technique was studied using catalysis to specifically detect airborne nanoparticles in presence of background particles in the workplace air. Catalytically active nanoparticles produced by spark discharge were used as aerosol catalysts. According to these particles suitable catalytic test reactions were chosen and investigated by two different approaches: catalysis on airborne nanoparticles and catalysis on deposited nanoparticles. The results indicate that catalysis is applicable for the specific measurement of nanoparticles in the workplace air. Catalysis on airborne particles is suitable for the specific detection of very active nanoparticles, e.g. platinum or nickel, at high concentrations of about 107 #/cm3. The approach of catalysis on deposited particles is better suited for nanoparticle aerosols at low concentrations, for slow catalytic reactions or less active nanoparticles like iron oxide (Fe2O3). On the basis of the experimental results detection limits in the range of μg or even ng were calculated which assure the good potential of catalysis for the specific detection of nanoparticles in the workplace air based on their catalytic activity.

  11. Reversible amorphization and the catalytically active state of crystalline Co3O4 during oxygen evolution.

    PubMed

    Bergmann, Arno; Martinez-Moreno, Elias; Teschner, Detre; Chernev, Petko; Gliech, Manuel; de Araújo, Jorge Ferreira; Reier, Tobias; Dau, Holger; Strasser, Peter

    2015-01-01

    Water splitting catalysed by earth-abundant materials is pivotal for global-scale production of non-fossil fuels, yet our understanding of the active catalyst structure and reactivity is still insufficient. Here we report on the structurally reversible evolution of crystalline Co3O4 electrocatalysts during oxygen evolution reaction identified using advanced in situ X-ray techniques. At electrode potentials facilitating oxygen evolution, a sub-nanometre shell of the Co3O4 is transformed into an X-ray amorphous CoOx(OH)y which comprises di-μ-oxo-bridged Co(3+/4+) ions. Unlike irreversible amorphizations, here, the formation of the catalytically-active layer is reversed by re-crystallization upon return to non-catalytic electrode conditions. The Co3O4 material thus combines the stability advantages of a controlled, stable crystalline material with high catalytic activity, thanks to the structural flexibility of its active amorphous oxides. We propose that crystalline oxides may be tailored for generating reactive amorphous surface layers at catalytic potentials, just to return to their stable crystalline state under rest conditions. PMID:26456525

  12. Open-mouthed hybrid microcapsules with elevated enzyme loading and enhanced catalytic activity.

    PubMed

    Shi, Jiafu; Zhang, Shaohua; Wang, Xiaoli; Jiang, Zhongyi

    2014-10-25

    Open-mouthed hybrid microcapsules (HMCs) are synthesized through a hard-templating method. When utilized for enzyme immobilization and enzymatic catalysis, the open-mouthed HMCs show high enzyme loading capability, enhanced catalytic activity and desirable recycling stability, due to their fully exposed outer and inner surfaces. PMID:25189769

  13. Reversible amorphization and the catalytically active state of crystalline Co3O4 during oxygen evolution

    NASA Astrophysics Data System (ADS)

    Bergmann, Arno; Martinez-Moreno, Elias; Teschner, Detre; Chernev, Petko; Gliech, Manuel; de Araújo, Jorge Ferreira; Reier, Tobias; Dau, Holger; Strasser, Peter

    2015-10-01

    Water splitting catalysed by earth-abundant materials is pivotal for global-scale production of non-fossil fuels, yet our understanding of the active catalyst structure and reactivity is still insufficient. Here we report on the structurally reversible evolution of crystalline Co3O4 electrocatalysts during oxygen evolution reaction identified using advanced in situ X-ray techniques. At electrode potentials facilitating oxygen evolution, a sub-nanometre shell of the Co3O4 is transformed into an X-ray amorphous CoOx(OH)y which comprises di-μ-oxo-bridged Co3+/4+ ions. Unlike irreversible amorphizations, here, the formation of the catalytically-active layer is reversed by re-crystallization upon return to non-catalytic electrode conditions. The Co3O4 material thus combines the stability advantages of a controlled, stable crystalline material with high catalytic activity, thanks to the structural flexibility of its active amorphous oxides. We propose that crystalline oxides may be tailored for generating reactive amorphous surface layers at catalytic potentials, just to return to their stable crystalline state under rest conditions.

  14. Reversible amorphization and the catalytically active state of crystalline Co3O4 during oxygen evolution

    PubMed Central

    Bergmann, Arno; Martinez-Moreno, Elias; Teschner, Detre; Chernev, Petko; Gliech, Manuel; de Araújo, Jorge Ferreira; Reier, Tobias; Dau, Holger; Strasser, Peter

    2015-01-01

    Water splitting catalysed by earth-abundant materials is pivotal for global-scale production of non-fossil fuels, yet our understanding of the active catalyst structure and reactivity is still insufficient. Here we report on the structurally reversible evolution of crystalline Co3O4 electrocatalysts during oxygen evolution reaction identified using advanced in situ X-ray techniques. At electrode potentials facilitating oxygen evolution, a sub-nanometre shell of the Co3O4 is transformed into an X-ray amorphous CoOx(OH)y which comprises di-μ-oxo-bridged Co3+/4+ ions. Unlike irreversible amorphizations, here, the formation of the catalytically-active layer is reversed by re-crystallization upon return to non-catalytic electrode conditions. The Co3O4 material thus combines the stability advantages of a controlled, stable crystalline material with high catalytic activity, thanks to the structural flexibility of its active amorphous oxides. We propose that crystalline oxides may be tailored for generating reactive amorphous surface layers at catalytic potentials, just to return to their stable crystalline state under rest conditions. PMID:26456525

  15. Confined iron nanowires enhance the catalytic activity of carbon nanotubes in the aerobic oxidation of cyclohexane.

    PubMed

    Yang, Xixian; Yu, Hao; Peng, Feng; Wang, Hongjuan

    2012-07-01

    Inside job: New applications of carbon materials pave the way towards greener chemical syntheses. The encapsulation of metallic Fe within CNTs improves electron transfer between the metal and the CNTs. The resulting material offers a high catalytic activity and easy magnetic separation of catalyst in the heterogeneous selective oxidation of cyclohexane. PMID:22488987

  16. Aligned carbon nanotube with electro-catalytic activity for oxygen reduction reaction

    DOEpatents

    Liu, Di-Jia; Yang, Junbing; Wang, Xiaoping

    2010-08-03

    A catalyst for an electro-chemical oxygen reduction reaction (ORR) of a bundle of longitudinally aligned carbon nanotubes having a catalytically active transition metal incorporated longitudinally in said nanotubes. A method of making an electro-chemical catalyst for an oxygen reduction reaction (ORR) having a bundle of longitudinally aligned carbon nanotubes with a catalytically active transition metal incorporated throughout the nanotubes, where a substrate is in a first reaction zone, and a combination selected from one or more of a hydrocarbon and an organometallic compound containing an catalytically active transition metal and a nitrogen containing compound and an inert gas and a reducing gas is introduced into the first reaction zone which is maintained at a first reaction temperature for a time sufficient to vaporize material therein. The vaporized material is then introduced to a second reaction zone maintained at a second reaction temperature for a time sufficient to grow longitudinally aligned carbon nanotubes over the substrate with a catalytically active transition metal incorporated throughout the nanotubes.

  17. HIGH-THROUGHPUT IDENTIFICATION OF CATALYTIC REDOX-ACTIVE CYSTEINE RESIDUES

    EPA Science Inventory

    Cysteine (Cys) residues often play critical roles in proteins; however, identification of their specific functions has been limited to case-by-case experimental approaches. We developed a procedure for high-throughput identification of catalytic redox-active Cys in proteins by se...

  18. Switchable catalytic activity: selenium-containing peptides with redox-controllable self-assembly properties.

    PubMed

    Miao, Xiaoming; Cao, Wei; Zheng, Wenting; Wang, Jingyu; Zhang, Xiaoli; Gao, Jie; Yang, Chengbiao; Kong, Deling; Xu, Huaping; Wang, Ling; Yang, Zhimou

    2013-07-22

    Mimicking nature: The reversible formation of self-assembled nanostructures of selenium-containing peptides can be controlled by redox triggers (see scheme, VC = vitamin C). As a consequence, the catalytic activity of these peptides is switchable. These results should lead to the development of nature-mimicking smart materials with promising properties. PMID:23784972

  19. Self-propulsion and interactions of catalytic particles in a chemically active medium

    NASA Astrophysics Data System (ADS)

    Banigan, Edward J.; Marko, John F.

    2016-01-01

    Enzymatic "machines," such as catalytic rods or colloids, can self-propel and interact by generating gradients of their substrates. We theoretically investigate the behaviors of such machines in a chemically active environment where their catalytic substrates are continuously synthesized and destroyed, as occurs in living cells. We show how the kinetic properties of the medium modulate self-propulsion and pairwise interactions between machines, with the latter controlled by a tunable characteristic interaction range analogous to the Debye screening length in an electrolytic solution. Finally, we discuss the effective force arising between interacting machines and possible biological applications, such as partitioning of bacterial plasmids.

  20. The nature of catalytically active complexes of Ziegler-type systems based on iron subgroup elements

    SciTech Connect

    Brodskii, A.R.; Noskova, N.F.

    1995-02-01

    Complexation processes that occur in Ziegler-type systems on the basis of the carboxylate compounds of elements belonging mainly to the Iron Subgroup are investigated. The influence of genesis on the composition and structure of the complexes forming in the catalytic systems is demonstrated. A general scheme to describe the interaction of the catalyst components depending on their formation conditions is proposed. It is established that, along with other complexes, polynuclear associated species are present in the catalysts and play a decisive role in the catalytic activity of the investigated systems.

  1. Non-catalytic site HIV-1 integrase inhibitors disrupt core maturation and induce a reverse transcription block in target cells.

    PubMed

    Balakrishnan, Mini; Yant, Stephen R; Tsai, Luong; O'Sullivan, Christopher; Bam, Rujuta A; Tsai, Angela; Niedziela-Majka, Anita; Stray, Kirsten M; Sakowicz, Roman; Cihlar, Tomas

    2013-01-01

    HIV-1 integrase (IN) is the target for two classes of antiretrovirals: i) the integrase strand-transfer inhibitors (INSTIs) and ii) the non-catalytic site integrase inhibitors (NCINIs). NCINIs bind at the IN dimer interface and are thought to interfere primarily with viral DNA (vDNA) integration in the target cell by blocking IN-vDNA assembly as well as the IN-LEDGF/p75 interaction. Herein we show that treatment of virus-producing cells, but not of mature virions or target cells, drives NCINI antiviral potency. NCINIs target an essential late-stage event in HIV replication that is insensitive to LEDGF levels in the producer cells. Virus particles produced in the presence of NCINIs displayed normal Gag-Pol processing and endogenous reverse transcriptase activity, but were defective at initiating vDNA synthesis following entry into the target cell. NCINI-resistant virus carrying a T174I mutation in the IN dimer interface was less sensitive to the compound-induced late-stage effects, including the reverse transcription block. Wild-type, but not T174I virus, produced in the presence of NCINIs exhibited striking defects in core morphology and an increased level of IN oligomers that was not observed upon treatment of mature cell-free particles. Collectively, these results reveal that NCINIs act through a novel mechanism that is unrelated to the previously observed inhibition of IN activity or IN-LEDGF interaction, and instead involves the disruption of an IN function during HIV-1 core maturation and assembly. PMID:24040198

  2. Non-Catalytic Site HIV-1 Integrase Inhibitors Disrupt Core Maturation and Induce a Reverse Transcription Block in Target Cells

    PubMed Central

    Tsai, Luong; O’Sullivan, Christopher; Bam, Rujuta A.; Tsai, Angela; Niedziela-Majka, Anita; Stray, Kirsten M.; Sakowicz, Roman; Cihlar, Tomas

    2013-01-01

    HIV-1 integrase (IN) is the target for two classes of antiretrovirals: i) the integrase strand-transfer inhibitors (INSTIs) and ii) the non-catalytic site integrase inhibitors (NCINIs). NCINIs bind at the IN dimer interface and are thought to interfere primarily with viral DNA (vDNA) integration in the target cell by blocking IN-vDNA assembly as well as the IN-LEDGF/p75 interaction. Herein we show that treatment of virus-producing cells, but not of mature virions or target cells, drives NCINI antiviral potency. NCINIs target an essential late-stage event in HIV replication that is insensitive to LEDGF levels in the producer cells. Virus particles produced in the presence of NCINIs displayed normal Gag-Pol processing and endogenous reverse transcriptase activity, but were defective at initiating vDNA synthesis following entry into the target cell. NCINI-resistant virus carrying a T174I mutation in the IN dimer interface was less sensitive to the compound-induced late-stage effects, including the reverse transcription block. Wild-type, but not T174I virus, produced in the presence of NCINIs exhibited striking defects in core morphology and an increased level of IN oligomers that was not observed upon treatment of mature cell-free particles. Collectively, these results reveal that NCINIs act through a novel mechanism that is unrelated to the previously observed inhibition of IN activity or IN-LEDGF interaction, and instead involves the disruption of an IN function during HIV-1 core maturation and assembly. PMID:24040198

  3. Evidence of the Participation of Remote Residues in the Catalytic Activity of Co-Type Nitrile Hydratase from Pseudomonas putida

    SciTech Connect

    Brodkin, Heather R.; Novak, Walter R.P.; Milne, Amy C.; D’Aquino, J. Alejandro; Karabacak, N.M.; Goldberg, Ilana G.; Agar, Jeffrey N.; Payne, Mark S.; Petsko, Gregory A.; Ondrechen, Mary Jo; Ringe, Dagmar

    2011-09-28

    Active sites may be regarded as layers of residues, whereby the residues that interact directly with substrate also interact with residues in a second shell and these in turn interact with residues in a third shell. These residues in the second and third layers may have distinct roles in maintaining the essential chemical properties of the first-shell catalytic residues, particularly their spatial arrangement relative to the substrate binding pocket, and their electrostatic and dynamic properties. The extent to which these remote residues participate in catalysis and precisely how they affect first-shell residues remains unexplored. To improve our understanding of the roles of second- and third-shell residues in catalysis, we used THEMATICS to identify residues in the second and third shells of the Co-type nitrile hydratase from Pseudomonas putida (ppNHase) that may be important for catalysis. Five of these predicted residues, and three additional, conserved residues that were not predicted, have been conservatively mutated, and their effects have been studied both kinetically and structurally. The eight residues have no direct contact with the active site metal ion or bound substrate. These results demonstrate that three of the predicted second-shell residues ({alpha}-Asp164, {beta}-Glu56, and {beta}-His147) and one predicted third-shell residue ({beta}-His71) have significant effects on the catalytic efficiency of the enzyme. One of the predicted residues ({alpha}-Glu168) and the three residues not predicted ({alpha}-Arg170, {alpha}-Tyr171, and {beta}-Tyr215) do not have any significant effects on the catalytic efficiency of the enzyme.

  4. Evidence for Participation of Remote Residues in the Catalytic Activity of Co-type Nitrile Hydratase from Pseudomonas putida†

    PubMed Central

    Brodkin, Heather R.; Novak, Walter R. P.; Milne, Amy C.; D’Aquino, J. Alejandro; Karabacak, N. M.; Agar, Jeffrey N.; Payne, Mark S.; Petsko, Gregory A.; Ondrechen, Mary Jo; Ringe, Dagmar

    2012-01-01

    Active sites may be regarded as layers of residues, whereby the residues that interact directly with substrate also interact with residues in a second shell, and these in turn interact with residues in a third shell. These residues in the second and third layers may have distinct roles in maintaining the essential chemical properties of the first-shell catalytic residues, particularly their spatial arrangement relative to the substrate binding pocket, and their electrostatic and dynamic properties. The extent to which these remote residues participate in catalysis and precisely how they affect first-shell residues remains unexplored. In order to better understand the roles of second- and third-shell residues in catalysis, we used THEMATICS to identify residues in the second- and third-shells of the Co-type nitrile hydratase from Pseudomonas putida (ppNHase) that may be important for catalysis. Five of these predicted residues, plus three additional, conserved residues that were not predicted, have been conservatively mutated, and their effects studied both kinetically and structurally. All of these eight residues have no direct contact with the active site metal ion or bound substrate. These results demonstrate that three of the predicted second-shell residues, α-Asp164, β-Glu56, and β-His147, and one predicted third-shell residue β-His71, have significant effects on the catalytic efficiency of the enzyme. One of the predicted residues, α-Glu168, and the three residues not predicted, α-Arg170, α-Tyr171, and β-Tyr215, do not show any significant effects on the catalytic efficiency of the enzyme. PMID:21473592

  5. Comparison of three microbial hosts for the expression of an active catalytic scFv.

    PubMed

    Robin, Sylvain; Petrov, Kliment; Dintinger, Thierry; Kujumdzieva, Anna; Tellier, Charles; Dion, Michel

    2003-01-01

    Antibodies represent an interesting protein framework on which catalytic functions can be grafted. In previous studies, we have reported the characterization of the catalytic antibody 4B2 obtained on the basis of the "bait and switch" strategy which catalyzes two different chemical reactions: the allylic isomerization of beta,gamma-unsaturated ketones and the Kemp elimination. We have cloned the antibody 4B2 and expressed it as a single-chain Fv (scFv) fragment in different expression systems, Escherichia coli and two yeasts species, in order to elicit the most suitable system to study its catalytic activity. The scFv4B2 was secreted as an active form in the culture medium of Pichia pastoris and Kluyveromyces lactis, which led respectively to 4 and 1.3mg/l after purification. In E. coli, different strategies were investigated to increase the cytoplasmic soluble fraction, which resulted, in all cases, in the expression of a low amount of functional antibodies. By contrast, substantial amount of scFv4B2 could be purified when it was expressed as inclusion bodies (12mg/l) and submitted to an in vitro refolding process. Its catalytic activity was measured and proved to be comparable to that of the whole IgG. However, the instability of the scFv4B2 in solution prevented from an exhaustive characterization of its activity and stabilization of this protein appears to be essential before designing strategies to improve its catalytic activity. PMID:12531284

  6. Improving the thermostability and catalytic efficiency of Bacillus deramificans pullulanase by site-directed mutagenesis.

    PubMed

    Duan, Xuguo; Chen, Jian; Wu, Jing

    2013-07-01

    Pullulanase (EC 3.2.1.41) is a well-known starch-debranching enzyme. Its instability and low catalytic efficiency are the major factors preventing its widespread application. To address these issues, Asp437 and Asp503 of the pullulanase from Bacillus deramificans were selected in this study as targets for site-directed mutagenesis based on a structure-guided consensus approach. Four mutants (carrying the mutations D503F, D437H, D503Y, and D437H/D503Y) were generated and characterized in detail. The results showed that the D503F, D437H, and D503Y mutants had an optimum temperature of 55°C and a pH optimum of 4.5, similar to that of the wild-type enzyme. However, the half-lives of the mutants at 60°C were twice as long as that of the wild-type enzyme. In addition, the D437H/D503Y double mutant displayed a larger shift in thermostability, with an optimal temperature of 60°C and a half-life at 60°C of more than 4.3-fold that of the wild-type enzyme. Kinetic studies showed that the Km values for the D503F, D437H, D503Y, and D437H/D503Y mutants decreased by 7.1%, 11.4%, 41.4%, and 45.7% and the Kcat/Km values increased by 10%, 20%, 140%, and 100%, respectively, compared to those of the wild-type enzyme. Mechanisms that could account for these enhancements were explored. Moreover, in conjunction with the enzyme glucoamylase, the D503Y and D437H/D503Y mutants exhibited an improved reaction rate and glucose yield during starch hydrolysis compared to those of the wild-type enzyme, confirming the enhanced properties of the mutants. The mutants generated in this study have potential applications in the starch industry. PMID:23624477

  7. Improving the Thermostability and Catalytic Efficiency of Bacillus deramificans Pullulanase by Site-Directed Mutagenesis

    PubMed Central

    Duan, Xuguo; Chen, Jian

    2013-01-01

    Pullulanase (EC 3.2.1.41) is a well-known starch-debranching enzyme. Its instability and low catalytic efficiency are the major factors preventing its widespread application. To address these issues, Asp437 and Asp503 of the pullulanase from Bacillus deramificans were selected in this study as targets for site-directed mutagenesis based on a structure-guided consensus approach. Four mutants (carrying the mutations D503F, D437H, D503Y, and D437H/D503Y) were generated and characterized in detail. The results showed that the D503F, D437H, and D503Y mutants had an optimum temperature of 55°C and a pH optimum of 4.5, similar to that of the wild-type enzyme. However, the half-lives of the mutants at 60°C were twice as long as that of the wild-type enzyme. In addition, the D437H/D503Y double mutant displayed a larger shift in thermostability, with an optimal temperature of 60°C and a half-life at 60°C of more than 4.3-fold that of the wild-type enzyme. Kinetic studies showed that the Km values for the D503F, D437H, D503Y, and D437H/D503Y mutants decreased by 7.1%, 11.4%, 41.4%, and 45.7% and the Kcat/Km values increased by 10%, 20%, 140%, and 100%, respectively, compared to those of the wild-type enzyme. Mechanisms that could account for these enhancements were explored. Moreover, in conjunction with the enzyme glucoamylase, the D503Y and D437H/D503Y mutants exhibited an improved reaction rate and glucose yield during starch hydrolysis compared to those of the wild-type enzyme, confirming the enhanced properties of the mutants. The mutants generated in this study have potential applications in the starch industry. PMID:23624477

  8. Two-dimensional structure Au nanosheets are super active for the catalytic reduction of 4-nitrophenol.

    PubMed

    Zhang, Yan; Cui, Zhimin; Li, Lidong; Guo, Lin; Yang, Shihe

    2015-06-14

    Two-dimensional structure Au nanosheets with a polygon morphology and controlled thicknesses of ∼15 nm, ∼35 nm, and ∼50 nm were successfully synthesized by a one-step solution reduction method. Scanning and transmission electron microscopy (SEM and TEM), selected area electron diffraction (SEAD) analyses, and X-ray diffraction (XRD) were used to thoroughly study the structure and the formation mechanism of the nanosheets. The catalytic activity of the Au nanosheets was investigated for the reduction of 4-nitrophenol (4-NP) by UV-visible absorption spectroscopy. Against all expectation, the Au nanosheets with such a big lateral (more than 1 μm) size exhibited superior catalytic activity on the selective reduction of 4-nitrophenol (4-NP) to 4-aminophenol (4-AP) in the presence of NaBH4. On the other hand, the catalytic activity does closely depend on the thickness of the nanosheets; that is, it decreases with increasing thickness. The reaction can be completed in less than 1 min when catalyzed by Au nanosheets about 15 nm thick. The 100% conversion efficiency was further demonstrated after two catalytic cycles with the thinnest Au nanosheets. PMID:25971868

  9. A computational analysis of the structural determinants of APOBEC3's catalytic activity and vulnerability to HIV-1 Vif

    PubMed Central

    Shandilya, M.D. Shivender; Bohn, Markus-Frederik; Schiffer, Celia A.

    2016-01-01

    APOBEC3s (A3) are Zn2+ dependent cytidine deaminases with diverse biological functions and implications for cancer and immunity. Four of the seven human A3s restrict HIV by 'hypermutating' the reverse-transcribed viral genomic DNA. HIV Virion Infectivity Factor (Vif) counters this restriction by targeting A3s to proteasomal degradation. However, there is no apparent correlation between catalytic activity, Vif binding, and sequence similarity between A3 domains. Our comparative structural analysis reveals features required for binding Vif and features influencing polynucleotide deaminase activity in A3 proteins. All Vif-binding A3s share a negatively charged surface region that includes residues previously implicated in binding the highly-positively charged Vif. Additionally, catalytically active A3s share a positively charged groove near the Zn2+ coordinating active site, which may accommodate the negatively charged polynucleotide substrate. Our findings suggest surface electrostatics, as well as the spatial extent of substrate accommodating region, are critical determinants of substrate and Vif binding across A3 proteins with implications for anti-retroviral and anti-cancer therapeutic design. PMID:25461536

  10. Preparation and Catalytic Activity for Aerobic Glucose Oxidation of Crown Jewel Structured Pt/Au Bimetallic Nanoclusters.

    PubMed

    Zhang, Haijun; Wang, Liqiong; Lu, Lilin; Toshima, Naoki

    2016-01-01

    Understanding of the "structure-activity" relations for catalysts at an atomic level has been regarded as one of the most important objectives in catalysis studies. Bimetallic nanoclusters (NCs) in its many types, such as core/shell, random alloy, cluster-in-cluster, bi-hemisphere, and crown jewel (one kind of atom locating at the top position of another kind of NC), attract significant attention owing to their excellent optical, electronic, and catalytic properties. PVP-protected crown jewel-structured Pt/Au (CJ-Pt/Au) bimetallic nanoclusters (BNCs) with Au atoms located at active top sites were synthesized via a replacement reaction using 1.4-nm Pt NCs as mother clusters even considering the fact that the replacement reaction between Pt and Au(3+) ions is difficult to be occurred. The prepared CJ-Pt/Au colloidal catalysts characterized by UV-Vis, TEM, HR-TEM and HAADF-STEM-EELS showed a high catalytic activity for aerobic glucose oxidation, and the top Au atoms decorating the Pt NCs were about 15 times more active than the Au atoms of Au NCs with similar particle size. PMID:27476577

  11. Importance of the Protein Framework for Catalytic Activity of [FeFe]-Hydrogenases

    PubMed Central

    Knörzer, Philipp; Silakov, Alexey; Foster, Carina E.; Armstrong, Fraser A.; Lubitz, Wolfgang; Happe, Thomas

    2012-01-01

    The active center (H-cluster) of [FeFe]-hydrogenases is embedded into a hydrophobic pocket within the protein. We analyzed several amino acids, located in the vicinity of this niche, by site-directed mutagenesis of the [FeFe]-hydrogenases from Clostridium pasteurianum (CpI) and Chlamydomonas reinhardtii (CrHydA1). These amino acids are highly conserved and predicted to be involved in H-cluster coordination. Characterization of two hydrogenase variants confirmed this hypothesis. The exchange of residues CrHydA1Met415 and CrHydA1Lys228 resulted in inactive proteins, which, according to EPR and FTIR analyses, contain no intact H-cluster. However, [FeFe]-hydrogenases in which CpIMet353 (CrHydA1Met223) and CpICys299 (CrHydA1Cys169) were exchanged to leucine and serine, respectively, showed a structurally intact H-cluster with catalytic activity either absent (CpIC299S) or strongly diminished (CpIM353L). In the case of CrHydA1C169S, the H-cluster was trapped in an inactive state exhibiting g values and vibrational frequencies that resembled the Htrans state of DdH from Desulfovibrio desulfuricans. This cysteine residue, interacting with the bridge head nitrogen of the di(methyl)amine ligand, seems therefore to represent an essential contribution of the immediate protein environment to the reaction mechanism. Exchanging methionine CpIM353 (CrHydA1M223) to leucine led to a strong decrease in turnover without affecting the Km value of the electron donor. We suggest that this methionine constitutes a “fine-tuning” element of hydrogenase activity. PMID:22110126

  12. Peptidase specificity characterization of C- and N-terminal catalytic sites of angiotensin I-converting enzyme.

    PubMed

    Araujo, M C; Melo, R L; Cesari, M H; Juliano, M A; Juliano, L; Carmona, A K

    2000-07-25

    Quenched fluorescence peptides were used to investigate the substrate specificity requirements for recombinant wild-type angiotensin I-converting enzyme (ACE) and two full-length mutants bearing a single functional active site (N- or C-domain). We assayed two series of bradykinin-related peptides flanked by o-aminobenzoic acid (Abz) and N-(2,4-dinitrophenyl)ethylenediamine (EDDnp), namely, Abz-GFSPFXQ-EDDnp and Abz-GFSPFRX-EDDnp (X = natural amino acids), in which the fluorescence appeared when Abz/EDDnp are separated by substrate hydrolysis. Abz-GFSPFFQ-EDDnp was preferentially hydrolyzed by the C-domain while Abz-GFSPFQQ-EDDnp exhibits higher N-domain specificity. Internally quenched fluorescent analogues of N-acetyl-SDKP-OH were also synthesized and assayed. Abz-SDK(Dnp)P-OH, in which Abz and Dnp (2,4-dinitrophenyl) are the fluorescent donor-acceptor pair, was cleaved at the D-K(Dnp) bond with high specificity by the ACE N-domain (k(cat)/K(m) = 1.1 microM(-)(1) s(-)(1)) being practically resistant to hydrolysis by the C-domain. The importance of hydroxyl-containing amino acids at the P(2) position for N-domain specificity was shown by performing the kinetics of hydrolysis of Abz-TDK(Dnp)P-OH and Abz-YDK(Dnp)P-OH. The peptides Abz-YRK(Dnp)P-OH and Abz-FRK(Dnp)P-OH which were hydrolyzed by wild-type ACE with K(m) values of 5.1 and 4.0 microM and k(cat) values of 246 and 210 s(-)(1), respectively, have been shown to be excellent substrates for ACE. The differentiation of the catalytic specificity of the C- and N-domains of ACE seems to depend on very subtle variations on substrate-specific amino acids. The presence of a free C-terminal carboxyl group or an aromatic moiety at the same substrate position determines specific interactions with the ACE active site which is regulated by chloride and seems to distinguish the activities of both domains. PMID:10913258

  13. Size-dependent catalytic activity and dynamics of gold nanoparticles at the single-molecule level.

    PubMed

    Zhou, Xiaochun; Xu, Weilin; Liu, Guokun; Panda, Debashis; Chen, Peng

    2010-01-13

    Nanoparticles are important catalysts for petroleum processing, energy conversion, and pollutant removal. As compared to their bulk counterparts, their often superior or new catalytic properties result from their nanometer size, which gives them increased surface-to-volume ratios and chemical potentials. The size of nanoparticles is thus pivotal for their catalytic properties. Here, we use single-molecule fluorescence microscopy to study the size-dependent catalytic activity and dynamics of spherical Au-nanoparticles under ambient solution conditions. By monitoring the catalysis of individual Au-nanoparticles of three different sizes in real time with single-turnover resolution, we observe clear size-dependent activities in both the catalytic product formation reaction and the product dissociation reaction. Within a model of classical thermodynamics, these size-dependent activities of Au-nanoparticles can be accounted for by the changes in the adsorption free energies of the substrate resazurin and the product resorufin because of the nanosize effect. We also observe size-dependent differential selectivity of the Au-nanoparticles between two parallel product dissociation pathways, with larger nanoparticles less selective between the two pathways. The particle size also strongly influences the surface-restructuring-coupled catalytic dynamics; both the catalysis-induced and the spontaneous dynamic surface restructuring occur more readily for smaller Au-nanoparticles due to their higher surface energies. Using a simple thermodynamic model, we analyze the catalysis- and size-dependent dynamic surface restructuring quantitatively; the results provide estimates on the activation energies and time scales of spontaneous dynamic surface restructuring that are fundamental to heterogeneous catalysis in both the nano- and the macro-scale. This study further exemplifies the power of the single-molecule approach in probing the intricate workings of nanoscale catalysts. PMID

  14. The Significance of Lewis Acid Sites for the Selective Catalytic Reduction of Nitric Oxide on Vanadium-Based Catalysts.

    PubMed

    Marberger, Adrian; Ferri, Davide; Elsener, Martin; Kröcher, Oliver

    2016-09-19

    The long debated reaction mechanisms of the selective catalytic reduction (SCR) of nitric oxide with ammonia (NH3 ) on vanadium-based catalysts rely on the involvement of Brønsted or Lewis acid sites. This issue has been clearly elucidated using a combination of transient perturbations of the catalyst environment with operando time-resolved spectroscopy to obtain unique molecular level insights. Nitric oxide reacts predominantly with NH3 coordinated to Lewis sites on vanadia on tungsta-titania (V2 O5 -WO3 -TiO2 ), while Brønsted sites are not involved in the catalytic cycle. The Lewis site is a mono-oxo vanadyl group that reduces only in the presence of both nitric oxide and NH3 . We were also able to verify the formation of the nitrosamide (NH2 NO) intermediate, which forms in tandem with vanadium reduction, and thus the entire mechanism of SCR. Our experimental approach, demonstrated in the specific case of SCR, promises to progress the understanding of chemical reactions of technological relevance. PMID:27553251

  15. Gold Sulfinyl Mesoionic Carbenes: Synthesis, Structure, and Catalytic Activity.

    PubMed

    Frutos, María; Avello, Marta G; Viso, Alma; Fernández de la Pradilla, Roberto; de la Torre, María C; Sierra, Miguel A; Gornitzka, Heinz; Hemmert, Catherine

    2016-08-01

    Gold mesoionic carbenes having a chiral sulfoxide group attached to the C4 position of the five membered ring have been prepared and tested as catalysts in the cycloisomerization of enynes. These new catalysts are very efficient, with the sulfoxide moiety playing a key role in their activity and the N1-substituent in control of the regioselectivity of these processes. PMID:27403763

  16. Flexible macrocycles as versatile supports for catalytically active metal clusters.

    PubMed

    Ryan, Jason D; Gagnon, Kevin J; Teat, Simon J; McIntosh, Ruaraidh D

    2016-07-12

    Here we present three structurally diverse clusters stabilised by the same macrocyclic polyphenol; t-butylcalix[8]arene. This work demonstrates the range of conformations the flexible ligand is capable of adopting, highlighting its versatility in metal coordination. In addition, a Ti complex displays activity for the ring-opening polymerisation of lactide. PMID:26892948

  17. Mutations Closer to the Active Site Improve the Promiscuous Aldolase Activity of 4-Oxalocrotonate Tautomerase More Effectively than Distant Mutations.

    PubMed

    Rahimi, Mehran; van der Meer, Jan-Ytzen; Geertsema, Edzard M; Poddar, Harshwardhan; Baas, Bert-Jan; Poelarends, Gerrit J

    2016-07-01

    The enzyme 4-oxalocrotonate tautomerase (4-OT), which catalyzes enol-keto tautomerization as part of a degradative pathway for aromatic hydrocarbons, promiscuously catalyzes various carbon-carbon bond-forming reactions. These include the aldol condensation of acetaldehyde with benzaldehyde to yield cinnamaldehyde. Here, we demonstrate that 4-OT can be engineered into a more efficient aldolase for this condensation reaction, with a >5000-fold improvement in catalytic efficiency (kcat /Km ) and a >10(7) -fold change in reaction specificity, by exploring small libraries in which only "hotspots" are varied. The hotspots were identified by systematic mutagenesis (covering each residue), followed by a screen for single mutations that give a strong improvement in the desired aldolase activity. All beneficial mutations were near the active site of 4-OT, thus underpinning the notion that new catalytic activities of a promiscuous enzyme are more effectively enhanced by mutations close to the active site. PMID:27238293

  18. Upregulation of RNase E activity by mutation of a site that uncompetitively interferes with RNA binding

    PubMed Central

    Lee, Minho; Shin, Eunkyoung; Jeon, Che Ok; Cha, Chang-Jun; Han, Seung Hyun; Kim, Su-Jin; Lee, Sang-Won; Lee, Younghoon; Ha, Nam-Chul

    2011-01-01

    Escherichia coli RNase E contains a site that selectively binds to RNAs containing 5′-monophosphate termini, increasing the efficiency of endonucleolytic cleavage of these RNAs. Random mutagenesis of N-Rne, the N-terminal catalytic region of RNase E, identified a hyperactive variant that remains preferentially responsive to phosphorylation at 5′ termini. Biochemical analyses showed that the mutation (Q36R), which replaces glutamine with arginine at a position distant from the catalytic site, increases formation of stable RNA-protein complexes without detectably affecting the enzyme's secondary or tertiary structure. Studies of cleavage of fluorogenic substrate and EMSA experiments indicated that the Q36R mutation increases catalytic activity and RNA binding. however, UV crosslinking and mass spectrometry studies suggested that the mutant enzyme lacks an RNA binding site present in its wild-type counterpart. Two substrate-bound tryptic peptides, 65HGFLPLK71—which includes amino acids previously implicated in substrate binding and catalysis—and 24LYDLDIESPGHEQK37—which includes the Q36 locus—were identified in wild-type enzyme complexes, whereas only the shorter peptide was observed for complexes containing Q36R. Our results identify a novel RNase E locus that disparately affects the number of substrate binding sites and catalytic activity of the enzyme. We propose a model that may account for these surprising effects. PMID:22186084

  19. Catalytic activity of baker's yeast in a mediatorless microbial fuel cell.

    PubMed

    Sayed, Enas Taha; Tsujiguchi, Takuya; Nakagawa, Nobuyoshi

    2012-08-01

    The catalytic activity of baker's yeast, Saccharomyces cerevisiae, as a biocatalyst was investigated in a mediatorless microbial fuel cell. The yeast cells that adhered on the anode surface were the active biocatalyst for glucose oxidation in a mediatorless biofuel cell, suggesting that the electron transfer took place through the surface confined species. The species in the anolyte solution including the dispersed yeast cells did not take a part in the electron transfer and thus in the power generation. PMID:22357359

  20. Development of High Activity, Coal-Derived, Promoted Catalytic Systems for NOx Reduction at Low Temperatures

    SciTech Connect

    J. M. Calo

    1998-05-01

    This project is directed at an investigation of catalytic NO{sub x} reduction mechanisms on coal-derived, activated carbon supports at low temperatures. Promoted carbon systems offer some potentially significant advantages for heterogeneous NO{sub x} reduction. These include: low cost; high activity at low temperatures, which minimizes carbon loss; oxygen resistance; and a support material which can be engineered with respect to porosity, transport and catalyst dispersion characteristics.

  1. Essential Nonredundant Function of the Catalytic Activity of Histone Deacetylase 2 in Mouse Development

    PubMed Central

    Hagelkruys, Astrid; Mattes, Katharina; Moos, Verena; Rennmayr, Magdalena; Ringbauer, Manuela; Sawicka, Anna

    2015-01-01

    The class I histone deacetylases (HDACs) HDAC1 and HDAC2 play partially redundant roles in the regulation of gene expression and mouse development. As part of multisubunit corepressor complexes, these two deacetylases exhibit both enzymatic and nonenzymatic functions. To examine the impact of the catalytic activities of HDAC1 and HDAC2, we generated knock-in mice expressing catalytically inactive isoforms, which are still incorporated into the HDAC1/HDAC2 corepressor complexes. Surprisingly, heterozygous mice expressing catalytically inactive HDAC2 die within a few hours after birth, while heterozygous HDAC1 mutant mice are indistinguishable from wild-type littermates. Heterozygous HDAC2 mutant mice show an unaltered composition but reduced associated deacetylase activity of corepressor complexes and exhibit a more severe phenotype than HDAC2-null mice. They display changes in brain architecture accompanied by premature expression of the key regulator protein kinase C delta. Our study reveals a dominant negative effect of catalytically inactive HDAC2 on specific corepressor complexes resulting in histone hyperacetylation, transcriptional derepression, and, ultimately, perinatal lethality. PMID:26598605

  2. Role of hydroxyl groups on the stability and catalytic activity of Au clusters on rutile surface

    SciTech Connect

    Kent, Paul R

    2011-01-01

    Hydroxyls are present as surface terminations of transition metal oxides under ambient conditions and may modify the properties of supported catalysts. We perform first-principles density functional theory calculations to investigate the role of hydroxyls on the catalytic activity of supported gold clusters on TiO{sub 2} (rutile). We find that they have a long-range effect increasing the adhesion of gold clusters on rutile. While hydroxyls make one gold atom more electronegative, a more complex charge-transfer scenario is observed on larger clusters which are important for catalytic applications. This enhances the molecular adsorption and coadsorption energies of CO and O{sub 2}, thereby increasing the catalytic activity of gold clusters for CO oxidation, consistent with reported experiments. Hydroxyls at the interface between gold and rutile surface are most important to this process, even when not directly bound to gold. As such, accurate models of catalytic processes on gold and other catalysts should include the effect of surface hydroxyls.

  3. An ultra-low Pd loading nanocatalyst with efficient catalytic activity

    NASA Astrophysics Data System (ADS)

    Jin, Yunxia; Xi, Jiangbo; Zhang, Zheye; Xiao, Junwu; Xiao, Fei; Qian, Lihua; Wang, Shuai

    2015-03-01

    An ultra-low Pd loading nanocatalyst is synthesized by a convenient solution route of photochemical reduction and aqueous chemical growth. The modification of nanocatalyst structures is investigated through changing morphologies of Pd nanoclusters on the surface of ZnO nanorods. A significant enhancement in photocatalytic properties has been achieved by decorating a trace amount of Pd clusters (0.05 at%) on the surface of ZnO nanorods. The reduction of 4-nitrophenol (4-NP) to 4-aminophenol (4-AP) is applied to demonstrate multiple catalytic activities in the Pd-ZnO hybrid nanocatalyst, which also provides a better understanding of the relationship between the unique nanoconfigured structure and catalytic performance.An ultra-low Pd loading nanocatalyst is synthesized by a convenient solution route of photochemical reduction and aqueous chemical growth. The modification of nanocatalyst structures is investigated through changing morphologies of Pd nanoclusters on the surface of ZnO nanorods. A significant enhancement in photocatalytic properties has been achieved by decorating a trace amount of Pd clusters (0.05 at%) on the surface of ZnO nanorods. The reduction of 4-nitrophenol (4-NP) to 4-aminophenol (4-AP) is applied to demonstrate multiple catalytic activities in the Pd-ZnO hybrid nanocatalyst, which also provides a better understanding of the relationship between the unique nanoconfigured structure and catalytic performance. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr00599j

  4. Site-specific growth of AgPd nanodendrites on highly purified Au bipyramids with remarkable catalytic performance

    NASA Astrophysics Data System (ADS)

    Zhou, Lin; Liu, Zeke; Zhang, Han; Cheng, Si; Fan, Li-Juan; Ma, Wanli

    2014-10-01

    Au nanorods have been extensively explored in various applications as the template for heterogeneous metallic nanostructures. However, Au bipyramids (AuBPs) have been paid much less attention although they possess an intriguing crystalline structure and extremely superior plasmonic properties which are absent in AuNRs. The state-of-the-art synthesis cannot produce pure AuBPs, which has become a major barrier to their various applications like catalysis since purity is often critical for achieving the desired performance. Herein, we have shown a facile approach to obtain large-scale high-purity AuBPs. The purity of AuBPs can be improved from 30 to 50% for the as-synthesized AuBP solution to over 95% for the purified solution. Site-specific growth of AgPd nanodendrites on multiply twinned AuBPs from core-shell to tipped nanostructures was achieved for the first time by coupling a galvanic replacement with a co-reduction process, which show remarkable catalytic activity in the reduction reaction of 4-nitrophenol (4-NP) by NaBH4. The use of ascorbic acid (AA) as a reductant in the co-reduction process and the intriguing crystalline structure of AuBPs play a critical role in forming these unique structures. We believe that this work would provide a general strategy to prepare high-purity AuBP based trimetallic nanostructures, which offers the opportunity for AuBPs to be widely used in catalysis or other plasmonic-effect related applications in the near future.Au nanorods have been extensively explored in various applications as the template for heterogeneous metallic nanostructures. However, Au bipyramids (AuBPs) have been paid much less attention although they possess an intriguing crystalline structure and extremely superior plasmonic properties which are absent in AuNRs. The state-of-the-art synthesis cannot produce pure AuBPs, which has become a major barrier to their various applications like catalysis since purity is often critical for achieving the desired

  5. TRAIL-induced caspase/p38 activation is responsible for the increased catalytic and invasive activities of Akt

    PubMed Central

    SUN, BO K.; KIM, JOO-HANG; NGUYEN, HOAN N.; KIM, SO Y.; OH, SEEUN; LEE, YONG J.; SONG, JAE J.

    2010-01-01

    We previously observed that TRAIL induces acquired TRAIL resistance coinciding with increased Akt phosphorylation brought about by the Src-PI3K-Akt signaling pathways and mediated by c-Cbl. c-Cbl, a ubiquitously expressed cytoplasmic adaptor protein, is simultaneously involved in the rapid degradation of TRAIL receptors and Akt phosphorylation during TRAIL treatment. Here, we show that Akt phosphorylation is not exclusively responsible for acquired TRAIL resistance. Akt catalytic activation is known to increase during metabolic oxidative stress, but we show that TRAIL also dramatically induces the catalytic activation of Akt in TRAIL-sensitive cells, but not in TRAIL-resistant cells. This suggests that Akt catalytic activation during TRAIL-induced apoptosis is likely to play a compensatory role in the maintenance of cell homeostasis. In addition, activated p38 and phosphorylated HSP27 were found to act as downstream effector molecules of p38 during TRAIL treatment and were shown to be responsible for increased Akt catalytic and invasive activities. PMID:21109947

  6. Preparation and Catalytic Activity for Aerobic Glucose Oxidation of Crown Jewel Structured Pt/Au Bimetallic Nanoclusters

    NASA Astrophysics Data System (ADS)

    Zhang, Haijun; Wang, Liqiong; Lu, Lilin; Toshima, Naoki

    2016-08-01

    Understanding of the “structure-activity” relations for catalysts at an atomic level has been regarded as one of the most important objectives in catalysis studies. Bimetallic nanoclusters (NCs) in its many types, such as core/shell, random alloy, cluster-in-cluster, bi-hemisphere, and crown jewel (one kind of atom locating at the top position of another kind of NC), attract significant attention owing to their excellent optical, electronic, and catalytic properties. PVP-protected crown jewel-structured Pt/Au (CJ-Pt/Au) bimetallic nanoclusters (BNCs) with Au atoms located at active top sites were synthesized via a replacement reaction using 1.4-nm Pt NCs as mother clusters even considering the fact that the replacement reaction between Pt and Au3+ ions is difficult to be occurred. The prepared CJ-Pt/Au colloidal catalysts characterized by UV-Vis, TEM, HR-TEM and HAADF-STEM-EELS showed a high catalytic activity for aerobic glucose oxidation, and the top Au atoms decorating the Pt NCs were about 15 times more active than the Au atoms of Au NCs with similar particle size.

  7. Study of the carburization of an iron catalyst during the Fischer-Tropsch synthesis: influence on its catalytic activity

    SciTech Connect

    Pijolat, M.; Perrichon, V.; Bussiere, P.

    1987-09-01

    The fast transformation of an ironalumina catalyst into Fe/sub 2+x/C during the H/sub 2/ + CO reaction was followed by in situ Moessbauer spectroscopy at 523 K and the behavior was compared with changes in catalytic activity for Fischer-Tropsch synthesis. After a few hours of synthesis, no metallic iron could be detected by either Moessbauer or IR spectroscopy, whereas the CO conversion was still half of that observed initially. The nature of the sites responsible for the remaining activity is discussed. The interpretation of the Moessbauer spectra has permitted the determination of the stoichiometry of the Fe/sub 2+x/C carbide (0 less than or equal to x less than or equal to 0.4), and hence the following of the change of x during the reaction. Thus, the activity in CO hydrogenation could be related to the number of carbon vacancies in the iron carbide, i.e., to the extent of the metallic character of this carbide. This concept of the variation of hydrogenating properties of the carbide with the carbon content has been supported by similar catalytic results obtained in the room temperature hydrogenation of ethylene performed on carbides of different stoichiometry

  8. Preparation and Catalytic Activity for Aerobic Glucose Oxidation of Crown Jewel Structured Pt/Au Bimetallic Nanoclusters

    PubMed Central

    Zhang, Haijun; Wang, Liqiong; Lu, Lilin; Toshima, Naoki

    2016-01-01

    Understanding of the “structure-activity” relations for catalysts at an atomic level has been regarded as one of the most important objectives in catalysis studies. Bimetallic nanoclusters (NCs) in its many types, such as core/shell, random alloy, cluster-in-cluster, bi-hemisphere, and crown jewel (one kind of atom locating at the top position of another kind of NC), attract significant attention owing to their excellent optical, electronic, and catalytic properties. PVP-protected crown jewel-structured Pt/Au (CJ-Pt/Au) bimetallic nanoclusters (BNCs) with Au atoms located at active top sites were synthesized via a replacement reaction using 1.4-nm Pt NCs as mother clusters even considering the fact that the replacement reaction between Pt and Au3+ ions is difficult to be occurred. The prepared CJ-Pt/Au colloidal catalysts characterized by UV-Vis, TEM, HR-TEM and HAADF-STEM-EELS showed a high catalytic activity for aerobic glucose oxidation, and the top Au atoms decorating the Pt NCs were about 15 times more active than the Au atoms of Au NCs with similar particle size. PMID:27476577

  9. Dissecting the Catalytic Mechanism of Betaine-Homocysteine S-Methyltransferase Using Intrinsic Tryptophan Fluorescence and Site-Directed Mutagenesis

    SciTech Connect

    Castro, C.; Gratson, A.A.; Evans, J.C.; Jiracek, J.; Collinsova, M.; Ludwig, M.L.; Garrow, T.A.

    2010-03-05

    Betaine-homocysteine S-methyltransferase (BHMT) is a zinc-dependent enzyme that catalyzes the transfer of a methyl group from glycine betaine (Bet) to homocysteine (Hcy) to form dimethylglycine (DMG) and methionine (Met). Previous studies in other laboratories have indicated that catalysis proceeds through the formation of a ternary complex, with a transition state mimicked by the inhibitor S-({delta}-carboxybutyl)-l-homocysteine (CBHcy). Using changes in intrinsic tryptophan fluorescence to determine the affinity of human BHMT for substrates, products, or CBHcy, we now demonstrate that the enzyme-substrate complex reaches its transition state through an ordered bi-bi mechanism in which Hcy is the first substrate to bind and Met is the last product released. Hcy, Met, and CBHcy bind to the enzyme to form binary complexes with K{sub d} values of 7.9, 6.9, and 0.28 {micro}M, respectively. Binary complexes with Bet and DMG cannot be detected with fluorescence as a probe, but Bet and DMG bind tightly to BHMT-Hcy to form ternary complexes with K{sub d} values of 1.1 and 0.73 {micro}M, respectively. Mutation of each of the seven tryptophan residues in human BHMT provides evidence that the enzyme undergoes two distinct conformational changes that are reflected in the fluorescence of the enzyme. The first is induced when Hcy binds, and the second, when Bet binds. As predicted by the crystal structure of BHMT, the amino acids Trp44 and Tyr160 are involved in binding Bet, and Glu159 in binding Hcy. Replacing these residues by site-directed mutagenesis significantly reduces the catalytic efficiency (V{sub max}/K{sub m}) of the enzyme. Replacing Tyr77 with Phe abolishes enzyme activity.

  10. Comparative catalytic activity of PET track-etched membranes with embedded silver and gold nanotubes

    NASA Astrophysics Data System (ADS)

    Mashentseva, Anastassiya; Borgekov, Daryn; Kislitsin, Sergey; Zdorovets, Maxim; Migunova, Anastassiya

    2015-12-01

    Irradiated by heavy ions nanoporous polyethylene terephthalate track-etched membranes (PET TeMs) after +15Kr84 ions bombardment (1.75 MeV/nucl with the ion fluency of 1 × 109 cm-2) and sequential etching was applied in this research as a template for development of composites with catalytically enriched properties. A highly ordered silver and gold nanotubes arrays were embedded in 100 nm pores of PET TeMs via electroless deposition technique at 4 °C during 1 h. All "as-prepared" composites were examined for catalytic activity using reduction of 4-nitrophenol (4-NP) to 4-aminophenol (4-AP) by sodium borohydride as a common reaction to test metallic nanostructures catalysts. The effect of temperature on the catalytic activity was investigated in range of 292-313 K and activation energy were calculated. Kapp of Ag/PET composites linearly increase with an increase of the temperature thus normal Arrhenius behavior have been seen and the activation energy was calculated to be 42.13 kJ/mol. Au/PET composites exhibit not only more powerful catalytic activity but also non-linear dependence of rate constant from temperature. Kapp increased with increasing temperature throughout the 292-308 K temperature range; the reaction had an activation energy 65.32 kJ/mol. In range 311-313 K rate constant dramatically decreased and the apparent activation energy at this temperature rang was -91.44 kJ/mol due some structural changes, i.e. agglomeration of Au nanoparticles on the surface of composite.

  11. Educational Activity Sites for High School Students

    ERIC Educational Resources Information Center

    Troutner, Joanne

    2005-01-01

    Finding quality Internet resources for high school students is a continuing challenge. Several high-quality web sites are presented for educators and students. These sites offer activities to learn how an art conservator looks at paintings, create a newspaper, research and develop an end product, build geometry and physics skills, explore science…

  12. The doping effect on the catalytic activity of graphene for oxygen evolution reaction in a lithium-air battery: a first-principles study.

    PubMed

    Ren, Xiaodong; Wang, Beizhou; Zhu, Jinzhen; Liu, Jianjun; Zhang, Wenqing; Wen, Zhaoyin

    2015-06-14

    A lithium-air battery as an energy storage technology can be used in electric vehicles due to its large energy density. However, its poor rate capability, low power density and large overpotential problems limit its practical usage. In this paper, the first-principles thermodynamic calculations were performed to study the catalytic activity of X-doped graphene (X = B, N, Al, Si, and P) materials as potential cathodes to enhance charge reactions in a lithium-air battery. Among these materials, P-doped graphene exhibits the highest catalytic activity in reducing the charge voltage by 0.25 V, while B-doped graphene has the highest catalytic activity in decreasing the oxygen evolution barrier by 0.12 eV. By combining these two catalytic effects, B,P-codoped graphene was demonstrated to have an enhanced catalytic activity in reducing the O2 evolution barrier by 0.70 eV and the charge voltage by 0.13 V. B-doped graphene interacts with Li2O2 by Li-sited adsorption in which the electron-withdrawing center can enhance charge transfer from Li2O2 to the substrate, facilitating reduction of O2 evolution barrier. In contrast, X-doped graphene (X = N, Al, Si, and P) prefers O-sited adsorption toward Li2O2, forming a X-O2(2-)···Li(+) interface structure between X-O2(2-) and the rich Li(+) layer. The active structure of X-O2(2-) can weaken the surrounding Li-O2 bonds and significantly reduce Li(+) desorption energy at the interface. Our investigation is helpful in developing a novel catalyst to enhance oxygen evolution reaction (OER) in Li-air batteries. PMID:25970821

  13. Single-molecule catalysis mapping quantifies site-specific activity and uncovers radial activity gradient on single 2D nanocrystals.

    PubMed

    Andoy, Nesha May; Zhou, Xiaochun; Choudhary, Eric; Shen, Hao; Liu, Guokun; Chen, Peng

    2013-02-01

    Shape-controlled metal nanocrystals are a new generation of nanoscale catalysts. Depending on their shapes, these nanocrystals exhibit various surface facets, and the assignments of their surface facets have routinely been used to rationalize or predict their catalytic activity in a variety of chemical transformations. Recently we discovered that for 1-dimensional (1D) nanocrystals (Au nanorods), the catalytic activity is not constant along the same side facets of single nanorods but rather differs significantly and further shows a gradient along its length, which we attributed to an underlying gradient of surface defect density resulting from their linear decay in growth rate during synthesis (Nat. Nanotechnol.2012, 7, 237-241). Here we report that this behavior also extends to 2D nanocrystals, even for a different catalytic reaction. By using super-resolution fluorescence microscopy to map out the locations of catalytic events within individual triangular and hexagonal Au nanoplates in correlation with scanning electron microscopy, we find that the catalytic activity within the flat {111} surface facet of a Au nanoplate exhibits a 2D radial gradient from the center toward the edges. We propose that this activity gradient results from a growth-dependent surface defect distribution. We also quantify the site-specific activity at different regions within a nanoplate: The corner regions have the highest activity, followed by the edge regions and then the flat surface facets. These discoveries highlight the spatial complexity of catalytic activity at the nanoscale as well as the interplay amid nanocrystal growth, morphology, and surface defects in determining nanocatalyst properties. PMID:23320465

  14. Fabrication of Pt-loaded NiCo nanochains with superior catalytic dehydrogenation activity.

    PubMed

    Wen, Ming; Wu, Qingnan; Peng, Jin; Wu, Qingsheng; Wang, Chenxiang

    2014-02-15

    A new magnetic Pt-loaded NiCo nanochain, with the diameter from 80 nm to 120 nm, has been prepared through microwave-induced assembly process followed by the galvanic displacement performance. Pt nanoparticles are distributed on the surface of NiCo nanochains. The products are investigated as hydrolytic dehydrogenation catalyst for potential hydrogen energy applications. Compared with NiCo nanochains, the Pt-loaded NiCo nanochains present exceedingly high catalytic activity toward the hydrolytic dehydrogenation of ammonia borane aqueous under ambient atmosphere at room temperature, where the Ni16Co80/Pt4 nanochains exhibit high catalytic activity with a lower activation energy of 45.72 kJ mol(-1) and a superior dehydrogenation rate of 1.17 × 10(4) mL min(-1) g(-1), suggesting the potential application in hydrogen fuel and chemical industry. PMID:24370425

  15. Molecular Basis of Reduced Pyridoxine 5′-Phosphate Oxidase Catalytic Activity in Neonatal Epileptic Encephalopathy Disorder*

    PubMed Central

    Musayev, Faik N.; Di Salvo, Martino L.; Saavedra, Mario A.; Contestabile, Roberto; Ghatge, Mohini S.; Haynes, Alexina; Schirch, Verne; Safo, Martin K.

    2009-01-01

    Mutations in pyridoxine 5′-phosphate oxidase are known to cause neonatal epileptic encephalopathy. This disorder has no cure or effective treatment and is often fatal. Pyridoxine 5′-phosphate oxidase catalyzes the oxidation of pyridoxine 5′-phosphate to pyridoxal 5′-phosphate, the active cofactor form of vitamin B6 required by more than 140 different catalytic activities, including enzymes involved in amino acid metabolism and biosynthesis of neurotransmitters. Our aim is to elucidate the mechanism by which a homozygous missense mutation (R229W) in the oxidase, linked to neonatal epileptic encephalopathy, leads to reduced oxidase activity. The R229W variant is ∼850-fold less efficient than the wild-type enzyme due to an ∼192-fold decrease in pyridoxine 5′-phosphate affinity and an ∼4.5-fold decrease in catalytic activity. There is also an ∼50-fold reduction in the affinity of the R229W variant for the FMN cofactor. A 2.5 Å crystal structure of the R229W variant shows that the substitution of Arg-229 at the FMN binding site has led to a loss of hydrogen-bond and/or salt-bridge interactions between FMN and Arg-229 and Ser-175. Additionally, the mutation has led to an alteration of the configuration of a β-strand-loop-β-strand structure at the active site, resulting in loss of two critical hydrogen-bond interactions involving residues His-227 and Arg-225, which are important for substrate binding and orientation for catalysis. These results provide a molecular basis for the phenotype associated with the R229W mutation, as well as providing a foundation for understanding the pathophysiological consequences of pyridoxine 5′-phosphate oxidase mutations. PMID:19759001

  16. Reversible Regulation of Catalytic Activity of Gold Nanoparticles with DNA Nanomachines

    PubMed Central

    Zhou, Peipei; Jia, Sisi; Pan, Dun; Wang, Lihua; Gao, Jimin; Lu, Jianxin; Shi, Jiye; Tang, Zisheng; Liu, Huajie

    2015-01-01

    Reversible catalysis regulation has gained much attention and traditional strategies utilized reversible ligand coordination for switching catalyst’s conformations. However, it remains challenging to regulate the catalytic activity of metal nanoparticle-based catalysts. Herein, we report a new DNA nanomachine-driven reversible nano-shield strategy for circumventing this problem. The basic idea is based on the fact that the conformational change of surface-attached DNA nanomachines will cause the variation of the exposed surface active area on metal nanoparticles. As a proof-of-concept study, we immobilized G-rich DNA strands on gold nanoparticles (AuNPs) which have glucose oxidase (GOx) like activity. Through the reversible conformational change of the G-rich DNA between a flexible single-stranded form and a compact G-quadruplex form, the catalytic activity of AuNPs has been regulated reversibly for several cycles. This strategy is reliable and robust, which demonstrated the possibility of reversibly adjusting catalytic activity with external surface coverage switching, rather than coordination interactions. PMID:26395968

  17. When ruthenia met titania: Achieving extraordinary catalytic activity at low temperature by nanostructuring of oxides

    SciTech Connect

    Graciani, J.; Stacchiola, D.; Yang, F.; Evans, J.; Vidal, A. B.; Rodriguez, J. A.; Sanz, J. F.

    2015-09-09

    Nanostructured RuOx/TiO2(110) catalysts have a remarkable catalytic activity for CO oxidation at temperatures in the range of 350–375 K. Furthermore, the RuO2(110) surface has no activity. The state-of-the-art DFT calculations indicate that the main reasons for such an impressive improvement in the catalytic activity are: (i) a decrease of the diffusion barrier of adsorbed O atoms by around 40%, from 1.07 eV in RuO2(110) to 0.66 eV in RuOx/TiO2(110), which explains the shift of the activity to lower temperatures and (ii) a lowering of the barrier by 20% for the association of adsorbed CO and O species to give CO2 (the main barrier for the CO oxidation reaction) passing from around 0.7 eV in RuO2(110) to 0.55 eV in RuOx/TiO2(110). We show that the catalytic properties of ruthenia are strongly modified when supported as nanostructures on titania, attaining higher activity at temperatures 100 K lower than that needed for pure ruthenia. As in other systems consisting of ceria nanostructures supported on titania, nanostructured ruthenia shows strongly modified properties compared to the pure oxide, consolidating the fact that the nanostructuring of oxides is a main way to attain higher catalytic activity at lower temperatures.

  18. When ruthenia met titania: Achieving extraordinary catalytic activity at low temperature by nanostructuring of oxides

    DOE PAGESBeta

    Graciani, J.; Stacchiola, D.; Yang, F.; Evans, J.; Vidal, A. B.; Rodriguez, J. A.; Sanz, J. F.

    2015-09-09

    Nanostructured RuOx/TiO2(110) catalysts have a remarkable catalytic activity for CO oxidation at temperatures in the range of 350–375 K. Furthermore, the RuO2(110) surface has no activity. The state-of-the-art DFT calculations indicate that the main reasons for such an impressive improvement in the catalytic activity are: (i) a decrease of the diffusion barrier of adsorbed O atoms by around 40%, from 1.07 eV in RuO2(110) to 0.66 eV in RuOx/TiO2(110), which explains the shift of the activity to lower temperatures and (ii) a lowering of the barrier by 20% for the association of adsorbed CO and O species to give CO2more » (the main barrier for the CO oxidation reaction) passing from around 0.7 eV in RuO2(110) to 0.55 eV in RuOx/TiO2(110). We show that the catalytic properties of ruthenia are strongly modified when supported as nanostructures on titania, attaining higher activity at temperatures 100 K lower than that needed for pure ruthenia. As in other systems consisting of ceria nanostructures supported on titania, nanostructured ruthenia shows strongly modified properties compared to the pure oxide, consolidating the fact that the nanostructuring of oxides is a main way to attain higher catalytic activity at lower temperatures.« less

  19. Hydrodechlorination catalytic activity of gold nanoparticles supported on TiO 2 modified SBA-15 investigated by IR spectroscopy

    NASA Astrophysics Data System (ADS)

    Hannus, I.; Búza, M.; Beck, A.; Guczi, L.; Sáfrán, G.

    2009-04-01

    The hydrodechlorination catalytic activity of gold nanoparticles on SBA-15 silica modified by TiO 2 promoters has been investigated. Comparing the hydrodechlorination catalytic activity platinum nanoparticles supported on TiO 2 catalyst was used in the hydrodechlorination of CCl 4 as model compound. The IR spectroscopic experimental results showed that the gold nanoparticles have higher catalytic activity, than platinum ones. The two samples were tested also in CO oxidation, in which Au/TiO 2/SBA-15 possess also somewhat higher activity than Pt/TiO 2.

  20. Small-Pore Molecular Sieves SAPO-34 with Chabazite Structure: Theoretical Study of Silicon Incorporation and Interrelated Catalytic Activity

    NASA Astrophysics Data System (ADS)

    Wang, Hong; Lewis, James; Liu, Zhongmin

    2011-03-01

    The catalytic conversion of methonal to olefin (MTO) has attracted attention both in industrial and academic fields. Strong evidence shows that small-pore molecular sieves with certain amount silicon incorporated (SAPO) present promising high catalytic activity in MTO conversion. Using DFT, we study the structural and electronic properties of chabazite SAPO-34. Although there are extensively experimental results show that silicon incorporation does not change the overall structure as the original AlPO structure, local structural changes are still created by silicon substitution, which probably accounted for the high catalytic activity. It is noted that the catalytic activity of SAPO-34 presents increasing trend along with the silicon incorporation amount increasing and maintain a flat peak even with more silicon incorporated. Hence, there is an optimal silicon incorporation amount which possibly yields the highest catalytic MTO conversion.

  1. Factor IX Amagasaki: A new mutation in the catalytic domain resulting in the loss of both coagulant and esterase activities

    SciTech Connect

    Miyata, Toshiyuki; Iwanaga, Sadaaki ); Sakai, Toshiyuki; Sugimoto, Mitsuhiko; Naka, Hiroyuki; Yamamoto, Kazukuni; Yoshioka, Akira; Fukui, Hiromu ); Mitsui, Kotoko; Kamiya, Kensyu; Umeyama, Hideaki )

    1991-11-26

    Factor IX Amagasaki (AMG) is a naturally occurring mutant of factor IX having essentially no coagulant activity, even though normal levels of antigen are detected in plasma. Factor IX AMG was purified from the patient's plasma by immunoaffinity chromatography with an anti-factor IX monoclonal antibody column. Factor IX AMG was cleaved normally by factor VIIa-tissue factor complex, yielding a two-chain factor IXa. Amino acid composition and sequence analysis of one of the tryptic peptides isolated from factor IX AMG revealed that Gly-311 had been replaced by Glu. The authors identified a one-base substitution of guanine to adenine in exon VIII by amplifying exon VIII using the polymerase chain reaction method and sequencing the product. This base mutation also supported the replacement of Gly-311 by Glu. In the purified system, factor IXa AMG did not activate for factor X in the presence of factor VIII, phospholipids, and Ca{sup 2+}, and no esterase activity toward Z-Arg-p-nitrobenzyl ester was observed. The model building of the serine protease domain of factor IXa suggests that the Gly-311 {yields} Glu exchange would disrupt the specific conformational state in the active site environment, resulting in the substrate binding site not forming properly. This is the first report to show the experimental evidence for importance of a highly conserved Gly-142 (chymotrypsinogen numbering) located in the catalytic site of mammalian serine proteases so far known.

  2. High Catalytic Activity and Chemoselectivity of Sub-nanometric Pd Clusters on Porous Nanorods of CeO2 for Hydrogenation of Nitroarenes.

    PubMed

    Zhang, Sai; Chang, Chun-Ran; Huang, Zheng-Qing; Li, Jing; Wu, Zhemin; Ma, Yuanyuan; Zhang, Zhiyun; Wang, Yong; Qu, Yongquan

    2016-03-01

    Sub-nanometric Pd clusters on porous nanorods of CeO2 (PN-CeO2) with a high Pd dispersion of 73.6% exhibit the highest catalytic activity and best chemoselectivity for hydrogenation of nitroarenes to date. For hydrogenation of 4-nitrophenol, the catalysts yield a TOF of ∼44059 h(-1) and a chemoselectivity to 4-aminophenol of >99.9%. The superior catalytic performance can be attributed to a cooperative effect between the highly dispersed sub-nanometric Pd clusters for hydrogen activation and unique surface sites of PN-CeO2 with a high concentration of oxygen vacancy for an energetically and geometrically preferential adsorption of nitroarenes via nitro group. The high concentration of surface defects of PN-CeO2 and large Pd dispersion contribute to the enhanced catalytic activity for the hydrogenation reactions. The high chemoselectivity is mainly governed by the high Pd dispersion on the support. The catalysts also deliver high catalytic activity and selectivity for nitroaromatics with various reducible substituents into the corresponding aminoarenes. PMID:26828123

  3. Catalytic diamination of olefins via N-N bond activation.

    PubMed

    Zhu, Yingguang; Cornwall, Richard G; Du, Haifeng; Zhao, Baoguo; Shi, Yian

    2014-12-16

    CONSPECTUS: Vicinal diamines are important structural motifs present in various biologically and chemically significant molecules. Direct diamination of olefins provides an effective approach to this class of compounds. Unlike well-established oxidation processes such as epoxidation, dihydroxylation, and aminohydroxylation, direct diamination of olefins had remained a long-standing challenge and had been less well developed. In this Account, we summarize our recent studies on Pd(0)- and Cu(I)-catalyzed diaminations of olefins using di-tert-butyldiaziridinone and its related analogues as nitrogen sources via N-N bond activation. A wide variety of imidazolidinones, cyclic sulfamides, indolines, imidazolinones, and cyclic guanidines can be obtained from conjugated dienes and terminal olefins. For conjugated dienes, the diamination proceeds regioselectively at the internal double bond with the Pd(0) catalyst. Mechanistic studies show that the diamination likely involves a four-membered Pd(II) species resulting from the insertion of Pd(0) into the N-N bond of di-tert-butyldiaziridinone. Interestingly, the Cu(I)-catalyzed process occurs regioselectively at either the terminal or internal double bond depending on the reaction conditions via two mechanistically distinct pathways. The Cu(I) catalyst cleaves the N-N bond of di-tert-butyldiaziridinone to form a Cu(II) nitrogen radical and a four-membered Cu(III) species, which are likely in rapid equilibrium. The Cu(II) nitrogen radical and the four-membered Cu(III) species lead to the terminal and internal diamination, respectively. Terminal olefins are effectively C-H diaminated at the allylic and homoallylic carbons with Pd(0) as catalyst and di-tert-butyldiaziridinone as nitrogen source, likely involving a diene intermediate generated in situ from the terminal olefin via formation of a π-allyl Pd complex and subsequent β-hydride elimination. When di-tert-butylthiadiaziridine 1,1-dioxide is used as nitrogen source

  4. Catalytic Diamination of Olefins via N–N Bond Activation

    PubMed Central

    2015-01-01

    Conspectus Vicinal diamines are important structural motifs present in various biologically and chemically significant molecules. Direct diamination of olefins provides an effective approach to this class of compounds. Unlike well-established oxidation processes such as epoxidation, dihydroxylation, and aminohydroxylation, direct diamination of olefins had remained a long-standing challenge and had been less well developed. In this Account, we summarize our recent studies on Pd(0)- and Cu(I)-catalyzed diaminations of olefins using di-tert-butyldiaziridinone and its related analogues as nitrogen sources via N–N bond activation. A wide variety of imidazolidinones, cyclic sulfamides, indolines, imidazolinones, and cyclic guanidines can be obtained from conjugated dienes and terminal olefins. For conjugated dienes, the diamination proceeds regioselectively at the internal double bond with the Pd(0) catalyst. Mechanistic studies show that the diamination likely involves a four-membered Pd(II) species resulting from the insertion of Pd(0) into the N–N bond of di-tert-butyldiaziridinone. Interestingly, the Cu(I)-catalyzed process occurs regioselectively at either the terminal or internal double bond depending on the reaction conditions via two mechanistically distinct pathways. The Cu(I) catalyst cleaves the N–N bond of di-tert-butyldiaziridinone to form a Cu(II) nitrogen radical and a four-membered Cu(III) species, which are likely in rapid equilibrium. The Cu(II) nitrogen radical and the four-membered Cu(III) species lead to the terminal and internal diamination, respectively. Terminal olefins are effectively C–H diaminated at the allylic and homoallylic carbons with Pd(0) as catalyst and di-tert-butyldiaziridinone as nitrogen source, likely involving a diene intermediate generated in situ from the terminal olefin via formation of a π-allyl Pd complex and subsequent β-hydride elimination. When di-tert-butylthiadiaziridine 1,1-dioxide is used as nitrogen source

  5. Domain function dissection and catalytic properties of Listeria monocytogenes p60 protein with bacteriolytic activity.

    PubMed

    Yu, Minfeng; Zuo, Jinrong; Gu, Hao; Guo, Minliang; Yin, Yuelan

    2015-12-01

    The major extracellular protein p60 of Listeria monocytogenes (Lm-p60) is an autolysin that can hydrolyze the peptidoglycan of bacterial cell wall and has been shown to be required for L. monocytogenes virulence. The predicted three-dimensional structure of Lm-p60 showed that Lm-p60 could be split into two independent structural domains at the amino acid residue 270. Conserved motif analysis showed that V30, D207, S395, and H444 are the key amino acid residues of the corresponding motifs. However, not only the actual functions of these two domains but also the catalytic properties of Lm-p60 are unclear. We try to express recombinant Lm-p60 and identify the functions of two domains by residue substitution (V30A, D207A, S395A, and H444A) and peptide truncation. The C-terminal domain was identified as catalytic element and N-terminal domain as substrate recognition and binding element. Either N-terminal domain truncation or C-terminal domain truncation presents corresponding biological activity. The catalytic activity of Lm-p60 with a malfunctioned substrate-binding domain was decreased, while the substrate binding was not affected by a mulfunctioned catalytic domain. With turbidimetric method, we determined the optimal conditions for the bacteriolytic activity of Lm-p60 against Micrococcus lysodeikficus. The assay for the effect of Lm-p60 on the bacteriolytic activity of lysozyme revealed that the combined use of Lm-p60 protein with lysozyme showed a strong synergistic effect on the bacteriolytic activity. PMID:26363556

  6. Active Site Loop Conformation Regulates Promiscuous Activity in a Lactonase from Geobacillus kaustophilus HTA426

    PubMed Central

    Zhang, Yu; An, Jiao; Yang, Guang-Yu; Bai, Aixi; Zheng, Baisong; Lou, Zhiyong; Wu, Geng; Ye, Wei; Chen, Hai-Feng; Feng, Yan; Manco, Giuseppe

    2015-01-01

    Enzyme promiscuity is a prerequisite for fast divergent evolution of biocatalysts. A phosphotriesterase-like lactonase (PLL) from Geobacillus kaustophilus HTA426 (GkaP) exhibits main lactonase and promiscuous phosphotriesterase activities. To understand its catalytic and evolutionary mechanisms, we investigated a “hot spot” in the active site by saturation mutagenesis as well as X-ray crystallographic analyses. We found that position 99 in the active site was involved in substrate discrimination. One mutant, Y99L, exhibited 11-fold improvement over wild-type in reactivity (kcat/Km) toward the phosphotriesterase substrate ethyl-paraoxon, but showed 15-fold decrease toward the lactonase substrate δ-decanolactone, resulting in a 157-fold inversion of the substrate specificity. Structural analysis of Y99L revealed that the mutation causes a ∼6.6 Å outward shift of adjacent loop 7, which may cause increased flexibility of the active site and facilitate accommodation and/or catalysis of organophosphate substrate. This study provides for the PLL family an example of how the evolutionary route from promiscuity to specificity can derive from very few mutations, which promotes alteration in the conformational adjustment of the active site loops, in turn draws the capacity of substrate binding and activity. PMID:25706379

  7. CO Oxidation on Au/TiO2: Condition-Dependent Active Sites and Mechanistic Pathways.

    PubMed

    Wang, Yang-Gang; Cantu, David C; Lee, Mal-Soon; Li, Jun; Glezakou, Vassiliki-Alexandra; Rousseau, Roger

    2016-08-24

    We present results of ab initio electronic structure and molecular dynamics simulations (AIMD), as well as a microkinetic model of CO oxidation catalyzed by TiO2 supported Au nanocatalysts. A coverage-dependent microkinetic analysis, based on energetics obtained with density functional methods, shows that the dominant kinetic pathway, activated oxygen species, and catalytic active sites are all strongly depended on both temperature and oxygen partial pressure. Under oxidizing conditions and T < 400 K, the prevalent pathway involves a dynamic single atom catalytic mechanism. This reaction is catalyzed by a transient Au-CO species that migrates from the Au-cluster onto a surface oxygen adatom. It subsequently reacts with the TiO2 support via a Mars van Krevelen mechanism to form CO2 and finally the Au atom reintegrates back into the gold cluster to complete the catalytic cycle. At 300 ≤ T ≤ 600 K, oxygen-bound single Oad-Au(+)-CO sites and the perimeter Au-sites of the nanoparticle work in tandem to optimally catalyze the reaction. Above 600 K, a variety of alternate pathways associated with both single-atom and the perimeter sites of the Au nanoparticle are found to be active. Under low oxygen pressures, Oad-Au(+)-CO species can be a source of catalyst deactivation and the dominant pathway involves only Au-perimeter sites. A detailed comparison of the current model and the existing literature resolves many apparent inconsistencies in the mechanistic interpretations. PMID:27480512

  8. Engineering catalytic activity via ion beam bombardment of catalyst supports for vertically aligned carbon nanotube growth

    SciTech Connect

    Islam, A. E.; Zakharov, D.; Stach, E. A.; Nikoleav, P.; Amama, P. B.; Sargent, G.; Saber, S.; Huffman, D.; Erford, M.; Semiatin, S. L.; Maruyama, B.

    2015-09-16

    Carbon nanotube growth depends on the catalytic activity of metal nanoparticles on alumina or silica supports. The control on catalytic activity is generally achieved by variations in water concentration, carbon feed, and sample placement on a few types of alumina or silica catalyst supports obtained via thin film deposition. We have recently expanded the choice of catalyst supports by engineering inactive substrates like c-cut sapphire via ion beam bombardment. The deterministic control on the structure and chemistry of catalyst supports obtained by tuning the degree of beam-induced damage have enabled better regulation of the activity of Fe catalysts only in the ion beam bombarded areas and hence enabled controllable super growth of carbon nanotubes. A wide range of surface characterization techniques were used to monitor the catalytically active surface engineered via ion beam bombardment. The proposed method offers a versatile way to control carbon nanotube growth in patterned areas and also enhances the current understanding of the growth process. As a result, with the right choice of water concentration, carbon feed and sample placement, engineered catalyst supports may extend the carbon nanotube growth yield to a level that is even higher than the ones reported here, and thus offers promising applications of carbon nanotubes in electronics, heat exchanger, and energy storage.

  9. Engineering catalytic activity via ion beam bombardment of catalyst supports for vertically aligned carbon nanotube growth

    DOE PAGESBeta

    Islam, A. E.; Zakharov, D.; Stach, E. A.; Nikoleav, P.; Amama, P. B.; Sargent, G.; Saber, S.; Huffman, D.; Erford, M.; Semiatin, S. L.; et al

    2015-09-16

    Carbon nanotube growth depends on the catalytic activity of metal nanoparticles on alumina or silica supports. The control on catalytic activity is generally achieved by variations in water concentration, carbon feed, and sample placement on a few types of alumina or silica catalyst supports obtained via thin film deposition. We have recently expanded the choice of catalyst supports by engineering inactive substrates like c-cut sapphire via ion beam bombardment. The deterministic control on the structure and chemistry of catalyst supports obtained by tuning the degree of beam-induced damage have enabled better regulation of the activity of Fe catalysts only inmore » the ion beam bombarded areas and hence enabled controllable super growth of carbon nanotubes. A wide range of surface characterization techniques were used to monitor the catalytically active surface engineered via ion beam bombardment. The proposed method offers a versatile way to control carbon nanotube growth in patterned areas and also enhances the current understanding of the growth process. As a result, with the right choice of water concentration, carbon feed and sample placement, engineered catalyst supports may extend the carbon nanotube growth yield to a level that is even higher than the ones reported here, and thus offers promising applications of carbon nanotubes in electronics, heat exchanger, and energy storage.« less

  10. Identification of promiscuous ene-reductase activity by mining structural databases using active site constellations

    PubMed Central

    Steinkellner, Georg; Gruber, Christian C.; Pavkov-Keller, Tea; Binter, Alexandra; Steiner, Kerstin; Winkler, Christoph; Łyskowski, Andrzej; Schwamberger, Orsolya; Oberer, Monika; Schwab, Helmut; Faber, Kurt; Macheroux, Peter; Gruber, Karl

    2014-01-01

    The exploitation of catalytic promiscuity and the application of de novo design have recently opened the access to novel, non-natural enzymatic activities. Here we describe a structural bioinformatic method for predicting catalytic activities of enzymes based on three-dimensional constellations of functional groups in active sites (‘catalophores’). As a proof-of-concept we identify two enzymes with predicted promiscuous ene-reductase activity (reduction of activated C–C double bonds) and compare them with known ene-reductases, that is, members of the Old Yellow Enzyme family. Despite completely different amino acid sequences, overall structures and protein folds, high-resolution crystal structures reveal equivalent binding modes of typical Old Yellow Enzyme substrates and ligands. Biochemical and biocatalytic data show that the two enzymes indeed possess ene-reductase activity and reveal an inverted stereopreference compared with Old Yellow Enzymes for some substrates. This method could thus be a tool for the identification of viable starting points for the development and engineering of novel biocatalysts. PMID:24954722

  11. A facile reflux procedure to increase active surface sites form highly active and durable supported palladium@platinum bimetallic nanodendrites

    NASA Astrophysics Data System (ADS)

    Wang, Qin; Li, Yingjun; Liu, Baocang; Xu, Guangran; Zhang, Geng; Zhao, Qi; Zhang, Jun

    2015-11-01

    A series of well-dispersed bimetallic Pd@Pt nanodendrites uniformly supported on XC-72 carbon black are fabricated by using different capping agents. These capping agents are essential for the branched morphology control. However, the surfactant adsorbed on the nanodendrites surface blocks the access of reactant molecules to the active surface sites, and the catalytic activities of these bimetallic nanodendrites are significantly restricted. Herein, a facile reflux procedure to effectively remove the capping agent molecules without significantly affecting their sizes is reported for activating supported nanocatalysts. More significantly, the structure and morphology of the nanodendrites can also be retained, enhancing the numbers of active surface sites, catalytic activity and stability toward methanol and ethanol electro-oxidation reactions. The as-obtained hot water reflux-treated Pd@Pt/C catalyst manifests superior catalytic activity and stability both in terms of surface and mass specific activities, as compared to the untreated catalysts and the commercial Pt/C and Pd/C catalysts. We anticipate that this effective and facile removal method has more general applicability to highly active nanocatalysts prepared with various surfactants, and should lead to improvements in environmental protection and energy production.

  12. Designing the synthesis of catalytically active Ti-β by using various new templates in the presence of fluoride anion.

    PubMed

    Sasidharan, Manickam; Bhaumik, Asim

    2011-09-28

    Crystallization of large-pore Ti-β by using a variety of diquaternary ammonium derivatives of dibromoalkane and amines such as triethylamine, 1,4-diazabicyclo[2,2,2]octane (DABCO), and quinuclidine as structure-directing agents (SDA) is described. The size of hydrophobic bridging alkyl-chain length of the template [R(3)N(+)-(CH(2))(x)-N(+)R(3)](OH(-))(2) directs the final crystalline product: Ti-β, Ti-ZSM-12, Ti-nonasil or Ti-ZSM-5, as x gradually changes from 6 to 1, in the fluoride medium under hydrothermal conditions. A dense phase such as Ti-nonasil (clathrasil type) is crystallized as the size of hydrophobic bridging alkyl-chain length decreases. The use of F(-) anions as a mineralizer and Ti(4+) as a heteroatom in the synthesis gel also influences the selectivity of final crystalline product. The phase purity and incorporation of Ti(4+) into the lattice of β (BEA) and ZSM-12 frameworks are confirmed using XRD, UV-visible, FT-IR, (29)Si NMR spectroscopes, elemental analysis (ICP), surface area measurements and catalytic test reactions. The morphology of Ti-β samples is dependent on the nature of the structure-directing agent as revealed by the scanning electron microscopic (SEM) observations. The catalytic activity in the epoxidation of 4-vinyl-1-cyclohexene is increased with the amount of tetrahedral Ti(4+) atoms in the framework. The new templates can be effectively used for preparation of catalytically active Ti-β with the minimum number of framework defect sites. PMID:21833381

  13. Pin1 cysteine-113 oxidation inhibits its catalytic activity and cellular function in Alzheimer’s disease

    PubMed Central

    Chen, Chun-Hau; Li, Wenzong; Sultana, Rukhsana; You, Mi-Hyeon; Kondo, Asami; Shahpasand, Kooroch; Kim, Byeong Mo; Luo, ManLi; Nechama, Morris; Lin, Yu-Min; Yao, Yandan; Lee, Tae Ho; Zhou, Xiao Zhen; Swomley, Aaron M.; Butterfield, D. Allan; Zhang, Yan; Lu, Kun Ping

    2015-01-01

    The unique proline isomerase Pin1 is pivotal for protecting against age-dependent neurodegeneration in Alzheimer’s disease (AD), with its inhibition providing a molecular link between tangle and plaque pathologies. Pin1 is oxidatively modified in human AD brains, but little is known about its regulatory mechanisms and pathological significance of such Pin1 modification. In this paper, our determination of crystal structures of oxidized Pin1 reveals a series of Pin1 oxidative modifications on Cys113 in a sequential fashion. Cys113 oxidization is further confirmed by generating antibodies specifically recognizing oxidized Cys113 of Pin1. Furthermore, Pin1 oxidation on Cys113 inactivates its catalytic activity in vitro, and Ala point substitution of Cys113 inactivates the ability of Pin1 to isomerize tau as well as to promote protein turnover of tau and APP. Moreover, redox regulation affects Pin1 subcellular localization and Pin1-mediated neuronal survival in response to hypoxia treatment. Importantly, Cys113-oxidized Pin1 is significantly increased in human AD brain comparing to age-matched controls. These results not only identify a novel Pin1 oxidation site to be the critical catalytic residue Cys113, but also provide a novel oxidative regulation mechanism for inhibiting Pin1 activity in AD. These results suggest that preventing Pin1 oxidization might help to reduce the risk of AD. PMID:25576397

  14. Aqueous synthesis of hierarchical bismuth nanobundles with high catalytic activity to organic dyes

    NASA Astrophysics Data System (ADS)

    Ma, Dechong; Zhao, Yan; Zhao, Jingzhe; Li, Yawen; Lu, Yan; Zhao, Duijia

    2015-07-01

    Bundle-like bismuth (Bi) nanoarchitectures were successfully prepared on a large scale by an aqueous reducing strategy with polyethylene glycol (PEG) as directing agent at 90 °C for 55 min. The bundle-like Bi nanoarchitectures have a length of 4-5 μm and diameter of 0.5-1 μm with fairly uniform construction. Catalytic activities of the as-prepared hierarchical Bi nanobundles were investigated for degrading Rhodamine B (RhB) dye solution under visible-light irradiation. The Bi nanostructures extended excellent catalytic activity and good cycling performance toward photodegradation of RhB. Possible mechanism was proposed for Bi-assisted photocatalytic degradation of RhB under visible-light.

  15. Gold Incorporated Mesoporous Silica Thin Film Model Surface as a Robust SERS and Catalytically Active Substrate.

    PubMed

    Sunil Sekhar, Anandakumari Chandrasekharan; Vinod, Chathakudath Prabhakaran

    2016-01-01

    Ultra-small gold nanoparticles incorporated in mesoporous silica thin films with accessible pore channels perpendicular to the substrate are prepared by a modified sol-gel method. The simple and easy spin coating technique is applied here to make homogeneous thin films. The surface characterization using FESEM shows crack-free films with a perpendicular pore arrangement. The applicability of these thin films as catalysts as well as a robust SERS active substrate for model catalysis study is tested. Compared to bare silica film our gold incorporated silica, GSM-23F gave an enhancement factor of 10³ for RhB with a laser source 633 nm. The reduction reaction of p-nitrophenol with sodium borohydride from our thin films shows a decrease in peak intensity corresponding to -NO₂ group as time proceeds, confirming the catalytic activity. Such model surfaces can potentially bridge the material gap between a real catalytic system and surface science studies. PMID:27213321

  16. Improving the catalytic activity of isopentenyl phosphate kinase through protein coevolution analysis

    PubMed Central

    Liu, Ying; Yan, Zhihui; Lu, Xiaoyun; Xiao, Dongguang; Jiang, Huifeng

    2016-01-01

    Protein rational design has become more and more popular for protein engineering with the advantage of biological big-data. In this study, we described a method of rational design that is able to identify desired mutants by analyzing the coevolution of protein sequence. We employed this approach to evolve an archaeal isopentenyl phosphate kinase that can convert dimethylallyl alcohol (DMA) into precursor of isoprenoids. By designing 9 point mutations, we improved the catalytic activities of IPK about 8-fold in vitro. After introducing the optimal mutant of IPK into engineered E. coli strain for β-carotenoids production, we found that β-carotenoids production exhibited 97% increase over the starting strain. The process of enzyme optimization presented here could be used to improve the catalytic activities of other enzymes. PMID:27052337

  17. Improving the catalytic activity of isopentenyl phosphate kinase through protein coevolution analysis.

    PubMed

    Liu, Ying; Yan, Zhihui; Lu, Xiaoyun; Xiao, Dongguang; Jiang, Huifeng

    2016-01-01

    Protein rational design has become more and more popular for protein engineering with the advantage of biological big-data. In this study, we described a method of rational design that is able to identify desired mutants by analyzing the coevolution of protein sequence. We employed this approach to evolve an archaeal isopentenyl phosphate kinase that can convert dimethylallyl alcohol (DMA) into precursor of isoprenoids. By designing 9 point mutations, we improved the catalytic activities of IPK about 8-fold in vitro. After introducing the optimal mutant of IPK into engineered E. coli strain for β-carotenoids production, we found that β-carotenoids production exhibited 97% increase over the starting strain. The process of enzyme optimization presented here could be used to improve the catalytic activities of other enzymes. PMID:27052337

  18. ALD Functionalized Nanoporous Gold: Thermal Stability, Mechanical Properties, and Catalytic Activity

    SciTech Connect

    Biener, M M; Biener, J; Wichmann, A; Wittstock, A; Baumann, T F; Baeumer, M; Hamza, A V

    2011-03-24

    Nanoporous metals have many technologically promising applications but their tendency to coarsen limits their long-term stability and excludes high temperature applications. Here, we demonstrate that atomic layer deposition (ALD) can be used to stabilize and functionalize nanoporous metals. Specifically, we studied the effect of nanometer-thick alumina and titania ALD films on thermal stability, mechanical properties, and catalytic activity of nanoporous gold (np-Au). Our results demonstrate that even only one-nm-thick oxide films can stabilize the nanoscale morphology of np-Au up to 1000 C, while simultaneously making the material stronger and stiffer. The catalytic activity of np-Au can be drastically increased by TiO{sub 2} ALD coatings. Our results open the door to high temperature sensor, actuator, and catalysis applications and functionalized electrodes for energy storage and harvesting applications.

  19. Characterization and catalytic activity of gold nanoparticles synthesized using ayurvedic arishtams

    NASA Astrophysics Data System (ADS)

    Aswathy Aromal, S.; Dinesh Babu, K. V.; Philip, Daizy

    2012-10-01

    The development of new synthesis methods for monodispersed nanocrystals using cheap and nontoxic chemicals, environmentally benign solvents and renewable materials remains a challenge to the scientific community. The present work reports a new green method for the synthesis of gold nanoparticles. Four different ayurvedic arishtams are used for the reduction of Au3+ to Au nanoparticles. This method is simple, efficient, economic and nontoxic. Gold nanoparticles having different sizes in the range from 15 to 23 nm could be obtained. The nanoparticles have been characterized by UV-Visible spectroscopy, transmission electron microscopy (TEM), X-ray diffraction (XRD) and FTIR analysis. The high crystallinity of nanoparticles is evident from bright circular spots in the SAED pattern and peaks in the XRD pattern. The synthesized gold nanoparticles show good catalytic activity for the reduction of 4-nitrophenol to 4-aminophenol by excess NaBH4. The synthesized nanoparticles are found to exhibit size dependent catalytic property, the smaller nanoparticles showing faster activity.

  20. Hydrogenation under high pressure enhancing catalytic activity of Cu-Zr amorphous alloys

    NASA Astrophysics Data System (ADS)

    Szummer, A.; Janik-Czachor, M.; Molnár, Á.; Marchuk, I.; Varga, M.; Filipek, S. M.

    2002-11-01

    High pressures of hydrogen up to 3.0 GPa and temperatures up to 373 K were used as a pretreatment to introduce structural changes in the bulk and on the surface of Cu-Zr amorphous alloys which then were examined by means of x-ray diffraction and microscopy. The hydrogenative pretreatment of high hydrogen fugacity followed by annealing at 623 K, aimed at causing desorption of hydrogen, and an eventual exposure of the samples to air at room temperature to oxidize Zr, resulted in a distinct increase of catalytic activity in the dehydrogenation of 2-propanol. A tentative mechanism to account for the enhancement of the catalytic activity induced by the above combined pretreatment is discussed.

  1. Discovery of catalytically active orthologues of the Parkinson's disease kinase PINK1: analysis of substrate specificity and impact of mutations.

    PubMed

    Woodroof, Helen I; Pogson, Joe H; Begley, Mike; Cantley, Lewis C; Deak, Maria; Campbell, David G; van Aalten, Daan M F; Whitworth, Alexander J; Alessi, Dario R; Muqit, Miratul M K

    2011-11-01

    Missense mutations of the phosphatase and tensin homolog (PTEN)-induced kinase 1 (PINK1) gene cause autosomal-recessive Parkinson's disease. To date, little is known about the intrinsic catalytic properties of PINK1 since the human enzyme displays such low kinase activity in vitro. We have discovered that, in contrast to mammalian PINK1, insect orthologues of PINK1 we have investigated-namely Drosophila melanogaster (dPINK1), Tribolium castaneum (TcPINK1) and Pediculus humanus corporis (PhcPINK1)-are active as judged by their ability to phosphorylate the generic substrate myelin basic protein. We have exploited the most active orthologue, TcPINK1, to assess its substrate specificity and elaborated a peptide substrate (PINKtide, KKWIpYRRSPRRR) that can be employed to quantify PINK1 kinase activity. Analysis of PINKtide variants reveal that PINK1 phosphorylates serine or threonine, but not tyrosine, and we show that PINK1 exhibits a preference for a proline at the +1 position relative to the phosphorylation site. We have also, for the first time, been able to investigate the effect of Parkinson's disease-associated PINK1 missense mutations, and found that nearly all those located within the kinase domain, as well as the C-terminal non-catalytic region, markedly suppress kinase activity. This emphasizes the crucial importance of PINK1 kinase activity in preventing the development of Parkinson's disease. Our findings will aid future studies aimed at understanding how the activity of PINK1 is regulated and the identification of physiological substrates. PMID:22645651

  2. Engineered catalytic biofilms: Site-specific enzyme immobilization onto E. coli curli nanofibers.

    PubMed

    Botyanszki, Zsofia; Tay, Pei Kun R; Nguyen, Peter Q; Nussbaumer, Martin G; Joshi, Neel S

    2015-10-01

    Biocatalytic transformations generally rely on purified enzymes or whole cells to perform complex transformations that are used on industrial scale for chemical, drug, and biofuel synthesis, pesticide decontamination, and water purification. However, both of these systems have inherent disadvantages related to the costs associated with enzyme purification, the long-term stability of immobilized enzymes, catalyst recovery, and compatibility with harsh reaction conditions. We developed a novel strategy for producing rationally designed biocatalytic surfaces based on Biofilm Integrated Nanofiber Display (BIND), which exploits the curli system of E. coli to create a functional nanofiber network capable of covalent immobilization of enzymes. This approach is attractive because it is scalable, represents a modular strategy for site-specific enzyme immobilization, and has the potential to stabilize enzymes under denaturing environmental conditions. We site-specifically immobilized a recombinant α-amylase, fused to the SpyCatcher attachment domain, onto E. coli curli fibers displaying complementary SpyTag capture domains. We characterized the effectiveness of this immobilization technique on the biofilms and tested the stability of immobilized α-amylase in unfavorable conditions. This enzyme-modified biofilm maintained its activity when exposed to a wide range of pH and organic solvent conditions. In contrast to other biofilm-based catalysts, which rely on high cellular metabolism, the modified curli-based biofilm remained active even after cell death due to organic solvent exposure. This work lays the foundation for a new and versatile method of using the extracellular polymeric matrix of E. coli for creating novel biocatalytic surfaces. PMID:25950512

  3. Methods and apparatuses for preparing a surface to have catalytic activity

    SciTech Connect

    Cooks, Robert G.; Peng, Wen-Ping; Ouyang, Zheng; Goodwin, Michael P.

    2011-03-22

    The invention provides methods and apparatuses that utilize mass spectrometry for preparation of a surface to have catalytic activity through molecular soft-landing of mass selected ions. Mass spectrometry is used to generate combinations of atoms in a particular geometrical arrangement, and ion soft-landing selects this molecular entity or combination of entities and gently deposits the entity or combination intact onto a surface.

  4. The Catalytic Activity of Proline Racemase: a QM/MM Study

    NASA Astrophysics Data System (ADS)

    Stenta, Marco; Calvaresi, Matteo; Altoè, Piero; Spinelli, Domenico; Garavelli, Marco; Bottoni, Andrea

    2007-12-01

    The catalytic activity of an interesting enzyme (involved in the life cycle of the Trypanosoma Cruzi eucariotic parasite) has been elucidated by mean of a QM/MM study. The reaction mechanism of the stereo-inversion of the substrate has been studied by characterizing the associated PES. The nature of the found critical point has been checked by means of numerical frequencies calculations. The role of the various residues in the catalysis has been pointed out.

  5. Synthesis of Pt-Mo-N Thin Film and Catalytic Activity for Fuel Cells

    SciTech Connect

    Miura, Akira; Tague, Michele E.; Gregoire, John M.; Wen, Xiao-Dong; van Dover, R. Bruce; Abruña, Héctor D.; DiSalvo, Francis J.

    2010-05-13

    Pt-Mo-N composition gradient film was synthesized by combining thin-film deposition techniques and subsequent thermal nitridation. A ternary platinum-based nitride, Pt2Mo3N, showed catalytic activities for fuel cell applications and higher electrochemical stability when it was compared with a PtMo alloy with the same Pt:Mo ratio.

  6. Nanorods of cryptomelane via soft chemistry method and their catalytic activity

    NASA Astrophysics Data System (ADS)

    Grigorieva, Anastasia V.; Melnik, Denis M.; Goodilin, Eugene A.; Anufrieva, Tatyana A.; Derlyukova, Lyudmila E.; Tretyakov, Yuri D.

    2012-07-01

    α-MnO2 nanorods were obtained by a fast redox transformation of aqueous solution of potassium permanganate. The formation mechanism of 1D nanocrystals proceeds via a first pH- and temperature sensitive stage followed by cation/anion control of the nanorod growth. A high surface area and nanostructuring allowed to achieve superb catalytic activity in a CO oxidation process compared to a conventionally prepared manganese dioxide.

  7. Briefly Bound to Activate: Transient Binding of a Second Catalytic Magnesium Activates the Structure and Dynamics of CDK2 Kinase for Catalysis

    SciTech Connect

    Bao, Zhao Qin; Jacobsen, Douglas M.; Young, Matthew A.

    2014-10-02

    We have determined high-resolution crystal structures of a CDK2/Cyclin A transition state complex bound to ADP, substrate peptide, and MgF{sub 3}{sup -}. Compared to previous structures of active CDK2, the catalytic subunit of the kinase adopts a more closed conformation around the active site and now allows observation of a second Mg{sup 2+} ion in the active site. Coupled with a strong [Mg{sup 2+}] effect on in vitro kinase activity, the structures suggest that the transient binding of the second Mg{sup 2+} ion is necessary to achieve maximum rate enhancement of the chemical reaction, and Mg{sup 2+} concentration could represent an important regulator of CDK2 activity in vivo. Molecular dynamics simulations illustrate how the simultaneous binding of substrate peptide, ATP, and two Mg{sup 2+} ions is able to induce a more rigid and closed organization of the active site that functions to orient the phosphates, stabilize the buildup of negative charge, and shield the subsequently activated {gamma}-phosphate from solvent.

  8. Crystal structure and site-directed mutagenesis of 3-ketosteroid Δ1-dehydrogenase from Rhodococcus erythropolis SQ1 explain its catalytic mechanism.

    PubMed

    Rohman, Ali; van Oosterwijk, Niels; Thunnissen, Andy-Mark W H; Dijkstra, Bauke W

    2013-12-01

    3-Ketosteroid Δ(1)-dehydrogenases are FAD-dependent enzymes that catalyze the 1,2-desaturation of 3-ketosteroid substrates to initiate degradation of the steroid nucleus. Here we report the 2.0 Å resolution crystal structure of the 56-kDa enzyme from Rhodococcus erythropolis SQ1 (Δ(1)-KSTD1). The enzyme contains two domains: an FAD-binding domain and a catalytic domain, between which the active site is situated as evidenced by the 2.3 Å resolution structure of Δ(1)-KSTD1 in complex with the reaction product 1,4-androstadiene-3,17-dione. The active site contains four key residues: Tyr(119), Tyr(318), Tyr(487), and Gly(491). Modeling of the substrate 4-androstene-3,17-dione at the position of the product revealed its interactions with these residues and the FAD. The C1 and C2 atoms of the substrate are at reaction distance to the N5 atom of the isoalloxazine ring of FAD and the hydroxyl group of Tyr(318), respectively, whereas the C3 carbonyl group is at hydrogen bonding distance from the hydroxyl group of Tyr(487) and the backbone amide of Gly(491). Site-directed mutagenesis of the tyrosines to phenylalanines confirmed their importance for catalysis. The structural features and the kinetic properties of the mutants suggest a catalytic mechanism in which Tyr(487) and Gly(491) work in tandem to promote keto-enol tautomerization and increase the acidity of the C2 hydrogen atoms of the substrate. With assistance of Tyr(119), the general base Tyr(318) abstracts the axial β-hydrogen from C2 as a proton, whereas the FAD accepts the axial α-hydrogen from the C1 atom of the substrate as a hydride ion. PMID:24165124

  9. Crystal Structure and Site-directed Mutagenesis of 3-Ketosteroid Δ1-Dehydrogenase from Rhodococcus erythropolis SQ1 Explain Its Catalytic Mechanism*

    PubMed Central

    Rohman, Ali; van Oosterwijk, Niels; Thunnissen, Andy-Mark W. H.; Dijkstra, Bauke W.

    2013-01-01

    3-Ketosteroid Δ1-dehydrogenases are FAD-dependent enzymes that catalyze the 1,2-desaturation of 3-ketosteroid substrates to initiate degradation of the steroid nucleus. Here we report the 2.0 Å resolution crystal structure of the 56-kDa enzyme from Rhodococcus erythropolis SQ1 (Δ1-KSTD1). The enzyme contains two domains: an FAD-binding domain and a catalytic domain, between which the active site is situated as evidenced by the 2.3 Å resolution structure of Δ1-KSTD1 in complex with the reaction product 1,4-androstadiene-3,17-dione. The active site contains four key residues: Tyr119, Tyr318, Tyr487, and Gly491. Modeling of the substrate 4-androstene-3,17-dione at the position of the product revealed its interactions with these residues and the FAD. The C1 and C2 atoms of the substrate are at reaction distance to the N5 atom of the isoalloxazine ring of FAD and the hydroxyl group of Tyr318, respectively, whereas the C3 carbonyl group is at hydrogen bonding distance from the hydroxyl group of Tyr487 and the backbone amide of Gly491. Site-directed mutagenesis of the tyrosines to phenylalanines confirmed their importance for catalysis. The structural features and the kinetic properties of the mutants suggest a catalytic mechanism in which Tyr487 and Gly491 work in tandem to promote keto-enol tautomerization and increase the acidity of the C2 hydrogen atoms of the substrate. With assistance of Tyr119, the general base Tyr318 abstracts the axial β-hydrogen from C2 as a proton, whereas the FAD accepts the axial α-hydrogen from the C1 atom of the substrate as a hydride ion. PMID:24165124

  10. Synthesis, Characterization, and Catalytic Oxygen Electroreduction Activities of Carbon-Supported PtW Nanoparticle Catalysts

    SciTech Connect

    Xiong, Liufeng; More, Karren Leslie; He, Ting

    2010-01-01

    Carbon-supported PtW (PtW/C) alloy nanoparticle catalysts with well-controlled particle size, dispersion, and composition uniformity, have been synthesized by wet chemical methods of decomposition of carbonyl cluster complexes, hydrolysis of metal salts, and chemical reactions within a reverse microemulsion. The synthesized PtW/C catalysts were characterized by X-ray diffraction, high-resolution transmission electron microscopy, and energy-dispersive spectroscopy. The catalytic oxygen electroreduction activities were measured by the hydrodynamic rotating disk electrode technique in an acidic electrolyte. The influence of the synthesis method on PtW particle size, size distribution, composition uniformity, and catalytic oxygen electroreduction activity, have been investigated. Among the synthesis methods studied, PtW/C catalysts prepared by the decomposition of carbonyl cluster complexes displayed the best platinum mass activity for oxygen reduction reaction under the current small scale production; a 3.4-fold catalytic enhancement was achieved in comparison to a benchmark Pt/C standard.

  11. A microreactor array for spatially resolved measurement of catalytic activity for high-throughput catalysis science

    SciTech Connect

    Kondratyuk, Petro; Gumuslu, Gamze; Shukla, Shantanu; Miller, James B; Morreale, Bryan D; Gellman, Andrew J

    2013-04-01

    We describe a 100 channel microreactor array capable of spatially resolved measurement of catalytic activity across the surface of a flat substrate. When used in conjunction with a composition spread alloy film (CSAF, e.g. Pd{sub x}Cu{sub y}Au{sub 1-x-y}) across which component concentrations vary smoothly, such measurements permit high-throughput analysis of catalytic activity and selectivity as a function of catalyst composition. In the reported implementation, the system achieves spatial resolution of 1 mm{sup 2} over a 10×10 mm{sup 2} area. During operation, the reactant gases are delivered at constant flow rate to 100 points of differing composition on the CSAF surface by means of a 100-channel microfluidic device. After coming into contact with the CSAF catalyst surface, the product gas mixture from each of the 100 points is withdrawn separately through a set of 100 isolated channels for analysis using a mass spectrometer. We demonstrate the operation of the device on a Pd{sub x}Cu{sub y}Au{sub 1-x-y} CSAF catalyzing the H{sub 2}-D{sub 2} exchange reaction at 333 K. In essentially a single experiment, we measured the catalytic activity over a broad swathe of concentrations from the ternary composition space of the Pd{sub x}Cu{sub y}Au{sub 1-x-y} alloy.

  12. Effect of the synthetic method on the catalytic activity of alumina: Epoxidation of cyclohexene

    SciTech Connect

    Valderruten, N.E.; Peña, W.F.; Ramírez, A.E.; Rodríguez-Páez, J.E.

    2015-02-15

    Graphical abstract: Temperature influence on percent conversion and selectivity in the epoxidation of cyclohexene using commercial alumina as a catalyst. - Highlights: • Aluminum oxide was synthesized using Pechini method. • The alumina obtained showed a mix of boehmite and γ-alumina phases. • We research an economically feasible method to obtain alumina for use as a catalyst. • Alumina obtained by Pechini showed high percent conversion and/or selectivity. • The best results were 78% conversion and 78% selectivity to epoxidation reactions. - Abstract: Al{sub 2}O{sub 3} was prepared from different inorganic precursors via the Pechini method and compared with Al{sub 2}O{sub 3} prepared by the sol–gel method. Structural characterization of these materials was carried out by FTIR, X-ray diffraction (XRD), N{sub 2} adsorption at −196 °C and transmission electron microscopy (TEM). The solids were tested in the epoxidation of cyclohexene and a difference in their catalytic activities was observed. The characterization results indicate that the samples prepared by Pechini have a mixture of γ-alumina and boehmite, a condition favoring catalytic activity, whereas the sol–gel sample is less crystalline due to higher boehmite content. These results indicate that both the nature of the precursor and the method of synthesis strongly affect the catalytic activity of Al{sub 2}O{sub 3}.

  13. Supercritical CO{sub 2} mediated synthesis and catalytic activity of graphene/Pd nanocomposites

    SciTech Connect

    Tang, Lulu; Nguyen, Van Hoa; Shim, Jae-Jin

    2015-11-15

    Highlights: • RGO/Pd composite was efficiently prepared via a facile method in supercritical CO{sub 2}. • Graphene sheets were coated uniformly with Pd nanoparticles with a size of ∼8 nm. • Composites exhibited excellent catalytic activity in the Suzuki reaction even after 10 cycles. - Abstract: Graphene sheets were decorated with palladium nanoparticles using a facile and efficient method in supercritical CO{sub 2}. The nanoparticles were formed on the graphene sheets by the simple hydrogen reduction of palladium(II) hexafluoroacetylacetonate precursor in supercritical CO{sub 2}. The product was characterized by X-ray diffraction, Fourier transform infrared spectroscopy, scanning electron microscopy, transmission electron microscopy, and X-ray photoelectron spectroscopy. Highly dispersed nanoparticles with various sizes and shapes adhered well to the graphene sheets. The composites showed high catalytic activities for the Suzuki reaction under aqueous and aerobic conditions within 5 min. The effects of the different Pd precursor loadings on the catalytic activities of the composites were also examined.

  14. Catalytic activity of cobalt on nanotextured polymer films for hydrogen production

    NASA Astrophysics Data System (ADS)

    Malvadkar, Niranjan A.; Sekeroglu, Koray; Dressick, Walter J.; Demirel, Melik C.

    2011-10-01

    We describe the mechanism of cobalt and ligand binding on nanotextured poly(chloro-p-xylylene) (PPX) films as supports for catalytic release of H2 from alkaline aqueous solutions of sodium borohydride. Cobalt catalysts are prepared on nanotextured PPX substrates via electroless plating using a Sn-free Pd(II) colloid with adsorbed pyridine ligand as an adhesion promoter. Gas physisorption studies on PPX, using N2 and CO2 as probe gases, indicate the presence of micropores (∼1 to 2 nm width) responsible for the adsorption and non-covalent stabilization of pyridine molecules on the nanotextured surface. The strongly adsorbed pyridine molecules promote Co adhesion onto the PPX surface during subsequent electroless deposition, thereby retaining the metal's catalytic activity for H2 evolution even after multiple reaction cycles. In contrast, conventionally deposited PPX is devoid of any nanotexture and contains fewer micropores capable of stabilizing pyridine adsorption, resulting in poor metallization and catalytic activity for H2 evolution. We also demonstrate the effect of patterning the PPX substrate as a means to further improve the activity of the Co catalyst to achieve H2 evolution rates comparable to those obtained using precious metal catalysts.

  15. Catalytic activity of human carbonic anhydrase isoform IX is displayed both extra- and intracellularly.

    PubMed

    Klier, Michael; Jamali, Somayeh; Ames, Samantha; Schneider, Hans-Peter; Becker, Holger M; Deitmer, Joachim W

    2016-01-01

    Most carbonic anhydrases catalyse the reversible conversion of carbon dioxide to protons and bicarbonate, either as soluble cytosolic enzymes, in or at intracellular organelles, or at the extracellular face of the cell membrane as membrane-anchored proteins. Carbonic anhydrase isoform IX (CA IX), a membrane-bound enzyme with catalytic activity at the extracellular membrane surface, has come to prominence in recent years because of its association with hypoxic tissue, particularly tumours, often indicating poor prognosis. We have evaluated the catalytic activity of CA IX heterologously expressed in Xenopus laevis oocytes by measuring the amplitude and rate of cytosolic pH changes as well as pH changes at the outer membrane surface (pHs ) during addition and removal of 5% CO2 /25 mm HCO3-, and by mass spectrometry. Our results indicate both extracellular and intracellular catalytic activity of CA IX. Reduced rates of CO2 -dependent intracellular pH changes after knockdown of CA IX confirmed these findings in two breast cancer cell lines: MCF-7 and MDA-MB-231. Our results demonstrate a new function of CA IX that may be important in the search for therapeutic cancer drugs targeting CA IX. PMID:26470855

  16. Insight into the Mechanism of Intramolecular Inhibition of the Catalytic Activity of Sirtuin 2 (SIRT2)

    PubMed Central

    Li, Jinyu; Flick, Franziska; Verheugd, Patricia; Carloni, Paolo; Lüscher, Bernhard; Rossetti, Giulia

    2015-01-01

    Sirtuin 2 (SIRT2) is a NAD+-dependent deacetylase that has been associated with neurodegeneration and cancer. SIRT2 is composed of a central catalytic domain, the structure of which has been solved, and N- and C-terminal extensions that are thought to control SIRT2 function. However structural information of these N- and C-terminal regions is missing. Here, we provide the first full-length molecular models of SIRT2 in the absence and presence of NAD+. We also predict the structural alterations associated with phosphorylation of SIRT2 at S331, a modification that inhibits catalytic activity. Bioinformatics tools and molecular dynamics simulations, complemented by in vitro deacetylation assays, provide a consistent picture based on which the C-terminal region of SIRT2 is suggested to function as an autoinhibitory region. This has the capacity to partially occlude the NAD+ binding pocket or stabilize the NAD+ in a non-productive state. Furthermore, our simulations suggest that the phosphorylation at S331 causes large conformational changes in the C-terminal region that enhance the autoinhibitory activity, consistent with our previous findings that phosphorylation of S331 by cyclin-dependent kinases inhibits SIRT2 catalytic activity. The molecular insight into the role of the C-terminal region in controlling SIRT2 function described in this study may be useful for future design of selective inhibitors targeting SIRT2 for therapeutic applications. PMID:26407304

  17. Conformational coupling, bridge helix dynamics and active site dehydration in catalysis by RNA polymerase

    PubMed Central

    Seibold, Steve A.; Singh, Badri Nath; Zhang, Chunfen; Kireeva, Maria; Domecq, Céline; Bouchard, Annie; Nazione, Anthony M.; Feig, Michael; Cukier, Robert I.; Coulombe, Benoit; Kashlev, Mikhail; Hampsey, Michael; Burton, Zachary F.

    2010-01-01

    Molecular dynamics simulation of Thermus thermophilus (Tt) RNA polymerase (RNAP) in a catalytic conformation demonstrates that the active site dNMP-NTP base pair must be substantially dehydrated to support full active site closing and optimum conditions for phosphodiester bond synthesis. In silico mutant β R428A RNAP, which was designed based on substitutions at the homologous position (Rpb2 R512) of Saccharomyces cerevisiae (Sc) RNAP II, was used as a reference structure to compare to Tt RNAP in simulations. Long range conformational coupling linking a dynamic segment of the bridge α-helix, the extended fork loop, the active site, and the trigger loop-trigger helix is apparent and adversely affected in β R428A RNAP. Furthermore, bridge helix bending is detected in the catalytic structure, indicating that bridge helix dynamics may regulate phosphodiester bond synthesis as well as translocation. An active site “latch” assembly that includes a key trigger helix residue Tt β’ H1242 and highly conserved active site residues β E445 and R557 appears to help regulate active site hydration/dehydration. The potential relevance of these observations in understanding RNAP and DNAP induced fit and fidelity is discussed. PMID:20478425

  18. Catalytic supports on the base of activated anthracites and synthetic carbons

    NASA Astrophysics Data System (ADS)

    Lyubchik, S. B.; Tikhonova, L. P.; Tarasenko, Yu. A.; Galushko, O. L.; Galushko, L. Ya.; Fonseca, I. M.

    2006-06-01

    Selective adsorption of platinum group metals (PMG) on activated carbons from a multi-component model and technological solutions was proposed for the preparation of heterogeneous-supported catalysts. Activated natural anthracites and a nitrogen-containing synthetic carbon are considered as carriers for Pd-supported catalysts. Their catalytic activity was studied in the Pd-catalyzed reactions of hydrogen peroxide decomposition and chloride ions oxidation by manganese(III). On the base of the obtained results, novel high sensitive analytical methods both for direct determination of supported-metal quantity and palladium oxidation states on the surface of spent adsorbents are suggested.

  19. Structural and biochemical characterization of an active arylamine N-acetyltransferase possessing a non-canonical Cys-His-Glu catalytic triad.

    PubMed

    Kubiak, Xavier; Li de la Sierra-Gallay, Inès; Chaffotte, Alain F; Pluvinage, Benjamin; Weber, Patrick; Haouz, Ahmed; Dupret, Jean-Marie; Rodrigues-Lima, Fernando

    2013-08-01

    Arylamine N-acetyltransferases (NATs), a class of xenobiotic-metabolizing enzymes, catalyze the acetylation of aromatic amine compounds through a strictly conserved Cys-His-Asp catalytic triad. Each residue is essential for catalysis in both prokaryotic and eukaryotic NATs. Indeed, in (HUMAN)NAT2 variants, mutation of the Asp residue to Asn, Gln, or Glu dramatically impairs enzyme activity. However, a putative atypical NAT harboring a catalytic triad Glu residue was recently identified in Bacillus cereus ((BACCR)NAT3) but has not yet been characterized. We report here the crystal structure and functional characterization of this atypical NAT. The overall fold of (BACCR)NAT3 and the geometry of its Cys-His-Glu catalytic triad are similar to those present in functional NATs. Importantly, the enzyme was found to be active and to acetylate prototypic arylamine NAT substrates. In contrast to (HUMAN) NAT2, the presence of a Glu or Asp in the triad of (BACCR)NAT3 did not significantly affect enzyme structure or function. Computational analysis identified differences in residue packing and steric constraints in the active site of (BACCR)NAT3 that allow it to accommodate a Cys-His-Glu triad. These findings overturn the conventional view, demonstrating that the catalytic triad of this family of acetyltransferases is plastic. Moreover, they highlight the need for further study of the evolutionary history of NATs and the functional significance of the predominant Cys-His-Asp triad in both prokaryotic and eukaryotic forms. PMID:23770703

  20. Low dielectric response in enzyme active site

    PubMed Central

    Mertz, Edward L.; Krishtalik, Lev I.

    2000-01-01

    The kinetics of charge transfer depend crucially on the dielectric reorganization of the medium. In enzymatic reactions that involve charge transfer, atomic dielectric response of the active site and of its surroundings determines the efficiency of the protein as a catalyst. We report direct spectroscopic measurements of the reorganization energy associated with the dielectric response in the active site of α-chymotrypsin. A chromophoric inhibitor of the enzyme is used as a spectroscopic probe. We find that water strongly affects the dielectric reorganization in the active site of the enzyme in solution. The reorganization energy of the protein matrix in the vicinity of the active site is similar to that of low-polarity solvents. Surprisingly, water exhibits an anomalously high dielectric response that cannot be described in terms of the dielectric continuum theory. As a result, sequestering the active site from the aqueous environment inside low-dielectric enzyme body dramatically reduces the dielectric reorganization. This reduction is particularly important for controlling the rate of enzymatic reactions. PMID:10681440

  1. Nanorods, nanospheres, nanocubes: Synthesis, characterization and catalytic activity of nanoferrites of Mn, Co, Ni, Part-89

    SciTech Connect

    Singh, Supriya; Srivastava, Pratibha; Singh, Gurdip

    2013-02-15

    Graphical abstract: Prepared nanoferrites were characterized by FE-SEM and bright field TEM micrographs. The catalytic effect of these nanoferrites was evaluated on the thermal decomposition of ammonium perchlorate using TG and TG–DSC techniques. The kinetics of thermal decomposition of AP was evaluated using isothermal TG data by model fitting as well as isoconversional method. Display Omitted Highlights: ► Synthesis of ferrite nanostructures (∼20.0 nm) by wet-chemical method under different synthetic conditions. ► Characterization using XRD, FE-SEM, EDS, TEM, HRTEM and SAED pattern. ► Catalytic activity of ferrite nanostructures on AP thermal decomposition by thermal techniques. ► Burning rate measurements of CSPs with ferrite nanostructures. ► Kinetics of thermal decomposition of AP + nanoferrites. -- Abstract: In this paper, the nanoferrites of Mn, Co and Ni were synthesized by wet chemical method and characterized by X-ray diffraction (XRD), field emission scanning electron microscopy (FE-SEM), energy dispersive, X-ray spectra (EDS), transmission electron microscopy (TEM) and high resolution transmission electron microscopy (HR-TEM). It is catalytic activity were investigated on the thermal decomposition of ammonium perchlorate (AP) and composite solid propellants (CSPs) using thermogravimetry (TG), TG coupled with differential scanning calorimetry (TG–DSC) and ignition delay measurements. Kinetics of thermal decomposition of AP + nanoferrites have also been investigated using isoconversional and model fitting approaches which have been applied to data for isothermal TG decomposition. The burning rate of CSPs was considerably enhanced by these nanoferrites. Addition of nanoferrites to AP led to shifting of the high temperature decomposition peak toward lower temperature. All these studies reveal that ferrite nanorods show the best catalytic activity superior to that of nanospheres and nanocubes.

  2. The support effect on the size and catalytic activity of thiolated Au25 nanoclusters as precatalysts

    NASA Astrophysics Data System (ADS)

    Fang, Jun; Li, Jingguo; Zhang, Bin; Yuan, Xun; Asakura, Hiroyuki; Tanaka, Tsunehiro; Teramura, Kentaro; Xie, Jianping; Yan, Ning

    2015-03-01

    In this study, 6-mercaptohexanoic (MHA) protected Au25(MHA)18 nanoclusters (or thiolated Au NCs) deposited on various inorganic supports, including hydroxyapatite (HAP), TiO2 (Degussa P25), activated carbon (AC), pyrolyzed graphene oxide (PGO), and fumed SiO2 were prepared via a conventional impregnation method. Following that, calcination under a N2 stream was conducted to produce surface ligand free, highly dispersed Au NCs catalysts. The effects of supports on the size and catalytic activity of Au NCs were systematically investigated. No obvious size growth was observed for Au NCs on HAP and P25 after thermally induced ligand removal, due to the strong interaction between the metal and the supports. However, severe aggregations of Au NCs were seen after thermal treatment on three other supports, including AC, PGO, and SiO2. The removal of surface thiol ligands from the Au NCs is crucial to catalyze nitrobenzene hydrogenation, where only calcined Au/HAP and Au/P25 exhibited good catalytic activity. On the other hand, all the supported Au NCs were active for the styrene oxidation, where Au/HAP exhibited the best catalytic performance. Altogether, both the size effect and metal-support interaction are crucial for the design of supported Au NCs as efficient catalysts for targeted reactions.In this study, 6-mercaptohexanoic (MHA) protected Au25(MHA)18 nanoclusters (or thiolated Au NCs) deposited on various inorganic supports, including hydroxyapatite (HAP), TiO2 (Degussa P25), activated carbon (AC), pyrolyzed graphene oxide (PGO), and fumed SiO2 were prepared via a conventional impregnation method. Following that, calcination under a N2 stream was conducted to produce surface ligand free, highly dispersed Au NCs catalysts. The effects of supports on the size and catalytic activity of Au NCs were systematically investigated. No obvious size growth was observed for Au NCs on HAP and P25 after thermally induced ligand removal, due to the strong interaction between the

  3. Triosephosphate isomerase I170V alters catalytic site, enhances stability and induces pathology in a Drosophila model of TPI deficiency

    DOE PAGESBeta

    Roland, Bartholomew P.; Amrich, Christopher G.; Kammerer, Charles J.; Stuchul, Kimberly A.; Larsen, Samantha B.; Rode, Sascha; Aslam, Anoshe A.; Heroux, Annie; Wetzel, Ronald; VanDemark, Andrew P.; et al

    2014-10-16

    Triosephosphate isomerase (TPI) is a glycolytic enzyme which homodimerizes for full catalytic activity. Mutations of the TPI gene elicit a disease known as TPI Deficiency, a glycolytic enzymopathy noted for its unique severity of neurological symptoms. Evidence suggests that TPI Deficiency pathogenesis may be due to conformational changes of the protein, likely affecting dimerization and protein stability. In this report, we genetically and physically characterize a human disease-associated TPI mutation caused by an I170V substitution. Human TPII170V elicits behavioral abnormalities in Drosophila. An examination of hTPII170V enzyme kinetics revealed this substitution reduced catalytic turnover, while assessments of thermal stability demonstratedmore » an increase in enzyme stability. Furthermore, the crystal structure of the homodimeric I170V mutant reveals changes in the geometry of critical residues within the catalytic pocket. In the end, collectively these data reveal new observations of the structural and kinetic determinants of TPI deficiency pathology, providing new insights into disease pathogenesis.« less

  4. An Iron Reservoir to the Catalytic Metal

    PubMed Central

    Liu, Fange; Geng, Jiafeng; Gumpper, Ryan H.; Barman, Arghya; Davis, Ian; Ozarowski, Andrew; Hamelberg, Donald; Liu, Aimin

    2015-01-01

    The rubredoxin motif is present in over 74,000 protein sequences and 2,000 structures, but few have known functions. A secondary, non-catalytic, rubredoxin-like iron site is conserved in 3-hydroxyanthranilate 3,4-dioxygenase (HAO), from single cellular sources but not multicellular sources. Through the population of the two metal binding sites with various metals in bacterial HAO, the structural and functional relationship of the rubredoxin-like site was investigated using kinetic, spectroscopic, crystallographic, and computational approaches. It is shown that the first metal presented preferentially binds to the catalytic site rather than the rubredoxin-like site, which selectively binds iron when the catalytic site is occupied. Furthermore, an iron ion bound to the rubredoxin-like site is readily delivered to an empty catalytic site of metal-free HAO via an intermolecular transfer mechanism. Through the use of metal analysis and catalytic activity measurements, we show that a downstream metabolic intermediate can selectively remove the catalytic iron. As the prokaryotic HAO is often crucial for cell survival, there is a need for ensuring its activity. These results suggest that the rubredoxin-like site is a possible auxiliary iron source to the catalytic center when it is lost during catalysis in a pathway with metabolic intermediates of metal-chelating properties. A spare tire concept is proposed based on this biochemical study, and this concept opens up a potentially new functional paradigm for iron-sulfur centers in iron-dependent enzymes as transient iron binding and shuttling sites to ensure full metal loading of the catalytic site. PMID:25918158

  5. The Roles of the Catalytic and Noncatalytic Activities of Rpd3L and Rpd3S in the Regulation of Gene Transcription in Yeast

    PubMed Central

    Yeheskely-Hayon, Daniella; Kotler, Anat; Stark, Michal; Hashimshony, Tamar; Sagee, Shira; Kassir, Yona

    2013-01-01

    In budding yeasts, the histone deacetylase Rpd3 resides in two different complexes called Rpd3L (large) and Rpd3S (small) that exert opposing effects on the transcription of meiosis-specific genes. By introducing mutations that disrupt the integrity and function of either Rpd3L or Rpd3S, we show here that Rpd3 function is determined by its association with either of these complexes. Specifically, the catalytic activity of Rpd3S activates the transcription of the two major positive regulators of meiosis, IME1 and IME2, under all growth conditions and activates the transcription of NDT80 only during vegetative growth. In contrast, the effects of Rpd3L depends on nutrients; it represses or activates transcription in the presence or absence of a nitrogen source, respectively. Further, we show that transcriptional activation does not correlate with histone H4 deacetylation, suggesting an effect on a nonhistone protein. Comparison of rpd3-null and catalytic-site point mutants revealed an inhibitory activity that is independent of either the catalytic activity of Rpd3 or the integrity of Rpd3L and Rpd3S. PMID:24358376

  6. The roles of the catalytic and noncatalytic activities of Rpd3L and Rpd3S in the regulation of gene transcription in yeast.

    PubMed

    Yeheskely-Hayon, Daniella; Kotler, Anat; Stark, Michal; Hashimshony, Tamar; Sagee, Shira; Kassir, Yona

    2013-01-01

    In budding yeasts, the histone deacetylase Rpd3 resides in two different complexes called Rpd3L (large) and Rpd3S (small) that exert opposing effects on the transcription of meiosis-specific genes. By introducing mutations that disrupt the integrity and function of either Rpd3L or Rpd3S, we show here that Rpd3 function is determined by its association with either of these complexes. Specifically, the catalytic activity of Rpd3S activates the transcription of the two major positive regulators of meiosis, IME1 and IME2, under all growth conditions and activates the transcription of NDT80 only during vegetative growth. In contrast, the effects of Rpd3L depends on nutrients; it represses or activates transcription in the presence or absence of a nitrogen source, respectively. Further, we show that transcriptional activation does not correlate with histone H4 deacetylation, suggesting an effect on a nonhistone protein. Comparison of rpd3-null and catalytic-site point mutants revealed an inhibitory activity that is independent of either the catalytic activity of Rpd3 or the integrity of Rpd3L and Rpd3S. PMID:24358376

  7. Tough and catalytically active hybrid biofibers wet-spun from nanochitin hydrogels.

    PubMed

    Das, Paramita; Heuser, Thomas; Wolf, Andrea; Zhu, Baolei; Demco, Dan Eugen; Ifuku, Shinsuke; Walther, Andreas

    2012-12-10

    Sustainable alternatives for high-performance and functional materials based on renewable resources are intensely needed as future alternatives for present-day, fossil-based materials. Nanochitin represents an emerging class of highly crystalline bionanoparticles with high intrinsic mechanical properties and the ability for conjugation into functional materials owing to reactive amine and hydroxyl groups. Herein we demonstrate that hydrogels containing surface-deacetylated chitin nanofibrils of micrometer length and average diameters of 9 nm, as imaged by cryogenic transmission electron microscopy, can be wet-spun into macrofibers via extrusion in a coagulation bath, a simple low energy and large-scale processing route. The resulting biofibers display attractive mechanical properties with a large plastic region of about 12% in strain, in which frictional sliding of nanofibrils allows dissipation of fracture energy and enables a high work-of-fracture of near 10 MJ/m3. We further show how to add functionality to these macrofibers by exploiting the amine functions of the surface chitosan groups to host catalytically active noble metal nanoparticles, furnishing biobased, renewable catalytic hybrids. These inorganic/organic macrofibers can be used repeatedly for fast catalytic reductions of model compounds without loss of activity, rendering the concept of hybridized chitin materials interesting as novel bioderived supports for nanoparticle catalysts. PMID:23102411

  8. Facile and green synthesis of cellulose nanocrystal-supported gold nanoparticles with superior catalytic activity.

    PubMed

    Yan, Wei; Chen, Chang; Wang, Ling; Zhang, Dan; Li, Ai-Jun; Yao, Zheng; Shi, Li-Yi

    2016-04-20

    The emphasis of science and technology shifts toward environmentally friendly and sustainable resources and processes. Herein, we report a facile, one-pot and green synthesis of biomaterial-supported gold nanoparticles (AuNPs) with superior catalytic activity. Cellulose nanocrystal (CNC)-supported AuNPs were prepared by heating the aqueous mixture of HAuCl4, CNCs and polyethylene glycol, avoiding toxic chemicals, extreme condition and complicated procedure. The resultant CNC-supported AuNPs exhibited catalytic activities for the reduction of 4-nitrophenol by sodium borohydride. The maximum apparent rate constant reached 1.47×10(-2)s(-1), and the turnover frequency reached 641h(-1). The superior catalytic performance can be ascribed to the large amount of highly dispersed AuNPs with few nanometers in size which are loaded on CNCs. About 90% of the AuNPs are smaller than 10nm, and nearly 60% of the AuNPs are smaller than 5nm. The synthesis is eco-friendly, facile and low-cost, thus has great potential for industrial and medical applications. PMID:26876829

  9. Catalytic Reduction of 4-Nitrophenol Using Silver Nanoparticles with Adjustable Activity.

    PubMed

    Kästner, Claudia; Thünemann, Andreas F

    2016-07-26

    We report on the development of ultrasmall core-shell silver nanoparticles synthesized by an upscaled modification of the polyol process. It is foreseen to use these thoroughly characterized particles as reference material to compare the catalytic and biological properties of functionalized silver nanoparticles. Small-angle X-ray scattering (SAXS) analysis reveals a narrow size distribution of the silver cores with a mean radius of Rc = 3.0 nm and a distribution width of 0.6 nm. Dynamic light scattering (DLS) provides a hydrodynamic radius of RH = 10.0 nm and a PDI of 0.09. The particles' surface is covered with poly(acrylic acid) (PAA) forming a shell with a thickness of 7.0 nm, which provides colloidal stability lasting for more than 6 months at ambient conditions. The PAA can be easily exchanged by biomolecules to modify the surface functionality. Replacements of PAA with glutathione (GSH) and bovine serum albumin (BSA) have been performed as examples. We demonstrate that the silver particles effectively catalyze the reduction of 4-nitrophenol to 4-aminophenol with sodium borohydride. With PAA as stabilizer, the catalytic activity of 436 ± 24 L g(-1) s(-1) is the highest reported in the literature for silver nanoparticles. GSH and BSA passivate the surface substantially, resulting in a catalytic activity of 77.6 ± 0.9 and 3.47 ± 0.50 L g(-1) s(-1), respectively. PMID:27380382

  10. A Novel miRNA Processing Pathway Independent of Dicer Requires Argonaute2 Catalytic Activity

    PubMed Central

    Cifuentes, Daniel; Xue, Huiling; Taylor, David W.; Patnode, Heather; Mishima, Yuichiro; Cheloufi, Sihem; Ma, Enbo; Mane, Shrikant; Hannon, Gregory J.; Lawson, Nathan D.; Wolfe, Scot A.; Giraldez, Antonio J.

    2011-01-01

    Dicer is a central enzyme in microRNA (miRNA) processing. We identified a Dicer-independent miRNA biogenesis pathway that uses Argonaute2 (Ago2) slicer catalytic activity. In contrast to other miRNAs, miR-451 levels were refractory to dicer loss of function but were reduced in MZago2 (maternal-zygotic) mutants. We found that pre-miR-451 processing requires Ago2 catalytic activity in vivo. MZago2 mutants showed delayed erythropoiesis that could be rescued by wild-type Ago2 or miR-451-duplex but not by catalytically dead Ago2. Changing the secondary structure of Dicer-dependent miRNAs to mimic that of pre-miR-451 restored miRNA function and rescued developmental defects in MZdicer mutants, indicating that the pre-miRNA secondary structure determines the processing pathway in vivo. We propose that Ago2-mediated cleavage of pre-miRNAs, followed by uridylation and trimming, generates functional miRNAs independently of Dicer. PMID:20448148

  11. A novel miRNA processing pathway independent of Dicer requires Argonaute2 catalytic activity.

    PubMed

    Cifuentes, Daniel; Xue, Huiling; Taylor, David W; Patnode, Heather; Mishima, Yuichiro; Cheloufi, Sihem; Ma, Enbo; Mane, Shrikant; Hannon, Gregory J; Lawson, Nathan D; Wolfe, Scot A; Giraldez, Antonio J

    2010-06-25

    Dicer is a central enzyme in microRNA (miRNA) processing. We identified a Dicer-independent miRNA biogenesis pathway that uses Argonaute2 (Ago2) slicer catalytic activity. In contrast to other miRNAs, miR-451 levels were refractory to dicer loss of function but were reduced in MZago2 (maternal-zygotic) mutants. We found that pre-miR-451 processing requires Ago2 catalytic activity in vivo. MZago2 mutants showed delayed erythropoiesis that could be rescued by wild-type Ago2 or miR-451-duplex but not by catalytically dead Ago2. Changing the secondary structure of Dicer-dependent miRNAs to mimic that of pre-miR-451 restored miRNA function and rescued developmental defects in MZdicer mutants, indicating that the pre-miRNA secondary structure determines the processing pathway in vivo. We propose that Ago2-mediated cleavage of pre-miRNAs, followed by uridylation and trimming, generates functional miRNAs independently of Dicer. PMID:20448148

  12. Co-Cu Nanoparticles: Synthesis by Galvanic Replacement and Phase Rearrangement during Catalytic Activation.

    PubMed

    Nafria, Raquel; Genç, Aziz; Ibáñez, Maria; Arbiol, Jordi; de la Piscina, Pilar Ramírez; Homs, Narcís; Cabot, Andreu

    2016-03-01

    The control of the phase distribution in multicomponent nanomaterials is critical to optimize their catalytic performance. In this direction, while impressive advances have been achieved in the past decade in the synthesis of multicomponent nanoparticles and nanocomposites, element rearrangement during catalyst activation has been frequently overseen. Here, we present a facile galvanic replacement-based procedure to synthesize Co@Cu nanoparticles with narrow size and composition distributions. We further characterize their phase arrangement before and after catalytic activation. When oxidized at 350 °C in air to remove organics, Co@Cu core-shell nanostructures oxidize to polycrystalline CuO-Co3O4 nanoparticles with randomly distributed CuO and Co3O4 crystallites. During a posterior reduction treatment in H2 atmosphere, Cu precipitates in a metallic core and Co migrates to the nanoparticle surface to form Cu@Co core-shell nanostructures. The catalytic behavior of such Cu@Co nanoparticles supported on mesoporous silica was further analyzed toward CO2 hydrogenation in real working conditions. PMID:26878153

  13. Graphdiyne oxides as excellent substrate for electroless deposition of Pd clusters with high catalytic activity.

    PubMed

    Qi, Hetong; Yu, Ping; Wang, Yuexiang; Han, Guangchao; Liu, Huibiao; Yi, Yuanping; Li, Yuliang; Mao, Lanqun

    2015-04-29

    Graphdiyne (GDY), a novel kind of two-dimensional carbon allotrope consisting of sp- and sp(2)-hybridized carbon atoms, is found to be able to serve as the reducing agent and stabilizer for electroless deposition of highly dispersed Pd nanoparticles owing to its low reduction potential and highly conjugated electronic structure. Furthermore, we observe that graphdiyne oxide (GDYO), the oxidation form of GDY, can be used as an even excellent substrate for electroless deposition of ultrafine Pd clusters to form Pd/GDYO nanocomposite that exhibits a high catalytic performance toward the reduction of 4-nitrophenol. The high catalytic performance is considered to benefit from the rational design and electroless deposition of active metal catalysts with GDYO as the support. PMID:25871853

  14. Green synthesis of silver nanoparticles, decorated on graphene oxide nanosheets and their catalytic activity

    NASA Astrophysics Data System (ADS)

    Sreekanth, T. V. M.; Jung, Min-Ji; Eom, In-Yong

    2016-01-01

    In this study, we develop an inexpensive and green route for the synthesis of silver nanoparticles (AgNPs) using Picrasma quassioides bark aqueous extract as reducing and capping agent and also eco-friendly decorate graphene oxide (GO) nanosheets with AgNPs (GO-AgNPs). Green synthesized AgNPs and GO-AgNPs composites were characterized by UV-Visible spectroscopy, SEM-EDX, and TEM-SAED techniques. The resulting GO-AgNPs contained about 41.35% of Ag and the AgNPs size ranges 17.5-66.5 nm, and GO-AgNPs size ranges 10-49.5 nm. Moreover, the GO-AgNPs exhibited excellent catalytic activity towards the methylene blue (MB) in the presence of sodium borohydride (NaBH4) at room temperature. This catalytic reaction completed within 15 min.

  15. Green synthesis, characterization and catalytic activity of palladium nanoparticles by xanthan gum

    NASA Astrophysics Data System (ADS)

    Santoshi kumari, Amrutham; Venkatesham, Maragoni; Ayodhya, Dasari; Veerabhadram, Guttena

    2015-03-01

    Here, we report the synthesis, characterization and catalytic evaluation of palladium nanoparticles (PdNPs) using xanthan gum, acting as both reducing and stabilizing agent without using any synthetic reagent. The uniqueness of our method lies in its fast synthesis rates using hydrothermal method in autoclave at a pressure of 15 psi and at 120 °C temperature by 10 min time. The formation and size of the PdNPs were characterized by UV-visible spectroscopy, X-ray diffraction, Fourier transform infrared spectroscopy and transmission electron microscopy. The catalytic activity of PdNPs was evaluated on the reduction of 4-nitrophenol to 4-aminophenol by sodium borohydride using spectrophotometry.

  16. Layered Double Hydroxide Nanoclusters: Aqueous, Concentrated, Stable, and Catalytically Active Colloids toward Green Chemistry.

    PubMed

    Tokudome, Yasuaki; Morimoto, Tsuyoshi; Tarutani, Naoki; Vaz, Pedro D; Nunes, Carla D; Prevot, Vanessa; Stenning, Gavin B G; Takahashi, Masahide

    2016-05-24

    Increasing attention has been dedicated to the development of nanomaterials rendering green and sustainable processes, which occur in benign aqueous reaction media. Herein, we demonstrate the synthesis of another family of green nanomaterials, layered double hydroxide (LDH) nanoclusters, which are concentrated (98.7 g/L in aqueous solvent), stably dispersed (transparent sol for >2 weeks), and catalytically active colloids of nano LDHs (isotropic shape with the size of 7.8 nm as determined by small-angle X-ray scattering). LDH nanoclusters are available as colloidal building blocks to give access to meso- and macroporous LDH materials. Proof-of-concept applications revealed that the LDH nanocluster works as a solid basic catalyst and is separable from solvents of catalytic reactions, confirming the nature of nanocatalysts. The present work closely investigates the unique physical and chemical features of this colloid, the formation mechanism, and the ability to act as basic nanocatalysts in benign aqueous reaction systems. PMID:27124717

  17. An ultra-low Pd loading nanocatalyst with efficient catalytic activity.

    PubMed

    Jin, Yunxia; Xi, Jiangbo; Zhang, Zheye; Xiao, Junwu; Xiao, Fei; Qian, Lihua; Wang, Shuai

    2015-03-12

    An ultra-low Pd loading nanocatalyst is synthesized by a convenient solution route of photochemical reduction and aqueous chemical growth. The modification of nanocatalyst structures is investigated through changing morphologies of Pd nanoclusters on the surface of ZnO nanorods. A significant enhancement in photocatalytic properties has been achieved by decorating a trace amount of Pd clusters (0.05 at%) on the surface of ZnO nanorods. The reduction of 4-nitrophenol (4-NP) to 4-aminophenol (4-AP) is applied to demonstrate multiple catalytic activities in the Pd-ZnO hybrid nanocatalyst, which also provides a better understanding of the relationship between the unique nanoconfigured structure and catalytic performance. PMID:25735825

  18. Influence of support hydroxides on the catalytic activity of oxidized gold clusters

    SciTech Connect

    Veith, Gabriel M; Lupini, Andrew R; Pennycook, Stephen J; Dudney, Nancy J

    2010-01-01

    Gold oxide nanoparticles were prepared on the native surface and a hydroxylated surface of a non-porous TiO2 support (Degussa P25). Scanning transmission electron microscopy results show the formation of similarly sized clusters on both support materials (1.86 and 1.61 nm clusters on the native oxide and the hydroxylated oxide respectively). X-ray absorption near edge spectroscopy and X-ray photoelectron spectroscopy clearly indicate the formation of Au3+ rich oxide nanoparticles. Despite the similar cluster sizes and oxidation states the gold oxide clusters grown on the hydroxylated surface were at least 180 times more catalytically active for the oxidation of carbon monoxide then those grown on the native oxide surface. These hydroxides are conveniently introduced during the solution phase synthesis of gold catalysts and play a dominate, but previously unrecognized, role in the catalytic properties of both oxidized and metallic gold particles.

  19. Nickel-doped ceria nanoparticles for promoting catalytic activity of Pt/C for ethanol electrooxidation

    NASA Astrophysics Data System (ADS)

    Tan, Qiang; Du, Chunyu; Sun, Yongrong; Du, Lei; Yin, Geping; Gao, Yunzhi

    2014-10-01

    This paper reports the facile synthesis of monodispersed nickel-doped ceria nanoparticles by a thermal decomposition method, which is used to promote catalytic properties of Pt/C. The Pt/Ni-doped CeO2/C catalyst obtained exhibits remarkably high activity and stability towards the ethanol electrooxidation in acidic media. This is attributed to higher oxygen releasing capacity and stronger interaction of Ni-doped CeO2 with Pt than pure CeO2 nanoparticles that contribute positively to the removal of poisoning intermediates. We believe that the design concept and synthetic strategy of metal doped oxides used for fuel cell catalysts can be potentially extended to other catalytic fields.

  20. Tailoring the assembly, interfaces, and porosity of nanostructures toward enhanced catalytic activity.

    PubMed

    Nguyen, Thanh-Dinh; Dinh, Cao-Thang; Do, Trong-On

    2015-01-14

    The evolution of nanotechnology has inspired materials scientists to invent nanostructures with achievements in numerous practical applications, particularly in catalysis. The great advancements typically involve flexible control over the unique properties of the nanomaterial through tuning their structural geometries and components. In this Feature Article, we present the recent progress of our recent research and that of other groups in tailoring the assembly, interfaces, and porosity of diverse inorganic nanostructures. The enhanced catalytic properties of the engineered nanostructures are discussed in relation to photocatalysis, with special emphasis on solar energy conversion, including water splitting, CO2 reduction, and organic photodecomposition. Considering their attributes of superior catalytic performance and long-term durability, the development of economical, active nanocatalysts opens up practical opportunities for endeavours in sustainable energy conversion and other applied fields. This review is expected to introduce readers to the general principles of engineering the nanostructured features of the inorganic nanomaterials capable of improving solar photocatalytic efficiency. PMID:25302344

  1. Structural and Kinetic Analyses of Macrophage Migration Inhibitory Factor Active Site Interactions

    SciTech Connect

    Crichlow, G.; Lubetsky, J; Leng, L; Bucala, R; Lolis, E

    2009-01-01

    Macrophage migration inhibitory factor (MIF) is a secreted protein expressed in numerous cell types that counters the antiinflammatory effects of glucocorticoids and has been implicated in sepsis, cancer, and certain autoimmune diseases. Interestingly, the structure of MIF contains a catalytic site resembling the tautomerase/isomerase sites of microbial enzymes. While bona fide physiological substrates remain unknown, model substrates have been identified. Selected compounds that bind in the tautomerase active site also inhibit biological functions of MIF. It had previously been shown that the acetaminophen metabolite, N-acetyl-p-benzoquinone imine (NAPQI), covalently binds to the active site of MIF. In this study, kinetic data indicate that NAPQI inhibits MIF both covalently and noncovalently. The structure of MIF cocrystallized with NAPQI reveals that the NAPQI has undergone a chemical alteration forming an acetaminophen dimer (bi-APAP) and binds noncovalently to MIF at the mouth of the active site. We also find that the commonly used protease inhibitor, phenylmethylsulfonyl fluoride (PMSF), forms a covalent complex with MIF and inhibits the tautomerase activity. Crystallographic analysis reveals the formation of a stable, novel covalent bond for PMSF between the catalytic nitrogen of the N-terminal proline and the sulfur of PMSF with complete, well-defined electron density in all three active sites of the MIF homotrimer. Conclusions are drawn from the structures of these two MIF-inhibitor complexes regarding the design of novel compounds that may provide more potent reversible and irreversible inhibition of MIF.

  2. Modulated mechanism of phosphatidylserine on the catalytic activity of Naja naja atra phospholipase A2 and Notechis scutatus scutatus notexin.

    PubMed

    Chiou, Yi-Ling; Lin, Shinne-Ren; Hu, Wan-Ping; Chang, Long-Sen

    2014-12-15

    Phosphatidylserine (PS) externalization is a hallmark for apoptotic death of cells. Previous studies showed that Naja naja atra phospholipase A2 (NnaPLA2) and Notechis scutatus scutatus notexin induced apoptosis of human cancer cells. However, NnaPLA2 and notexin did not markedly disrupt the integrity of cellular membrane as evidenced by membrane permeability of propidium iodide. These findings reflected that the ability of NnaPLA2 and notexin to hydrolyze membrane phospholipids may be affected by PS externalization. To address that question, this study investigated the membrane-interacted mode and catalytic activity of NnaPLA2 and notexin toward outer leaflet (phosphatidylcholine/sphingomyelin/cholesterol, PC/SM/Chol) and inner leaflet (phosphatidylserine/phosphatidylethanolamine/cholesterol, PS/PE/Chol) of plasma membrane-mimicking vesicles. PS incorporation promoted enzymatic activity of NnaPLA2 and notexin on PC and PC/SM vesicles, but suppressed NnaPLA2 and notexin activity on PC/SM/Chol and PE/Chol vesicles. PS incorporation increased the membrane fluidity of PC vesicles but reduced membrane fluidity of PC/SM, PC/SM/Chol and PE/Chol vesicles. PS increased the phospholipid order of all the tested vesicles. Moreover, PS incorporation did not greatly alter the binding affinity of notexin and NnaPLA2 with phospholipid vesicles. Acrylamide quenching studies and trinitrophenylation of Lys residues revealed that membrane-bound mode of notexin and NnaPLA2 varied with the targeted membrane compositions. The fine structure of catalytic site in NnaPLA2 and notexin in all the tested vesicles showed different changes. Collectively, the present data suggest that membrane-inserted PS modulates PLA2 interfacial activity via its effects on membrane structure and membrane-bound mode of NnaPLA2 and notexin, and membrane compositions determine the effect of PS on PLA2 activity. PMID:25449100

  3. A single mutation Gln142Lys doubles the catalytic activity of VPR, a cold adapted subtilisin-like serine proteinase.

    PubMed

    Óskarsson, Kristinn R; Nygaard, Mads; Ellertsson, Brynjar Ö; Thorbjarnardottir, Sigríður H; Papaleo, Elena; Kristjánsson, Magnús M

    2016-10-01

    Structural comparisons of the cold adapted subtilase VPR and its thermophilic homologue, aqualysin I (AQUI) indicated the presence of additional salt bridges in the latter. Few of those appear to contribute significantly to thermal stability of AQUI. This includes a putative salt bridge between residues Lys142 and Glu172 as its deletion did not have any significant effect on its stability or activity (Jónsdóttir et al. (2014)). Insertion of this putative salt bridge into the structure of VPR, in a double mutant (VPRΔC_Q142K/S172E), however was detrimental to the stability of the enzyme. Incorporation of either the Q142K or S172E mutations into VPR, were found to significantly affect the catalytic properties of the enzyme. The single mutation Q142K was highly effective, as it increased the kcat and kcat/Km more than twofold. When the Q142K mutation was inserted into a thermostabilized, but a low activity mutant of VPR (VPRΔC_N3P/I5P), the activity increased about tenfold in terms of kcat and kcat/Km, while retaining the stability of the mutant. Molecular dynamics simulations of the single mutants were carried out to provide structural rationale for these experimental observations. Based on root mean square fluctuation (RMSF) profiles, the two mutants were more flexible in certain regions of the structure and the Q142K mutant had the highest overall flexibility of the three enzymes. The results suggest that weakening of specific H-bonds resulting from the mutations may be propagated over some distance giving rise to higher flexibility in the active site regions of the enzyme, causing higher catalytic activity in the mutants. PMID:27456266

  4. The role of acidic sites and the catalytic reaction pathways on the Rh/ZrO2 catalysts for ethanol steam reforming.

    PubMed

    Zhong, Ziyi; Ang, Hanwee; Choong, Catherine; Chen, Luwei; Huang, Lin; Lin, Jianyi

    2009-02-01

    Rh catalysts supported on ZrO(2)-based oxides were studied for ethanol steam reforming (SR) reaction. Pure ZrO(2) as the support resulted in higher H(2) production yield compared to the ZrO(2) oxide decorated with CeO(2), Al(2)O(3), La(2)O(3) or Li(2)O at the reaction temperature of 300 degrees C. Above 450 degrees C, all the catalysts exhibited similar catalytic activity. However, at low reaction temperatures (below 400 degrees C), a significant enhancement in the catalytic activity, selectivity and stability was achieved by replacing the ZrO(2) support prepared by a precipitation method (ZrO(2)-CP) with that prepared by a hydrothermal method (ZrO(2)-HT). A deactivation was observed during the EtOH SR reaction at 300 degrees C on the two catalysts of Rh/ZrO(2)-CP and Rh/ZrO(2)-HT. NH(3)-TPD experiments confirmed that the ZrO(2)-HT support had two types of acidic sites while the ZrO(2)-CP support had only one type of weak acidic sites. DRIFTS studies showed that the absorption of EtOH molecules was strong on the Rh/ZrO(2)-HT catalyst and a number of C(2) oxygenates were accumulated on the catalyst surface. Meanwhile, the EtOH absorption on the Rh/ZrO(2)-CP catalyst was weak and the accumulation of CO, carbonate and CH(x) was observed. It is concluded that the relatively strong Lewis acidic sites in the Rh/ZrO(2)-HT catalyst is responsible for the strong absorption of EtOH molecules, and the subsequent C-H breakage step (formation of acetaldehyde or called as dehydrogenation reaction) is a fast reaction on it; on the Rh/ZrO(2)-CP catalyst, the EtOH adsorption was weak and the C-C breakage was the dominating reaction which led to the accumulation of surface CO, CH(x) and CO(2) species. Therefore, it is believed that, in order to promote the absorption of EtOH molecules and to reduce the formation of metastable carbonaceous species (C(2) oxygenates) during the reaction, the catalyst should be enhanced both with Lewis acidity and with C-C bond breakage function. Also

  5. Strongly coupled Pd nanotetrahedron/tungsten oxide nanosheet hybrids with enhanced catalytic activity and stability as oxygen reduction electrocatalysts.

    PubMed

    Lu, Yizhong; Jiang, Yuanyuan; Gao, Xiaohui; Wang, Xiaodan; Chen, Wei

    2014-08-20

    The design and synthesis of highly active oxygen reduction reaction (ORR) catalysts with strong durability at low cost is extremely desirable but still remains a significant challenge. Here we develop an efficient strategy that utilizes organopalladium(I) complexes containing palladium-palladium bonds as precursors for the synthesis of strongly coupled Pd tetrahedron-tungsten oxide nanosheet hybrids (Pd/W18O49) to improve the electrocatalytic activity and stability of Pd nanocrystals. The hybrid materials are synthesized by direct nucleation, growth, and anchoring of Pd tetrahedral nanocrystals on the in situ-synthesized W18O49 nanosheets. Compared to supportless Pd nanocrystals and W18O49, their hybrids exhibited not only surprisingly high activity but also superior stability to Pt for the ORR in alkaline solutions. X-ray photoelectron spectroscopy, high-resolution transmission electron microscopy, and electrochemical analyses indicated that the enhanced electrocatalytic activity and durability are associated with the increased number and improved catalytic activity of active sites, which is induced by the strong interaction between the Pd tetrahedrons and W18O49 nanosheet supports. The present study provides a novel strategy for synthesizing hybrid catalysts with strong chemical attachment and electrical coupling between nanocatalysts and supports. The strategy is expected to open up exciting opportunities for developing a novel class of metal-support hybrid nanoelectrocatalysts with improved ORR activity and durability for both fuel cells and metal-air batteries. PMID:25054583

  6. Catalytically active lead(ii)-imidazolium coordination assemblies with diversified lead(ii) coordination geometries.

    PubMed

    Naga Babu, Chatla; Suresh, Paladugu; Srinivas, Katam; Sathyanarayana, Arruri; Sampath, Natarajan; Prabusankar, Ganesan

    2016-05-10

    Five Pb(ii)-imidazolium carboxylate coordination assemblies with novel structural motifs were derived from the reaction between the corresponding flexible, semi flexible or rigid imidazolium carboxylic acid ligands and lead nitrate. The imidazolium linker present in these molecules likely plays a triple role such as the counter ion to balance the metal charge, the ligand being an integral part of the final product and the catalyst facilitating carbon-carbon bond formation reaction. These lead-imidazolium coordination assemblies exhibit, variable chemical and thermal stabilities, as well as catalytic activity. These newly prepared catalysts are highly active towards benzoin condensation reactions with good functional group tolerance. PMID:27093629

  7. Improving upon Nature: Active site remodeling produces highly efficient aldolase activity towards hydrophobic electrophilic substrates

    PubMed Central

    Cheriyan, Manoj; Toone, Eric J.; Fierke, Carol A.

    2012-01-01

    Substrate specificity of enzymes is frequently narrow and constrained by multiple interactions, limiting the use of natural enzymes in biocatalytic applications. Aldolases have important synthetic applications, but the usefulness of these enzymes is hampered by their narrow reactivity profile with unnatural substrates. To explore the determinants of substrate selectivity and alter the specificity of E. coli 2-keto-3-deoxy-6-phosphogluconate (KDPG) aldolase, we employed structure-based mutagenesis coupled with library screening of mutant enzymes localized to the bacterial periplasm. We identified two active site mutations (T161S/S184L) that work additively to enhance the substrate specificity of this aldolase to include catalysis of retro-aldol cleavage of (4S)-2-keto-4-hydroxy-4-(2′-pyridyl)butyrate (S-KHPB). These mutations improve the value of kcat/KMS-KHPB by >450-fold, resulting in a catalytic efficiency that is comparable to that of the wild-type enzyme with the natural substrate while retaining high stereoselectivity. Moreover, the value of kcatS-KHPB for this mutant enzyme, a parameter critical for biocatalytic applications, is 3-fold higher than the maximum value achieved by the natural aldolase with any substrate. This mutant also possesses high catalytic efficiency for the retro-aldol cleavage of the natural substrate, KDPG, and a >50-fold improved activity for cleavage of 2-keto-4-hydroxy-octonoate (KHO), a non-functionalized hydrophobic analog. These data suggest a substrate binding mode that illuminates the origin of facial selectivity in aldol addition reactions catalyzed by KDPG and 2-keto-3-deoxy-6-phosphogalactonate (KDPGal) aldolases. Furthermore, targeting mutations to the active site provides marked improvement in substrate selectivity, demonstrating that structure-guided active site mutagenesis combined with selection techniques can efficiently identify proteins with characteristics that compare favorably to naturally occurring enzymes. PMID

  8. The Contribution of Non-catalytic Carbohydrate Binding Modules to the Activity of Lytic Polysaccharide Monooxygenases*

    PubMed Central

    Crouch, Lucy I.; Labourel, Aurore; Walton, Paul H.; Davies, Gideon J.; Gilbert, Harry J.

    2016-01-01

    Lignocellulosic biomass is a sustainable industrial substrate. Copper-dependent lytic polysaccharide monooxygenases (LPMOs) contribute to the degradation of lignocellulose and increase the efficiency of biofuel production. LPMOs can contain non-catalytic carbohydrate binding modules (CBMs), but their role in the activity of these enzymes is poorly understood. Here we explored the importance of CBMs in LPMO function. The family 2a CBMs of two monooxygenases, CfLPMO10 and TbLPMO10 from Cellulomonas fimi and Thermobispora bispora, respectively, were deleted and/or replaced with CBMs from other proteins. The data showed that the CBMs could potentiate and, surprisingly, inhibit LPMO activity, and that these effects were both enzyme-specific and substrate-specific. Removing the natural CBM or introducing CtCBM3a, from the Clostridium thermocellum cellulosome scaffoldin CipA, almost abolished the catalytic activity of the LPMOs against the cellulosic substrates. The deleterious effect of CBM removal likely reflects the importance of prolonged presentation of the enzyme on the surface of the substrate for efficient catalytic activity, as only LPMOs appended to CBMs bound tightly to cellulose. The negative impact of CtCBM3a is in sharp contrast with the capacity of this binding module to potentiate the activity of a range of glycoside hydrolases including cellulases. The deletion of the endogenous CBM from CfLPMO10 or the introduction of a family 10 CBM from Cellvibrio japonicus LPMO10B into TbLPMO10 influenced the quantity of non-oxidized products generated, demonstrating that CBMs can modulate the mode of action of LPMOs. This study demonstrates that engineered LPMO-CBM hybrids can display enhanced industrially relevant oxygenations. PMID:26801613

  9. Reactions of hypochlorous acid with biological substrates are activated catalytically by tertiary amines.

    PubMed

    Prütz, W A

    1998-09-15

    The activation of reactions of HOCl with a variety of model substrates by tertiary amines was investigated spectroscopically by tandem-mix and stopped-flow techniques. HOCl-induced chlorination of salicylate can be sped up by several orders of magnitude by catalytic amounts of trimethylamine (TMN). The effect is obviously due to the fast generation of reactive quarternary chloramonium ions, TMN+ Cl, which act as chain carrier in a catalytic reaction cycle. Of various catalysts tested, quinine shows the highest activity; this is attributable to the quinuclidine (QN) substituent, a bicyclic tertiary amine, forming a particularly reactive chloro derivative, QN+ Cl, which does not decompose autocatalytically. The rate of catalytic salicylate chlorination as a function of pH (around pH 7) depends not at least on the basicity of the tertiary amine; the rate increases with pH in the cases of TMN and quinuclidine (high basicity), but decreases with pH in the case of MES (low basicity). Tertiary amines also catalyze the interaction between HOCl and alkenes, as shown using sorbate as model. Reaction of HOCl with the nucleotides GMP and CMP is sped up remarkably by catalytic amounts of tertiary amines. In the case of GMP the same product spectrum is produced by HOCl in absence and presence of catalyst, but a change in the product spectra is obtained when AMP and CMP are reacted with HOCl in presence of catalyst. Using poly(dA-dT).poly(dA-dT) as DNA model, it is shown that HOCl primarily induces an absorbance increase at 263 nm, which indicates unfolding of the double strand due to fast chlorination of thymidine; a subsequent secondary absorbance decrease can be explained by slow chlorination of adenosine. Both the primary and secondary processes are activated by catalytic amounts of quinine. No evidence was found for a radical pathway in TMN-mediated oxidation of formate by HOCl. The present results suggest that low concentrations of certain tertiary amines have the potential

  10. Stable and catalytically active iron porphyrin-based porous organic polymer: Activity as both a redox and Lewis acid catalyst

    PubMed Central

    Oveisi, Ali R.; Zhang, Kainan; Khorramabadi-zad, Ahmad; Farha, Omar K.; Hupp, Joseph T.

    2015-01-01

    A new porphyrin-based porous organic polymer (POP) with BET surface area ranging from 780 to 880 m2/g was synthesized in free-base form via the reaction of meso-tetrakis(pentafluorophenyl) porphyrin and a rigid trigonal building block, hexahydroxytriphenylene. The material was then metallated with Fe(III) imparting activity for Lewis acid catalysis (regioselective methanolysis ring-opening of styrene oxide), oxidative cyclization catalysis (conversion of bis(2-hydroxy-1-naphthyl)methanes to the corresponding spirodienone), and a tandem catalytic processes: an in situ oxidation-cyclic aminal formation-oxidation sequence, which selectively converts benzyl alcohol to 2-phenyl-quinazolin-4(3H)-one. Notably, the catalyst is readily recoverable and reusable, with little loss in catalytic activity. PMID:26177563

  11. Energy Efficient Catalytic Activation of Hydrogen peroxide for Green Chemical Processes: Final Report

    SciTech Connect

    Collins, Terrence J.; Horwitz, Colin

    2004-11-12

    A new, highly energy efficient approach for using catalytic oxidation chemistry in multiple fields of technology has been pursued. The new catalysts, called TAML® activators, catalyze the reactions of hydrogen peroxide and other oxidants for the exceptionally rapid decontamination of noninfectious simulants (B. atrophaeus) of anthrax spores, for the energy efficient decontamination of thiophosphate pesticides, for the facile, low temperature removal of color and organochlorines from pulp and paper mill effluent, for the bleaching of dyes from textile mill effluents, and for the removal of recalcitrant dibenzothiophene compounds from diesel and gasoline fuels. Highlights include the following: 1) A 7-log kill of Bacillus atrophaeus spores has been achieved unambiguously in water under ambient conditions within 15 minutes. 2) The rapid total degradation under ambient conditions of four thiophosphate pesticides and phosphonate degradation intermediates has been achieved on treatment with TAML/peroxide, opening up potential applications of the decontamination system for phosphonate structured chemical warfare agents, for inexpensive, easy to perform degradation of stored and aged pesticide stocks (especially in Africa and Asia), for remediation of polluted sites and water bodies, and for the destruction of chemical warfare agent stockpiles. 3) A mill trial conducted in a Pennsylvanian bleached kraft pulp mill has established that TAML catalyst injected into an alkaline peroxide bleach tower can significantly lower color from the effluent stream promising a new, more cost effective, energy-saving approach for color remediation adding further evidence of the value and diverse engineering capacity of the approach to other field trials conducted on effluent streams as they exit the bleach plant. 4) Dibenzothiophenes (DBTs), including 4,6-dimethyldibenzothiophene, the most recalcitrant sulfur compounds in diesel and gasoline, can be completely removed from model gasoline

  12. Catalytic oxidation of pulping effluent by activated carbon-supported heterogeneous catalysts.

    PubMed

    Yadav, Bholu Ram; Garg, Anurag

    2016-01-01

    The present study deals with the non-catalytic and catalytic wet oxidation (CWO) for the removal of persistent organic compounds from the pulping effluent. Two activated carbon-supported heterogeneous catalysts (Cu/Ce/AC and Cu/Mn/AC) were used for CWO after characterization by the following techniques: temperature-programmed reduction, Fourier transform infrared spectroscopy and thermo-gravimetric analysis. The oxidation reaction was performed in a batch high-pressure reactor (capacity = 0.7  L) at moderate oxidation conditions (temperature = 190°C and oxygen pressure = 0.9 MPa). With Cu/Ce/AC catalyst, the maximum chemical oxygen demand (COD), total organic carbon (TOC) and lignin removals of 79%, 77% and 88% were achieved compared to only 50% removal during the non-catalytic process. The 5-day biochemical oxygen demand (BOD5) to COD ratio (a measure for biodegradability) of the pulping effluent was improved to 0.52 from an initial value of 0.16. The mass balance calculations for solid recovered after CWO reaction showed 8% and 10% deduction in catalyst mass primarily attributed to the loss of carbon and metal leaching. After the CWO process, carbon deposition was also observed on the recovered catalyst which was responsible for around 3-4% TOC reduction. PMID:26508075

  13. Catalytic activity of silicon nanowires decorated with silver and copper nanoparticles

    NASA Astrophysics Data System (ADS)

    Amdouni, Sonia; Coffinier, Yannick; Szunerits, Sabine; Zaïbi, Mohammed Ali; Oueslati, Meherzi; Boukherroub, Rabah

    2016-01-01

    The paper reports on the elaboration of silicon nanowires decorated with silver (SiNWs-Ag NPs) or copper (SiNWs-Cu NPs) nanoparticles and the investigation of their catalytic properties for the reduction of 4-nitrophenol to 4-aminophenol. The SiNW arrays were produced through chemical etching of crystalline silicon in HF/AgNO3 aqueous solution. The metal nanoparticles were deposited on the SiNW substrates through chemical bath immersion in a metal salt/hydrofluoric acid aqueous solution. The SiNWs decorated with Ag NPs and Cu NPs were characterized by scanning electron microscopy (SEM), x-ray diffraction (XRD) and x-ray photoelectron spectroscopy (XPS). The catalytic activity of the SiNWs loaded with metal nanoparticles was evaluated for the reduction of 4-nitrophenol to 4-aminophenol in the presence of sodium borohydride (NaBH4). The substrates exhibited good catalytic performance toward nitrophenol with a full reduction in less than 30 s for the SiNWs-Cu NPs.

  14. Facile synthesis of magnetically separable reduced graphene oxide/magnetite/silver nanocomposites with enhanced catalytic activity.

    PubMed

    Ji, Zhenyuan; Shen, Xiaoping; Yue, Xiaoyang; Zhou, Hu; Yang, Juan; Wang, Yuqin; Ma, Lianbo; Chen, Kangmin

    2015-12-01

    In this study, the combination of magnetite (Fe3O4) with reduced graphene oxide (RGO) generates a new hybrid substrate for the dispersion of noble metal nanoparticles. Well-dispersed silver (Ag) nanoparticles loaded on the surface of Fe3O4 modified RGO are achieved by an efficient two-step approach. Through reducing Ag(+) ions, highly dispersed Ag nanoparticles are in-situ formed on the RGO/Fe3O4 substrate. It is found that the existence of Fe3O4 nanocrystals can significantly improve the dispersity and decrease the particle size of the in-situ formed Ag nanoparticles. Magnetic study reveals that the as-prepared RGO/Fe3O4/Ag ternary nanocomposites display room-temperature superparamagnetic behavior. The catalytic properties of the RGO/Fe3O4/Ag ternary nanocomposites were evaluated with the reduction of 4-nitrophenol into 4-aminophenol as a model reaction. The as-synthesized RGO/Fe3O4/Ag ternary catalysts exhibit excellent catalytic stability and much higher catalytic activity than the corresponding RGO/Ag catalyst. Moreover, the RGO/Fe3O4/Ag catalysts can be easily magnetically separated for reuse. This study further demonstrates that nanoparticles modified graphene can act as an effective hybrid substrate for the synthesis of multi-component and multifunctional graphene-based composites. PMID:26263498

  15. Key substrate recognition residues in the active site of a plant cytochrome P450, CYP73A1. Homology guided site-directed mutagenesis.

    PubMed

    Schoch, Guillaume A; Attias, Roger; Le Ret, Monique; Werck-Reichhart, Danièle

    2003-09-01

    CYP73 enzymes are highly conserved cytochromes P450 in plant species that catalyse the regiospecific 4-hydroxylation of cinnamic acid to form precursors of lignin and many other phenolic compounds. A CYP73A1 homology model based on P450 experimentally solved structures was used to identify active site residues likely to govern substrate binding and regio-specific catalysis. The functional significance of these residues was assessed using site-directed mutagenesis. Active site modelling predicted that N302 and I371 form a hydrogen bond and hydrophobic contacts with the anionic site or aromatic ring of the substrate. Modification of these residues led to a drastic decrease in substrate binding and metabolism without major perturbation of protein structure. Changes to residue K484, which is located too far in the active site model to form a direct contact with cinnamic acid in the oxidized enzyme, did not influence initial substrate binding. However, the K484M substitution led to a 50% loss in catalytic activity. K484 may affect positioning of the substrate in the reduced enzyme during the catalytic cycle, or product release. Catalytic analysis of the mutants with structural analogues of cinnamic acid, in particular indole-2-carboxylic acid that can be hydroxylated with different regioselectivities, supports the involvement of N302, I371 and K484 in substrate docking and orientation. PMID:12950252

  16. Biosynthesised palladium nanoparticles using Eucommia ulmoides bark aqueous extract and their catalytic activity.

    PubMed

    Duan, Liansheng; Li, Ming; Liu, Huihong

    2015-12-01

    Palladium nanoparticles (PdNPs) are of great importance as catalytic materials. Their synthesis has been widely studied and interest in their properties is growing. Bio-based methods might be a greener option for designing the PdNPs with reduced environmental impacts. This study reports the synthesis of PdNPs by utilising the aqueous extract of medicinally important Eucommia ulmoides (E. Ulmoides) bark which functions as both reducing and capping agent in moderate reaction conditions. Reduction potential of E. Ulmoides bark aqueous extract was about -0.08 V vs. saturated calomel electrode by open-circuit voltage method and the rich polyphenolics was confirmed by cyclic voltammetry, which helps to reduce palladium ions to PdNPs. The characterisation through high-resolution transmission electron microscopic, energy dispersive X-ray spectroscopy and X-ray diffraction infer that the as-synthesised PdNPs were spherical in shape with a face cubic crystal structure. The results from dynamic light scattering suggest the PdNPs have the narrow size distribution with an average size of 12.6 nm. The lower zeta potential (-25.3 mV) and the Fourier transform infrared spectra indicate that the as-synthesised PdNPs keep remarkably stable for a long period due to the capped biomolecules on the nanoparticle surface. This method for synthesis of PdNPs is simple, economic, non-toxic and efficient. The PdNPs show excellent catalytic activity for the electro-catalytic oxidation of hydrazine and the catalytic reducing degradation of p-aminoazobenzene, a model compound of azo-dyes. PMID:26647810

  17. Chemical modification studies on arginine kinase: essential cysteine and arginine residues at the active site.

    PubMed

    Zhu, Wen-Jing; Li, Miao; Wang, Xiao-Yun

    2007-12-01

    Chemical modification was used to elucidate the essential amino acids in the catalytic activity of arginine kinase (AK) from Migratoria manilensis. Among six cysteine (Cys) residues only one Cys residue was determined to be essential in the active site by Tsou's method. Furthermore, the AK modified by DTNB can be fully reactivated by dithiothreitol (DTT) in a monophasic kinetic course. At the same time, this reactivation can be slowed down in the presence of ATP, suggesting that the essential Cys is located near the ATP binding site. The ionizing groups at the AK active site were studied and the standard dissociation enthalpy (DeltaH degrees ) was 12.38kcal/mol, showing that the dissociation group may be the guanidino of arginine (Arg). Using the specific chemical modifier phenylglyoxal (PG) demonstrated that only one Arg, located near the ATP binding site, is essential for the activity of AK. PMID:17765964

  18. Dielectric characterization and catalytic activity studies of nickel chloride doped carboxymethyl cellulose films

    NASA Astrophysics Data System (ADS)

    El-Bahy, Zeinhom M.; Mahmoud, Khaled H.

    Cast technique was used to prepare films of sodium carboxymethyl cellulose (CMC) doped with different ratios of NiCl2·6H2O in the range of 0-40 Ni2+ wt.%. Thermal analysis (DTA) in the range of 25-600 °C and dielectric properties in the temperature range of 30-150 °C and frequency range of 0.1-100 kHz were measured for the prepared samples. DTA analysis showed new exothermic peaks which were attributed to structural phase transitions. Different molecular motions are separated via dielectric relaxation spectroscopy. In the high temperature range (higher than 100 °C), the σ-relaxation, which is associated with the hopping motion of ions through polymer material, was detected. The detailed analysis of the results showed that the dielectric dispersion consists of both dipolar and interfacial polarization. Measurements of ac conductivity as a function of frequency at different temperatures indicated that the correlated barrier hopping model (CBH) is the most suitable mechanism for the ac conduction behavior. The catalytic activity of CMC doped with Ni2+ was tested in the reduction of the hazardous pollutant 4-nitrophenol to the functional 4-aminophenol with an excess amount of NaBH4. Ni-free CMC did not exhibit any catalytic activity for the studied reaction. However, Ni2+-doped CMC showed a significant catalytic activity that is proportional to the ratio of Ni2+ included in CMC. The activation energy (Ea) was estimated in the temperature range of 25-40 °C. The estimated value of Ea decreased with increasing the ratio of Ni2+. Finally, the optimum catalyst mass was found to be ≈0.6 g/l.

  19. Flexibility and Stability Trade-Off in Active Site of Cold-Adapted Pseudomonas mandelii Esterase EstK.

    PubMed

    Truongvan, Ngoc; Jang, Sei-Heon; Lee, ChangWoo

    2016-06-28

    Cold-adapted enzymes exhibit enhanced conformational flexibility, especially in their active sites, as compared with their warmer-temperature counterparts. However, the mechanism by which cold-adapted enzymes maintain their active site stability is largely unknown. In this study, we investigated the role of conserved D308-Y309 residues located in the same loop as the catalytic H307 residue in the cold-adapted esterase EstK from Pseudomonas mandelii. Mutation of D308 and/or Y309 to Ala or deletion resulted in increased conformational flexibility. Particularly, the D308A or Y309A mutant showed enhanced substrate affinity and catalytic rate, as compared with wild-type EstK, via enlargement of the active site. However, all mutant EstK enzymes exhibited reduced thermal stability. The effect of mutation was greater for D308 than Y309. These results indicate that D308 is not preferable for substrate selection and catalytic activity, whereas hydrogen bond formation involving D308 is critical for active site stabilization. Taken together, conformation of the EstK active site is constrained via flexibility-stability trade-off for enzyme catalysis and thermal stability. Our study provides further insights into active site stabilization of cold-adapted enzymes. PMID:27259687

  20. Facile route to hierarchical silver microstructures with high catalytic activity for the reduction of p-nitrophenol

    SciTech Connect

    Gu, Sasa; Wang, Wei Tan, Fatang; Gu, Jian; Qiao, Xueliang; Chen, Jianguo

    2014-01-01

    Graphical abstract: - Highlights: • A facile route was developed to prepare hierarchical silver microstructures. • The shape and size of secondary units can be tailed by varying reaction conditions. • Hierarchical silver microstructures have excellent catalytic activity. • The morphology and crystallinity of silver particles affect the catalytic activity. - Abstract: A facile, cost-effective and environmentally friendly route was developed to synthesize hierarchical silver microstructures consisting of different shaped secondary units through reducing concentrated silver nitrate with ascorbic acid in the absence of any surfactant. The as-obtained samples were characterized by X-ray diffraction (XRD), field-emission scanning electron microscopy (FESEM) and transmission electron microscopy (TEM). The investigation on the morphology evolution revealed that the molar ratio of ascorbic acid to silver nitrate was critical to control the shape of secondary structures. The length of plate-like secondary structures which composed hierarchical silver particles could be controlled by changing the reactant concentrations, and it had a key relationship with the catalytic activity for the reduction of p-nitrophenol by NaBH{sub 4}. The catalytic activity of these surfactant-free silver microstructures was about ten times higher than that of silver nanoparticles, and even comparable to that of gold nanoplates, which indicates that the as-obtained silver microstructures are very promising candidates for the catalytic reduction of p-nitrophenol due to the simple synthesis route and high catalytic activity.

  1. State and catalytic activity of iridium compounds in the reaction of mercury(I) oxidation by cerium(IV)

    SciTech Connect

    Khomutova, E.G.; Rysev, A.P.; Romanovskaya, L.E.; Malysheva, N.M.

    1995-12-01

    Kinetic methods of determining Ir are insufficiently selective and sensitive as compared to the methods of determining Os and Ru. These characteristics may be improved by increasing the catalytic activity of iridium. All other factors being equal, catalytic activity depends on the state and form of iridium that enters the catalytic process. This is why one of the ways of improving the performance characteristics of a method of determining iridium involves searching for forms of the catalyst with higher catalytic activity. The aim of this work was to study the state and catalytic activity of iridium compounds. The method based on the iridium-catalyzed reaction of mercury(I) oxidation by cerium(IV) was chosen for the investigation. This method is most commonly used for analyzing complex samples. It was found previously that both the catalytic activity and selectivity of iridium determination increase when the reaction is conducted in the medium of perchloric acid or the sample is pretreated with nitric acid.

  2. Light chain of botulinum A neurotoxin expressed as an inclusion body from a synthetic gene is catalytically and functionally active.

    PubMed

    Ahmed, S A; Smith, L A

    2000-08-01

    Botulinum neurotoxins, the most potent of all toxins, induce lethal neuromuscular paralysis by inhibiting exocytosis at the neuromuscular junction. The light chains (LC) of these dichain neurotoxins are a new class of zinc-endopeptidases that specifically cleave the synaptosomal proteins, SNAP-25, VAMP, or syntaxin at discrete sites. To facilitate the structural and functional characterization of these unique endopeptidases, we constructed a synthetic gene for the LC of the botulinum neurotoxin serotype A (BoNT/A), overexpressed it in Escherichia coli, and purified the gene product from inclusion bodies. Our procedure can provide 1.1 g of the LC from 1 L of culture. The LC product was stable in solution at 4 degrees C for at least 6 months. This rBoNT/A LC was proteolytically active, specifically cleaving the Glu-Arg bond in a 17-residue synthetic peptide of SNAP-25, the reported cleavage site of BoNT/A. Its calculated catalytic efficiency kcat/Km was higher than that reported for the native BoNT/A dichain. Treating the rBoNT/A LC with mercuric compounds completely abolished its activity, most probably by modifying the cysteine-164 residue located in the vicinity of the active site. About 70% activity of the LC was restored by adding Zn2+ to a Zn2+-free, apo-LC preparation. The LC was nontoxic to mice and failed to elicit neutralizing epitope(s) when the animals were vaccinated with this protein. In addition, injecting rBoNT/A LC into sea urchin eggs inhibited exocytosis-dependent plasma membrane resealing. For the first time, results of our study make available a large amount of the biologically active toxin fragment in a soluble and stable form. PMID:11195972

  3. Characterization of a soluble, catalytically active form of Escherichia coli leader peptidase: requirement of detergent or phospholipid for optimal activity.

    PubMed

    Tschantz, W R; Paetzel, M; Cao, G; Suciu, D; Inouye, M; Dalbey, R E

    1995-03-28

    Leader peptidase is a novel serine protease in Escherichia coli, which functions to cleave leader sequences from exported proteins. Its catalytic domain extends into the periplasmic space and is anchored to the membrane by two transmembrane segments located at the N-terminal end of the protein. At present, there is no information on the structure of the catalytic domain. Here, we report on the properties of a soluble form of leader peptidase (delta 2-75), and we compare its properties to those of the wild-type enzyme. We find that the truncated leader peptidase has a kcat of 3.0 S-1 and a Km of 32 microM with a pro-OmpA nuclease A substrate. In contrast to the wild-type enzyme (pI of 6.8), delta 2-75 is water-soluble and has an acidic isoelectric point of 5.6. We also show with delta 2-75 that the replacement of serine 90 and lysine 145 with alanine residues results in a 500-fold reduction in activity, providing further evidence that leader peptidase employs a catalytic serine/lysine dyad. Finally, we find that the catalysis of delta 2-75 is accelerated by the presence of the detergent Triton X-100, regardless if the substrate is pro-OmpA nuclease A or a peptide substrate. Triton X-100 is required for optimal activity of delta 2-75 at a level far below the critical micelle concentration. Moreover, we find that E. coli phospholipids stimulate the activity of delta 2-75, suggesting that phospholipids may play an important physiological role in the catalytic mechanism of leader peptidase. PMID:7696258

  4. Functional role of TRIM E3 ligase oligomerization and regulation of catalytic activity.

    PubMed

    Koliopoulos, Marios G; Esposito, Diego; Christodoulou, Evangelos; Taylor, Ian A; Rittinger, Katrin

    2016-06-01

    TRIM E3 ubiquitin ligases regulate a wide variety of cellular processes and are particularly important during innate immune signalling events. They are characterized by a conserved tripartite motif in their N-terminal portion which comprises a canonical RING domain, one or two B-box domains and a coiled-coil region that mediates ligase dimerization. Self-association via the coiled-coil has been suggested to be crucial for catalytic activity of TRIMs; however, the precise molecular mechanism underlying this observation remains elusive. Here, we provide a detailed characterization of the TRIM ligases TRIM25 and TRIM32 and show how their oligomeric state is linked to catalytic activity. The crystal structure of a complex between the TRIM25 RING domain and an ubiquitin-loaded E2 identifies the structural and mechanistic features that promote a closed E2~Ub conformation to activate the thioester for ubiquitin transfer allowing us to propose a model for the regulation of activity in the full-length protein. Our data reveal an unexpected diversity in the self-association mechanism of TRIMs that might be crucial for their biological function. PMID:27154206

  5. Facile synthesis of pristine graphene-palladium nanocomposites with extraordinary catalytic activities using swollen liquid crystals.

    PubMed

    Vats, T; Dutt, S; Kumar, R; Siril, P F

    2016-01-01

    Amazing conductivity, perfect honeycomb sp(2) arrangement and the high theoretical surface area make pristine graphene as one of the best materials suited for application as catalyst supports. Unfortunately, the low reactivity of the material makes the formation of nanocomposite with inorganic materials difficult. Here we report an easy approach to synthesize nanocomposites of pristine graphene with palladium (Pd-G) using swollen liquid crystals (SLCs) as a soft template. The SLC template gives the control to deposit very small Pd particles of uniform size on G as well as RGO. The synthesized nanocomposite (Pd-G) exhibited exceptionally better catalytic activity compared with Pd-RGO nanocomposite in the hydrogenation of nitrophenols and microwave assisted C-C coupling reactions. The catalytic activity of Pd-G nanocomposite during nitrophenol reduction reaction was sixteen times higher than Pd nanoparticles and more than double than Pd-RGO nanocomposite. The exceptionally high activity of pristine graphene supported catalysts in the organic reactions is explained on the basis of its better pi interacting property compared to partially reduced RGO. The Pd-G nanocomposite showed exceptional stability under the reaction conditions as it could be recycled upto a minimum of 15 cycles for the C-C coupling reactions without any loss in activity. PMID:27619321

  6. Prediction of hammerhead ribozyme intracellular activity with the catalytic core fingerprint.

    PubMed

    Gabryelska, Marta Magdalena; Wyszko, Eliza; Szymański, Maciej; Popenda, Mariusz; Barciszewski, Jan

    2013-05-01

    Hammerhead ribozyme is a versatile tool for down-regulation of gene expression in vivo. Owing to its small size and high activity, it is used as a model for RNA structure-function relationship studies. In the present paper we describe a new extended hammerhead ribozyme HH-2 with a tertiary stabilizing motif constructed on the basis of the tetraloop receptor sequence. This ribozyme is very active in living cells, but shows low activity in vitro. To understand it, we analysed tertiary structure models of substrate-ribozyme complexes. We calculated six unique catalytic core geometry parameters as distances and angles between particular atoms that we call the ribozyme fingerprint. A flanking sequence and tertiary motif change the geometry of the general base, general acid, nucleophile and leaving group. We found almost complete correlation between these parameters and the decrease of target gene expression in the cells. The tertiary structure model calculations allow us to predict ribozyme intracellular activity. Our approach could be widely adapted to characterize catalytic properties of other RNAs. PMID:23418809

  7. Creation of catalytically active particles from enzymes crosslinked with a natural bifunctional agent--homocysteine thiolactone.

    PubMed

    Stroylova, Yulia Y; Semenyuk, Pavel I; Asriyantz, Regina A; Gaillard, Cedric; Haertlé, Thomas; Muronetz, Vladimir I

    2014-09-01

    The current study describes an approach to creation of catalytically active particles with increased stability from enzymes by N-homocysteinylation, a naturally presented protein modification. Enzymatic activities and properties of two globular tetrameric enzymes glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and lactate dehydrogenase (LDH) were studied before and after N-homocysteinylation. Modification of these proteins concerns the accessible lysine residues and introduces an average of 2-2,5 homocysteine residues per protein monomer. Formation of a range of aggregates was observed for both enzymes, which assemble via formation of intermolecular noncovalent bonds and by disulfide bonds. It was demonstrated that both studied enzymes retain their catalytic activities on modification and the subsequent formation of oligomeric forms. At low concentrations of homocysteine thiolactone, modification of GAPDH leads not only to prevention of spontaneous inactivation but also increases thermal stability of this enzyme on heating to 80°C. A moderate reduction of the activity of GAPDH observed in case of its crosslinking with 50-fold excess of homocysteine thiolactone per lysine is probably caused by hindered substrate diffusion. Spherical particles of 100 nm and larger diameters were observed by transmission electron microscopy and atomic force microscope techniques after modification of GAPDH with different homocysteine thiolactone concentrations. In case of LDH, branched fibril-like aggregates were observed under the same conditions. Interestingly, crosslinked samples of both proteins were found to have reversible thermal denaturation profiles, indicating that modification with homocysteine thiolactone stabilizes the spatial structure of these enzymes. PMID:24912753

  8. Activity, Expression and Function of a Second Drosophila Protein Kinase a Catalytic Subunit Gene

    PubMed Central

    Melendez, A.; Li, W.; Kalderon, D.

    1995-01-01

    The DC2 gene was isolated previously on the basis of sequence similarity to DCO, the major Drosophila protein kinase A (PKA) catalytic subunit gene. We show here that the 67-kD Drosophila DC2 protein behaves as a PKA catalytic subunit in vitro. DC2 is transcribed in mesodermal anlagen of early embryos. This expression depends on dorsal but on neither twist nor snail activity. DC2 transcriptional fusions mimic this embryonic expression and are also expressed in subsets of cells in the optic lamina, wing disc and leg discs of third instar larvae. A saturation screen of a small deficiency interval containing DC2 for recessive lethal mutations yielded no DC2 alleles. We therefore isolated new deficiencies to generate deficiency trans-heterozygotes that lacked DC2 activity. These animals were viable and fertile. The absence of DC2 did not affect the viability or phenotype of imaginal disc cells lacking DC0 activity or embryonic hatching of animals with reduced DC0 activity. Furthermore, transgenes expressing DC2 from a DC0 promoter did not efficiently rescue a variety of DC0 mutant phenotypes. These observations indicate that DC2 is not an essential gene and is unlikely to be functionally redundant with DC0, which has multiple unique functions during development. PMID:8601490

  9. A new CuZ active form in the catalytic reduction of N(2)O by nitrous oxide reductase from Pseudomonas nautica.

    PubMed

    Dell'Acqua, Simone; Pauleta, Sofia R; Paes de Sousa, Patrícia M; Monzani, Enrico; Casella, Luigi; Moura, José J G; Moura, Isabel

    2010-08-01

    The final step of bacterial denitrification, the two-electron reduction of N(2)O to N(2), is catalyzed by a multi-copper enzyme named nitrous oxide reductase. The catalytic centre of this enzyme is a tetranuclear copper site called CuZ, unique in biological systems. The in vitro reconstruction of the activity requires a slow activation in the presence of the artificial electron donor, reduced methyl viologen, necessary to reduce CuZ from the resting non-active state (1Cu(II)/3Cu(I)) to the fully reduced state (4Cu(I)), in contrast to the turnover cycle, which is very fast. In the present work, the direct reaction of the activated form of Pseudomonas nautica nitrous oxide reductase with stoichiometric amounts of N(2)O allowed the identification of a new reactive intermediate of the catalytic centre, CuZ degrees , in the turnover cycle, characterized by an intense absorption band at 680 nm. Moreover, the first mediated electrochemical study of Ps. nautica nitrous oxide reductase with its physiological electron donor, cytochrome c-552, was performed. The intermolecular electron transfer was analysed by cyclic voltammetry, under catalytic conditions, and a second-order rate constant of (5.5 +/- 0.9) x 10(5) M(-1 )s(-1) was determined. Both the reaction of stoichiometric amounts of substrate and the electrochemical studies show that the active CuZ degrees species, generated in the absence of reductants, can rearrange to the resting non-active CuZ state. In this light, new aspects of the catalytic and activation/inactivation mechanism of the enzyme are discussed. PMID:20422435

  10. Anisotropic Covalency Contributions to Superexchange Pathways in Type One Copper Active Sites

    PubMed Central

    2015-01-01

    Type one (T1) Cu sites deliver electrons to catalytic Cu active sites: the mononuclear type two (T2) Cu site in nitrite reductases (NiRs) and the trinuclear Cu cluster in the multicopper oxidases (MCOs). The T1 Cu and the remote catalytic sites are connected via a Cys-His intramolecular electron-transfer (ET) bridge, which contains two potential ET pathways: P1 through the protein backbone and P2 through the H-bond between the Cys and the His. The high covalency of the T1 Cu–S(Cys) bond is shown here to activate the T1 Cu site for hole superexchange via occupied valence orbitals of the bridge. This covalency-activated electronic coupling (HDA) facilitates long-range ET through both pathways. These pathways can be selectively activated depending on the geometric and electronic structure of the T1 Cu site and thus the anisotropic covalency of the T1 Cu–S(Cys) bond. In NiRs, blue (π-type) T1 sites utilize P1 and green (σ-type) T1 sites utilize P2, with P2 being more efficient. Comparing the MCOs to NiRs, the second-sphere environment changes the conformation of the Cys-His pathway, which selectively activates HDA for superexchange by blue π sites for efficient turnover in catalysis. These studies show that a given protein bridge, here Cys-His, provides different superexchange pathways and electronic couplings depending on the anisotropic covalencies of the donor and acceptor metal sites. PMID:25310460

  11. Catalytic Activity and Stability of Oxides: The Role of Near-Surface Atomic Structures and Compositions.

    PubMed

    Feng, Zhenxing; Hong, Wesley T; Fong, Dillon D; Lee, Yueh-Lin; Yacoby, Yizhak; Morgan, Dane; Shao-Horn, Yang

    2016-05-17

    the physical origin of segregation is discussed in comparison with (La1-ySry)2CoO4±δ/La1-xSrxCo0.2Fe0.8O3-δ. Sr enrichment in many electrocatalysts, such as La1-xSrxMO3-δ (M = Cr, Co, Mn, or Co and Fe) and Sm1-xSrxCoO3, has been probed using alternative techniques, including low energy ion scattering, secondary ion mass spectrometry, and X-ray fluorescence-based methods for depth-dependent, element-specific analysis. We highlight a strong connection between cation segregation and electrocatalytic properties, because cation segregation enhances oxygen transport and surface oxygen exchange kinetics. On the other hand, the formation of cation-enriched secondary phases can lead to the blocking of active sites, inhibiting oxygen exchange. With help from density functional theory, the links between cation migration, catalyst stability, and catalytic activity are provided, and the oxygen p-band center relative to the Fermi level can be identified as an activity descriptor. Based on these findings, we discuss strategies to increase a catalyst's activity while maintaining stability to design efficient, cost-effective electrocatalysts. PMID:27149528

  12. One-Step Synthesis of MoS₂/WS₂ Layered Heterostructures and Catalytic Activity of Defective Transition Metal Dichalcogenide Films.

    PubMed

    Woods, John M; Jung, Yeonwoong; Xie, Yujun; Liu, Wen; Liu, Yanhui; Wang, Hailiang; Cha, Judy J

    2016-02-23

    Transition metal dichalcogenides (TMDCs) are a promising class of two-dimensional (2D) materials for use in applications such as 2D electronics, optoelectronics, and catalysis. Due to the van der Waals (vdW) bonding between layers, vdW heterostructures can be constructed between two different species of TMDCs. Most studies employ exfoliation or co-vapor growth schemes, which are limited by the small size and uneven distribution of heterostructures on the growth substrate. In this work we demonstrate a one-step synthesis procedure for large-area vdW heterostructures between horizontal TMDCs MoS2 and WS2. The synthesis procedure is scalable and provides patterning ability, which is critical for electronic applications in integrated circuits. We demonstrate rectification characteristics of large-area MoS2/WS2 stacks. In addition, hydrogen evolution reaction performance was measured in these horizontal MoS2 and WS2 thin films, which indicate that, in addition to the catalytically active sulfur edge sites, defect sites may serve as catalyst sites. PMID:26836122

  13. Electro-catalytic activity of Ni–Co-based catalysts for oxygen evolution reaction

    SciTech Connect

    Ju, Hua; Li, Zhihu; Xu, Yanhui

    2015-04-15

    Graphical abstract: The electro-catalytic activity of different electro-catalysts with a porous electrode structure was compared considering the real electrode area that was evaluated by cyclic measurement. - Highlights: • Ni–Co-based electro-catalysts for OER have been studied and compared. • The real electrode area is calculated and used for assessing the electro-catalysts. • Exchange current and reaction rate constant are estimated. • Ni is more useful for OER reaction than Co. - Abstract: In the present work, Ni–Co-based electrocatalysts (Ni/Co = 0:6, 1:5, 2:4, 3:3, 4:2, 5:1 and 6:0) have been studied for oxygen evolution reaction. The phase structure has been analyzed by X-ray diffraction technique. Based on the XRD and SEM results, it is believed that the synthesized products are poorly crystallized. To exclude the disturbance of electrode preparation technology on the evaluation of electro-catalytic activity, the real electrode surface area is calculated based on the cyclic voltammetry data, assumed that the specific surface capacitance is 60 μF cm{sup −2} for metal oxide electrode. The real electrode area data are used to calculate the current density. The reaction rate constant of OER at different electrodes is also estimated based on basic reaction kinetic equations. It is found that the exchange current is 0.05–0.47 mA cm{sup −2} (the real surface area), and the reaction rate constant has an order of magnitude of 10{sup −7}–10{sup −6} cm s{sup −1}. The influence of the electrode potential on OER rate has been also studied by electrochemical impedance spectroscopy (EIS) technique. Our investigation has shown that the nickel element has more contribution than the cobalt; the nickel oxide has the best electro-catalytic activity toward OER.

  14. Acylpeptide hydrolase: inhibitors and some active site residues of the human enzyme.

    PubMed

    Scaloni, A; Jones, W M; Barra, D; Pospischil, M; Sassa, S; Popowicz, A; Manning, L R; Schneewind, O; Manning, J M

    1992-02-25

    Acylpeptide hydrolase may be involved in N-terminal deacetylation of nascent polypeptide chains and of bioactive peptides. The activity of this enzyme from human erythrocytes is sensitive to anions such as chloride, nitrate, and fluoride. Furthermore, blocked amino acids act as competitive inhibitors of the enzyme. Acetyl leucine chloromethyl ketone has been employed to identify one active site residue as His-707. Diisopropylfluorophosphate has been used to identify a second active site residue as Ser-587. Chemical modification studies with a water-soluble carbodiimide implicate a carboxyl group in catalytic activity. These results and the sequence around these active site residues, especially near Ser-587, suggest that acylpeptide hydrolase contains a catalytic triad. The presence of a cysteine residue in the vicinity of the active site is suggested by the inactivation of the enzyme by sulfhydryl-modifying agents and also by a low amount of modification by the peptide chloromethyl ketone inhibitor. Ebelactone A, an inhibitor of the formyl aminopeptidase, the bacterial counterpart of eukaryotic acylpeptide hydrolase, was found to be an effective inhibitor of this enzyme. These findings suggest that acylpeptidase hydrolase is a member of a family of enzymes with extremely diverse functions. PMID:1740429

  15. A new experimental setup for high-pressure catalytic activity measurements on surface deposited mass-selected Pt clusters

    SciTech Connect

    Watanabe, Yoshihide; Isomura, Noritake

    2009-09-15

    A new experimental setup to study catalytic and electronic properties of size-selected clusters on metal oxide substrates from the viewpoint of cluster-support interaction and to formulate a method for the development of heterogeneous catalysts such as automotive exhaust catalysts has been developed. The apparatus consists of a size-selected cluster source, a photoemission spectrometer, a scanning tunneling microscope (STM), and a high-pressure reaction cell. The high-pressure reaction cell measurements provided information on catalytic properties in conditions close to practical use. The authors investigated size-selected platinum clusters deposited on a TiO{sub 2}(110) surface using a reaction cell and STM. Catalytic activity measurements showed that the catalytic activities have a cluster-size dependency.

  16. Polyvinylpyrrolidone adsorption effects on the morphologies of synthesized platinum particles and its catalytic activity

    NASA Astrophysics Data System (ADS)

    Ooi, Mahayatun Dayana Johan; Aziz, Azlan Abdul

    2015-04-01

    Flower-like Platinum micro-structures were synthesized from different concentration of the PVP using solvothermal method. At 5.0×10-3 mmol of PVP, well-defined flower-like pattern consists of triangular petals radiating from the centre were produced whereas larger flower network developed at higher PVP concentration. High degree of crystallinity was obtained upon each increment of PVP. The well defined flower like pattern synthesized using 5.0×10-3 mmol PVP exhi