Sample records for catalytically competent active
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Jimenez-Sandoval, Pedro; Vique-Sanchez, Jose Luis; Hidalgo, Marisol López; Velazquez-Juarez, Gilberto; Diaz-Quezada, Corina; Arroyo-Navarro, Luis Fernando; Moran, Gabriela Montero; Fattori, Juliana; Jessica Diaz-Salazar, A; Rudiño-Pinera, Enrique; Sotelo-Mundo, Rogerio; Figueira, Ana Carolina Migliorini; Lara-Gonzalez, Samuel; Benítez-Cardoza, Claudia G; Brieba, Luis G
2017-11-01
The protozoan parasite Trichomonas vaginalis contains two nearly identical triosephosphate isomerases (TvTIMs) that dissociate into stable monomers and dimerize upon substrate binding. Herein, we compare the role of the "ball and socket" and loop 3 interactions in substrate assisted dimer assembly in both TvTIMs. We found that point mutants at the "ball" are only 39 and 29-fold less catalytically active than their corresponding wild-type counterparts, whereas Δloop 3 deletions are 1502 and 9400-fold less active. Point and deletion mutants dissociate into stable monomers. However, point mutants assemble as catalytic competent dimers upon binding of the transition state substrate analog PGH, whereas loop 3 deletions remain monomeric. A comparison between crystal structures of point and loop 3 deletion monomeric mutants illustrates that the catalytic residues in point mutants and wild-type TvTIMs are maintained in the same orientation, whereas the catalytic residues in deletion mutants show an increase in thermal mobility and present structural disorder that may hamper their catalytic role. The high enzymatic activity present in monomeric point mutants correlates with the formation of dimeric TvTIMs upon substrate binding. In contrast, the low activity and lack of dimer assembly in deletion mutants suggests a role of loop 3 in promoting the formation of the active site as well as dimer assembly. Our results suggest that in TvTIMs the active site is assembled during dimerization and that the integrity of loop 3 and ball and socket residues is crucial to stabilize the dimer. Copyright © 2017 Elsevier B.V. All rights reserved.
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Molecular Self-Assembly Strategy for Generating Catalytic Hybrid Polypeptides
Ikezoe, Yasuhiro; Pike, Douglas H.; Nanda, Vikas; Matsui, Hiroshi
2016-01-01
Recently, catalytic peptides were introduced that mimicked protease activities and showed promising selectivity of products even in organic solvents where protease cannot perform well. However, their catalytic efficiency was extremely low compared to natural enzyme counterparts presumably due to the lack of stable tertiary fold. We hypothesized that assembling these peptides along with simple hydrophobic pockets, mimicking enzyme active sites, could enhance the catalytic activity. Here we fused the sequence of catalytic peptide CP4, capable of protease and esterase-like activities, into a short amyloidogenic peptide fragment of Aβ. When the fused CP4-Aβ construct assembled into antiparallel β-sheets and amyloid fibrils, a 4.0-fold increase in the hydrolysis rate of p-nitrophenyl acetate (p-NPA) compared to neat CP4 peptide was observed. The enhanced catalytic activity of CP4-Aβ assembly could be explained both by pre-organization of a catalytically competent Ser-His-acid triad and hydrophobic stabilization of a bound substrate between the triad and p-NPA, indicating that a design strategy for self-assembled peptides is important to accomplish the desired functionality. PMID:27116246
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Molecular self-assembly strategy for generating catalytic hybrid polypeptides
Maeda, Yoshiaki; Fang, Justin; Ikezoe, Yasuhiro; ...
2016-04-26
Recently, catalytic peptides were introduced that mimicked protease activities and showed promising selectivity of products even in organic solvents where protease cannot perform well. However, their catalytic efficiency was extremely low compared to natural enzyme counterparts presumably due to the lack of stable tertiary fold. We hypothesized that assembling these peptides along with simple hydrophobic pockets, mimicking enzyme active sites, could enhance the catalytic activity. Here we fused the sequence of catalytic peptide CP4, capable of protease and esterase-like activities, into a short amyloidogenic peptide fragment of Aβ. When the fused CP4-Aβ construct assembled into antiparallel β- sheets and amyloidmore » fibrils, a 4.0-fold increase in the hydrolysis rate of p-nitrophenyl acetate (p-NPA) compared to neat CP4 peptide was observed. Furthermore, the enhanced catalytic activity of CP4-Aβ assembly could be explained both by pre-organization of a catalytically competent Ser-His-acid triad and hydrophobic stabilization of a bound substrate between the triad and p-NPA, indicating that a design strategy for self-assembled peptides is important to accomplish the desired functionality.« less
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USDA-ARS?s Scientific Manuscript database
Rubisco’s catalytic chaperone, Rubisco activase (Rca), uses the energy from ATP hydrolysis to restore catalytic competence to Rubisco. In Arabidopsis, inhibition of Rca activity by ADP is fine-tuned by redox regulation of the a-isoform. To elucidate the mechanism for Rca regulation in species contai...
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Structural assembly of the signaling competent ERK2–RSK1 heterodimeric protein kinase complex
Alexa, Anita; Gógl, Gergő; Glatz, Gábor; Garai, Ágnes; Zeke, András; Varga, János; Dudás, Erika; Jeszenői, Norbert; Bodor, Andrea; Hetényi, Csaba; Reményi, Attila
2015-01-01
Mitogen-activated protein kinases (MAPKs) bind and activate their downstream kinase substrates, MAPK-activated protein kinases (MAPKAPKs). Notably, extracellular signal regulated kinase 2 (ERK2) phosphorylates ribosomal S6 kinase 1 (RSK1), which promotes cellular growth. Here, we determined the crystal structure of an RSK1 construct in complex with its activator kinase. The structure captures the kinase–kinase complex in a precatalytic state where the activation loop of the downstream kinase (RSK1) faces the enzyme's (ERK2) catalytic site. Molecular dynamics simulation was used to show how this heterodimer could shift into a signaling-competent state. This structural analysis combined with biochemical and cellular studies on MAPK→MAPKAPK signaling showed that the interaction between the MAPK binding linear motif (residing in a disordered kinase domain extension) and the ERK2 “docking” groove plays the major role in making an encounter complex. This interaction holds kinase domains proximal as they “readjust,” whereas generic kinase domain surface contacts bring them into a catalytically competent state. PMID:25730857
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The activity of Rubisco's molecular chaperone, Rubisco activase, in leaf extracts
USDA-ARS?s Scientific Manuscript database
Rubisco frequently undergoes unproductive interactions with its sugar-phosphate substrate that stabilize active sites in an inactive conformation. Restoring catalytic competence to these sites requires the “molecular chiropractic” activity of Rubisco activase (activase). To make the study of activas...
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Conformational motions regulate phosphoryl transfer in related protein tyrosine phosphatases
Whittier, Sean K.; Hengge, Alvan C.; Loria, J. Patrick
2014-01-01
Many studies have implicated a role for conformational motions during the catalytic cycle, acting to optimize the binding pocket or facilitate product release, but a more intimate role in the chemical reaction has not been described. We address this by monitoring active-site loop motion in two protein tyrosine phosphatases (PTPs) using NMR spectroscopy. The PTPs, YopH and PTP1B, have very different catalytic rates, however we find in both that the active-site loop closes to its catalytically competent position at rates that mirror the phosphotyrosine cleavage kinetics. This loop contains the catalytic acid, suggesting that loop closure occurs concomitantly with the protonation of the leaving group tyrosine and explains the different kinetics of two otherwise chemically and mechanistically indistinguishable enzymes. PMID:23970698
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Kuznetsov, N A; Kiryutin, A S; Kuznetsova, A A; Panov, M S; Barsukova, M O; Yurkovskaya, A V; Fedorova, O S
2017-04-01
Human alkyladenine DNA glycosylase (AAG) protects DNA from alkylated and deaminated purine lesions. AAG flips out the damaged nucleotide from the double helix of DNA and catalyzes the hydrolysis of the N-glycosidic bond to release the damaged base. To understand better, how the step of nucleotide eversion influences the overall catalytic process, we performed a pre-steady-state kinetic analysis of AAG interaction with specific DNA-substrates, 13-base pair duplexes containing in the 7th position 1-N6-ethenoadenine (εA), hypoxanthine (Hx), and the stable product analogue tetrahydrofuran (F). The combination of the fluorescence of tryptophan, 2-aminopurine, and 1-N6-ethenoadenine was used to record conformational changes of the enzyme and DNA during the processes of DNA lesion recognition, damaged base eversion, excision of the N-glycosidic bond, and product release. The thermal stability of the duplexes characterized by the temperature of melting, T m , and the rates of spontaneous opening of individual nucleotide base pairs were determined by NMR spectroscopy. The data show that the relative thermal stability of duplexes containing a particular base pair in position 7, (T m (F/T) < T m (εA/T) < T m (Hx/T) < T m (A/T)) correlates with the rate of reversible spontaneous opening of the base pair. However, in contrast to that, the catalytic lesion excision rate is two orders of magnitude higher for Hx-containing substrates than for substrates containing εA, proving that catalytic activity is not correlated with the stability of the damaged base pair. Our study reveals that the formation of the catalytically competent enzyme-substrate complex is not the bottleneck controlling the catalytic activity of AAG.
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Locking the Active Conformation of c-Src Kinase through the Phosphorylation of the Activation Loop
Meng, Yilin; Roux, Benoît
2013-01-01
Molecular dynamics umbrella sampling simulations are used to compare the relative stability of the active conformation of the catalytic domain of c-Src kinase while the tyrosine 416 in the activation loop (A-loop) is either unphosphorylated or phosphorylated. When the A-loop is unphosphorylated, there is considerable flexiblity of the kinase. While the active conformation of the kinase is not forbidden and can be visited transiently, it is not the predominant state. This is consistent with the view that c-Src displays some catalytic activity even when the A-loop is unphosphorylated. In contrast, phosphorylation of the A-loop contributes to stabilize several structural features that are critical for catalysis, such as the hydrophobic regulatory spine, the HRD motif, and the electrostatic switch. In summary, the free energy landscape calculations demonstrate that phosphorylation of tyrosine 416 in the A-loop essentially “locks” the kinase into its catalytically competent conformation. PMID:24103328
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A minimal kinetic model for a viral DNA packaging machine.
Yang, Qin; Catalano, Carlos Enrique
2004-01-20
Terminase enzymes are common to both eukaryotic and prokaryotic double-stranded DNA viruses. These enzymes possess ATPase and nuclease activities that work in concert to "package" a viral genome into an empty procapsid, and it is likely that terminase enzymes from disparate viruses utilize a common packaging mechanism. Bacteriophage lambda terminase possesses a site-specific nuclease activity, a so-called helicase activity, a DNA translocase activity, and multiple ATPase catalytic sites that function to package viral DNA. Allosteric interactions between the multiple catalytic sites have been reported. This study probes these catalytic interactions using enzyme kinetic, photoaffinity labeling, and vanadate inhibition studies. The ensemble of data forms the basis for a minimal kinetic model for lambda terminase. The model incorporates an ADP-driven conformational reorganization of the terminase subunits assembled on viral DNA, which is central to the activation of a catalytically competent packaging machine. The proposed model provides a unifying mechanism for allosteric interaction between the multiple catalytic sites of the holoenzyme and explains much of the kinetic data in the literature. Given that similar packaging mechanisms have been proposed for viruses as dissimilar as lambda and the herpes viruses, the model may find general utility in our global understanding of the enzymology of virus assembly.
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Genth, Harald; Selzer, Jörg; Busch, Christian; Dumbach, Jürgen; Hofmann, Fred; Aktories, Klaus; Just, Ingo
2000-01-01
The family of the large clostridial cytotoxins, encompassing Clostridium difficile toxins A and B as well as the lethal and hemorrhagic toxins from Clostridium sordellii, monoglucosylate the Rho GTPases by transferring a glucose moiety from the cosubstrate UDP-glucose. Here we present a new detoxification procedure to block the enzyme activity by treatment with the reactive UDP-2′,3′-dialdehyde to result in alkylation of toxin A and B. Alkylation is likely to occur in the catalytic domain, because the native cosubstrate UDP-glucose completely protected the toxins from inactivation and the alkylated toxin competes with the native toxin at the cell receptor. Alkylated toxins are good antigens resulting in antibodies recognizing only the C-terminally located receptor binding domain, whereas formaldehyde treatment resulted in antibodies recognizing both the receptor binding domain and the catalytic domain, indicating that the catalytic domain is concealed under native conditions. Antibodies against the native catalytic domain (amino acids 1 through 546) and those holotoxin antibodies recognizing the catalytic domain inhibited enzyme activity. However, only antibodies against the receptor binding domain protected intact cells from the cytotoxic activity of toxin B, whereas antibodies against the catalytic domain were protective only when inside the cell. PMID:10678912
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Dutta, Saheb; Kundu, Soumya; Saha, Amrita; Nandi, Nilashis
2018-03-01
Aminoacylation reaction is the first step of protein biosynthesis. The catalytic reorganization at the active site of aminoacyl tRNA synthetases (aaRSs) is driven by the loop motions. There remain lacunae of understanding concerning the catalytic loop dynamics in aaRSs. We analyzed the functional loop dynamics in seryl tRNA synthetase from Methanopyrus kandleri ( mk SerRS) and histidyl tRNA synthetases from Thermus thermophilus ( tt HisRS), respectively, using molecular dynamics. Results confirm that the motif 2 loop and other active site loops are flexible spots within the catalytic domain. Catalytic residues of the loops form a network of interaction with the substrates to form a reactive state. The loops undergo transitions between closed state and open state and the relaxation of the constituent residues occurs in femtosecond to nanosecond time scale. Order parameters are higher for constituent catalytic residues which form a specific network of interaction with the substrates to form a reactive state compared to the Gly residues within the loop. The development of interaction is supported from mutation studies where the catalytic domain with mutated loop exhibits unfavorable binding energy with the substrates. During the open-close motion of the loops, the catalytic residues make relaxation by ultrafast librational motion as well as fast diffusive motion and subsequently relax rather slowly via slower diffusive motion. The Gly residues act as a hinge to facilitate the loop closing and opening by their faster relaxation behavior. The role of bound water is analyzed by comparing implicit solvent-based and explicit solvent-based simulations. Loops fail to form catalytically competent geometry in absence of water. The present result, for the first time reveals the nature of the active site loop dynamics in aaRS and their influence on catalysis.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Lee, Seongmin; Verdine, Gregory L.; Harvard)
2010-01-14
Adenine DNA glycosylase catalyzes the glycolytic removal of adenine from the promutagenic A {center_dot} oxoG base pair in DNA. The general features of DNA recognition by an adenine DNA glycosylase, Bacillus stearothermophilus MutY, have previously been revealed via the X-ray structure of a catalytically inactive mutant protein bound to an A:oxoG-containing DNA duplex. Although the structure revealed the substrate adenine to be, as expected, extruded from the DNA helix and inserted into an extrahelical active site pocket on the enzyme, the substrate adenine engaged in no direct contacts with active site residues. This feature was paradoxical, because other glycosylases havemore » been observed to engage their substrates primarily through direct contacts. The lack of direct contacts in the case of MutY suggested that either MutY uses a distinctive logic for substrate recognition or that the X-ray structure had captured a noncatalytically competent state in lesion recognition. To gain further insight into this issue, we crystallized wild-type MutY bound to DNA containing a catalytically inactive analog of 2'-deoxyadenosine in which a single 2'-H atom was replaced by fluorine. The structure of this fluorinated lesion-recognition complex (FLRC) reveals the substrate adenine buried more deeply into the active site pocket than in the prior structure and now engaged in multiple direct hydrogen bonding and hydrophobic interactions. This structure appears to capture the catalytically competent state of adenine DNA glycosylases, and it suggests a catalytic mechanism for this class of enzymes, one in which general acid-catalyzed protonation of the nucleobase promotes glycosidic bond cleavage.« less
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Hsiao, Ju-Chun; McGrath, Aaron P; Kielmann, Linda; Kalimuthu, Palraj; Darain, Farzana; Bernhardt, Paul V; Harmer, Jeffrey; Lee, Mihwa; Meyers, Kimberley; Maher, Megan J; Kappler, Ulrike
2018-01-01
A central conserved arginine, first identified as a clinical mutation leading to sulfite oxidase deficiency, is essential for catalytic competency of sulfite oxidizing molybdoenzymes, but the molecular basis for its effects on turnover and substrate affinity have not been fully elucidated. We have used a bacterial sulfite dehydrogenase, SorT, which lacks an internal heme group, but transfers electrons to an external, electron accepting cytochrome, SorU, to investigate the molecular functions of this arginine residue (Arg78). Assay of the SorT Mo centre catalytic competency in the absence of SorU showed that substitutions in the central arginine (R78Q, R78K and R78M mutations) only moderately altered SorT catalytic properties, except for R78M which caused significant reduction in SorT activity. The substitutions also altered the Mo-centre redox potentials (Mo VI/V potential lowered by ca. 60-80mV). However, all Arg78 mutations significantly impaired the ability of SorT to transfer electrons to SorU, where activities were reduced 17 to 46-fold compared to SorT WT , precluding determination of kinetic parameters. This was accompanied by the observation of conformational changes in both the introduced Gln and Lys residues in the crystal structure of the enzymes. Taking into account data collected by others on related SOE mutations we propose that the formation and maintenance of an electron transfer complex between the Mo centre and electron accepting heme groups is the main function of the central arginine, and that the reduced turnover and increases in K Msulfite are caused by the inefficient operation of the oxidative half reaction of the catalytic cycle in enzymes carrying these mutations. Copyright © 2017 Elsevier B.V. All rights reserved.
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Lee, Ting-Wai; Cherney, Maia M; Liu, Jie; James, Karen Ellis; Powers, James C; Eltis, Lindsay D; James, Michael N G
2007-02-23
The SARS coronavirus main peptidase (SARS-CoV M(pro)) plays an essential role in the life-cycle of the virus and is a primary target for the development of anti-SARS agents. Here, we report the crystal structure of M(pro) at a resolution of 1.82 Angstroms, in space group P2(1) at pH 6.0. In contrast to the previously reported structure of M(pro) in the same space group at the same pH, the active sites and the S1 specificity pockets of both protomers in the structure of M(pro) reported here are in the catalytically competent conformation, suggesting their conformational flexibility. We report two crystal structures of M(pro) having an additional Ala at the N terminus of each protomer (M(+A(-1))(pro)), both at a resolution of 2.00 Angstroms, in space group P4(3)2(1)2: one unbound and one bound by a substrate-like aza-peptide epoxide (APE). In the unbound form, the active sites and the S1 specificity pockets of both protomers of M(+A(-1))(pro) are observed in a collapsed (catalytically incompetent) conformation; whereas they are in an open (catalytically competent) conformation in the APE-bound form. The observed conformational flexibility of the active sites and the S1 specificity pockets suggests that these parts of M(pro) exist in dynamic equilibrium. The structural data further suggest that the binding of APE to M(pro) follows an induced-fit model. The substrate likely also binds in an induced-fit manner in a process that may help drive the catalytic cycle.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Sheng, Fang; Jia, Xiaofei; Yep, Alejandra
2009-07-06
Escherichia coli glycogen synthase (EcGS, EC 2.4.1.21) is a retaining glycosyltransferase (GT) that transfers glucose from adenosine diphosphate glucose to a glucan chain acceptor with retention of configuration at the anomeric carbon. EcGS belongs to the GT-B structural superfamily. Here we report several EcGS x-ray structures that together shed considerable light on the structure and function of these enzymes. The structure of the wild-type enzyme bound to ADP and glucose revealed a 15.2 degrees overall domain-domain closure and provided for the first time the structure of the catalytically active, closed conformation of a glycogen synthase. The main chain carbonyl groupmore » of His-161, Arg-300, and Lys-305 are suggested by the structure to act as critical catalytic residues in the transglycosylation. Glu-377, previously thought to be catalytic is found on the alpha-face of the glucose and plays an electrostatic role in the active site and as a glucose ring locator. This is also consistent with the structure of the EcGS(E377A)-ADP-HEPPSO complex where the glucose moiety is either absent or disordered in the active site« less
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Eckhard, Kathrin; Chen, Xingxing; Turcu, Florin; Schuhmann, Wolfgang
2006-12-07
In order to locally analyse catalytic activity on modified surfaces a transient redox competition mode of scanning electrochemical microscopy (SECM) has been developed. In a bi-potentiostatic experiment the SECM tip competes with the sample for the very same analyte. This leads to a current decrease at the SECM tip, if it is positioned in close proximity to an active catalyst site on the surface. Specifically, local catalytic activity of a Pt-catalyst modified sample with respect to the catalytic reduction of molecular oxygen was investigated. At higher local catalytic activity the local 02 partial pressure within the gap between accurately positioned SECM tip and sample is depleted, leading to a noticeable tip current decrease over active sites. A flexible software module has been implemented into the SECM to adapt the competition conditions by proper definition of tip and sample potentials. A potential pulse profile enables the localised electrochemically induced generation of molecular oxygen prior to the competition detection. The current decay curves are recorded over the entire duration of the applied reduction pulse. Hence, a time resolved processing of the acquired current values provides movies of the local oxygen concentration against x,y-position. The SECM redox competition mode was verified with a macroscopic Pt-disk electrode as a test sample to demonstrate the feasibility of the approach. Moreover, highly dispersed electro-deposited spots of gold and platinum on glassy carbon were visualised using the redox competition mode of SECM. Catalyst spots of different nature as well as activity inhomogeneities within one spot caused by local variations in Pt-loading were visualised successfully.
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Foley, Nicholas A; Lail, Marty; Lee, John P; Gunnoe, T Brent; Cundari, Thomas R; Petersen, Jeffrey L
2007-05-30
Complexes of the type TpRu(L)(NCMe)R [L = CO or PMe3; R = Ph or Me; Tp = hydridotris(pyrazolyl)borate] initiate C-H activation of benzene. Kinetic studies, isotopic labeling, and other experimental evidence suggest that the mechanism of benzene C-H activation involves reversible dissociation of acetonitrile, reversible benzene coordination, and rate-determining C-H activation of coordinated benzene. TpRu(PMe3)(NCMe)Ph initiates C-D activation of C6D6 at rates that are approximately 2-3 times more rapid than that for TpRu(CO)(NCMe)Ph (depending on substrate concentration); however, the catalytic hydrophenylation of ethylene using TpRu(PMe3)(NCMe)Ph is substantially less efficient than catalysis with TpRu(CO)(NCMe)Ph. For TpRu(PMe3)(NCMe)Ph, C-H activation of ethylene, to ultimately produce TpRu(PMe3)(eta3-C4H7), is found to kinetically compete with catalytic ethylene hydrophenylation. In THF solutions containing ethylene, TpRu(PMe3)(NCMe)Ph and TpRu(CO)(NCMe)Ph separately convert to TpRu(L)(eta3-C4H7) (L = PMe3 or CO, respectively) via initial Ru-mediated ethylene C-H activation. Heating mesitylene solutions of TpRu(L)(eta3-C4H7) under ethylene pressure results in the catalytic production of butenes (i.e., ethylene hydrovinylation) and hexenes.
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Liberato, Marcelo V; Silveira, Rodrigo L; Prates, Érica T; de Araujo, Evandro A; Pellegrini, Vanessa O A; Camilo, Cesar M; Kadowaki, Marco A; Neto, Mario de O; Popov, Alexander; Skaf, Munir S; Polikarpov, Igor
2016-04-01
Glycoside hydrolases (GHs) play fundamental roles in the decomposition of lignocellulosic biomaterials. Here, we report the full-length structure of a cellulase from Bacillus licheniformis (BlCel5B), a member of the GH5 subfamily 4 that is entirely dependent on its two ancillary modules (Ig-like module and CBM46) for catalytic activity. Using X-ray crystallography, small-angle X-ray scattering and molecular dynamics simulations, we propose that the C-terminal CBM46 caps the distal N-terminal catalytic domain (CD) to establish a fully functional active site via a combination of large-scale multidomain conformational selection and induced-fit mechanisms. The Ig-like module is pivoting the packing and unpacking motions of CBM46 relative to CD in the assembly of the binding subsite. This is the first example of a multidomain GH relying on large amplitude motions of the CBM46 for assembly of the catalytically competent form of the enzyme.
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NASA Astrophysics Data System (ADS)
Liberato, Marcelo V.; Silveira, Rodrigo L.; Prates, Érica T.; de Araujo, Evandro A.; Pellegrini, Vanessa O. A.; Camilo, Cesar M.; Kadowaki, Marco A.; Neto, Mario De O.; Popov, Alexander; Skaf, Munir S.; Polikarpov, Igor
2016-04-01
Glycoside hydrolases (GHs) play fundamental roles in the decomposition of lignocellulosic biomaterials. Here, we report the full-length structure of a cellulase from Bacillus licheniformis (BlCel5B), a member of the GH5 subfamily 4 that is entirely dependent on its two ancillary modules (Ig-like module and CBM46) for catalytic activity. Using X-ray crystallography, small-angle X-ray scattering and molecular dynamics simulations, we propose that the C-terminal CBM46 caps the distal N-terminal catalytic domain (CD) to establish a fully functional active site via a combination of large-scale multidomain conformational selection and induced-fit mechanisms. The Ig-like module is pivoting the packing and unpacking motions of CBM46 relative to CD in the assembly of the binding subsite. This is the first example of a multidomain GH relying on large amplitude motions of the CBM46 for assembly of the catalytically competent form of the enzyme.
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Anti-staphylococcal activities of lysostaphin and LytM catalytic domain
2012-01-01
Background Lysostaphin and the catalytic domain of LytM cleave pentaglycine crossbridges of Staphylococcus aureus peptidoglycan. The bacteriocin lysostaphin is secreted by Staphylococcus simulans biovar staphylolyticus and directed against the cell walls of competing S. aureus. LytM is produced by S. aureus as a latent autolysin and can be activated in vitro by the removal of an N-terminal domain and occluding region. Results We compared the efficacies of the lysostaphin and LytM catalytic domains using a newly developed model of chronic S. aureus infected eczema. Lysostaphin was effective, like in other models. In contrast, LytM was not significantly better than control. The different treatment outcomes could be correlated with in vitro properties of the proteins, including proteolytic stability, affinity to cell wall components other than peptidoglycan, and sensitivity to the ionic milieu. Conclusions Although lysostaphin and LytM cleave the same peptide bond in the peptidoglycan, the two enzymes have very different environmental requirements what is reflected in their contrasting performance in mouse eczema model. PMID:22672475
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Sebastián, María; Velázquez-Campoy, Adrián; Medina, Milagros
2018-12-01
Emergence of multidrug-resistant bacteria forces us to explore new therapeutic strategies, and proteins involved in key metabolic pathways are promising anti-bacterial targets. Bifunctional flavin-adenine dinucleotide (FAD) synthetases (FADS) are prokaryotic enzymes that synthesise the flavin mononucleotide (FMN) and FAD cofactors. The FADS from the human pathogen Streptococcus pneumoniae (SpnFADS)-causative agent of pneumonia in humans - shows relevant catalytic dissimilarities compared to other FADSs. Here, by integrating thermodynamic and kinetic data, we present a global description of the riboflavin kinase activity of SpnFADS, as well as of the inhibition mechanisms regulating this activity. Our data shed light on biophysical determinants that modulate species-specific conformational changes leading to catalytically competent conformations, as well as binding rates and affinities of substrates versus products. This knowledge paves the way for the development of tools - that taking advantage of the regulatory dissimilarities during FMN biosynthesis in different species - might be used in the discovery of specific anti-pneumococcal drugs.
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The report is part of a two-phase EPA effort to assess the performance, suitability, and costs of various technologies to control emissions of volatile organic compounds (VOCs). In Phase 1, information was assembled from the literature on the use and cost of using catalytic incin...
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Water Oxidation Catalysis for NiOOH by a Metropolis Monte Carlo Algorithm.
Hareli, Chen; Caspary Toroker, Maytal
2018-05-08
Understanding catalytic mechanisms is important for discovering better catalysts, particularly for water splitting reactions that are of great interest to the renewable energy field. One of the best performing catalysts for water oxidation is nickel oxyhydroxide (NiOOH). However, only one mechanism has been adopted so far for modeling catalysis of the active plane: β-NiOOH(01̅5). In order to understand how a second reaction mechanism affects catalysis, we perform Density Functional Theory + U (DFT+U) calculations of a second mechanism for water oxidation reaction of NiOOH. Then, we use a Metropolis Monte Carlo algorithm to calculate how many catalytic cycles are completed when two reaction mechanisms are competing. We find that within the Metropolis algorithm, the second mechanism has a higher overpotential and is therefore not active even for large applied biases.
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Heier, Christoph; Kien, Benedikt; Huang, Feifei; Eichmann, Thomas O; Xie, Hao; Zechner, Rudolf; Chang, Ping-An
2017-11-17
Mammalian patatin-like phospholipase domain-containing proteins (PNPLAs) are lipid-metabolizing enzymes with essential roles in energy metabolism, skin barrier development, and brain function. A detailed annotation of enzymatic activities and structure-function relationships remains an important prerequisite to understand PNPLA functions in (patho-)physiology, for example, in disorders such as neutral lipid storage disease, non-alcoholic fatty liver disease, and neurodegenerative syndromes. In this study, we characterized the structural features controlling the subcellular localization and enzymatic activity of PNPLA7, a poorly annotated phospholipase linked to insulin signaling and energy metabolism. We show that PNPLA7 is an endoplasmic reticulum (ER) transmembrane protein that specifically promotes hydrolysis of lysophosphatidylcholine in mammalian cells. We found that transmembrane and regulatory domains in the PNPLA7 N-terminal region cooperate to regulate ER targeting but are dispensable for substrate hydrolysis. Enzymatic activity is instead mediated by the C-terminal domain, which maintains full catalytic competence even in the absence of N-terminal regions. Upon elevated fatty acid flux, the catalytic domain targets cellular lipid droplets and promotes interactions of PNPLA7 with these organelles in response to increased cAMP levels. We conclude that PNPLA7 acts as an ER-anchored lysophosphatidylcholine hydrolase that is composed of specific functional domains mediating catalytic activity, subcellular positioning, and interactions with cellular organelles. Our study provides critical structural insights into an evolutionarily conserved class of phospholipid-metabolizing enzymes. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.
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Domain alternation and active site remodeling are conserved structural features of ubiquitin E1.
Lv, Zongyang; Yuan, Lingmin; Atkison, James H; Aldana-Masangkay, Grace; Chen, Yuan; Olsen, Shaun K
2017-07-21
E1 enzymes for ubiquitin (Ub) and Ub-like modifiers (Ubls) harbor two catalytic activities that are required for Ub/Ubl activation: adenylation and thioester bond formation. Structural studies of the E1 for the Ubl s mall u biquitin-like mo difier (SUMO) revealed a single active site that is transformed by a conformational switch that toggles its competency for catalysis of these two distinct chemical reactions. Although the mechanisms of adenylation and thioester bond formation revealed by SUMO E1 structures are thought to be conserved in Ub E1, there is currently a lack of structural data supporting this hypothesis. Here, we present a structure of Schizosaccharomyces pombe Uba1 in which the second catalytic cysteine half-domain (SCCH domain) harboring the catalytic cysteine has undergone a 106° rotation that results in a completely different network of intramolecular interactions between the SCCH and adenylation domains and translocation of the catalytic cysteine 12 Å closer to the Ub C terminus compared with previous Uba1 structures. SCCH domain alternation is accompanied by conformational changes within the Uba1 adenylation domains that effectively disassemble the adenylation active site. Importantly, the structural and biochemical data suggest that domain alternation and remodeling of the adenylation active site are interconnected and are intrinsic structural features of Uba1 and that the overall structural basis for adenylation and thioester bond formation exhibited by SUMO E1 is indeed conserved in Ub E1. Finally, the mechanistic insights provided by the novel conformational snapshot of Uba1 presented in this study may guide efforts to develop small molecule inhibitors of this critically important enzyme that is an active target for anticancer therapeutics. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.
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Propitious Dendritic Cu2O-Pt Nanostructured Anodes for Direct Formic Acid Fuel Cells.
El-Nagar, Gumaa A; Mohammad, Ahmad M; El-Deab, Mohamed S; El-Anadouli, Bahgat E
2017-06-14
This study introduces a novel competent dendritic copper oxide-platinum nanocatalyst (nano-Cu 2 O-Pt) immobilized onto a glassy carbon (GC) substrate for formic acid (FA) electro-oxidation (FAO); the prime reaction in the anodic compartment of direct formic acid fuel cells (DFAFCs). Interestingly, the proposed catalyst exhibited an outstanding improvement for FAO compared to the traditional platinum nanoparticles (nano-Pt) modified GC (nano-Pt/GC) catalyst. This was evaluated from steering the reaction mechanism toward the desired direct route producing carbon dioxide (CO 2 ); consistently with mitigating the other undesired indirect pathway producing carbon monoxide (CO); the potential poison deteriorating the catalytic activity of typical Pt-based catalysts. Moreover, the developed catalyst showed a reasonable long-term catalytic stability along with a significant lowering in onset potential of direct FAO that ultimately reduces the polarization and amplifies the fuel cell's voltage. The observed catalytic enhancement was believed to originate bifunctionally; while nano-Pt represented the base for the FA adsorption, nanostructured copper oxide (nano-Cu 2 O) behaved as a catalytic mediator facilitating the charge transfer during FAO and providing the oxygen atmosphere inspiring the poison's (CO) oxidation at relatively lower potential. Surprisingly, moreover, nano-Cu 2 O induced a surface retrieval of nano-Pt active sites by capturing the poisoning CO via "a spillover mechanism" to renovate the Pt surface for the direct FAO. Finally, the catalytic tolerance of the developed catalyst toward halides' poisoning was discussed.
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Discovery of a selective catalytic p300/CBP inhibitor that targets lineage-specific tumours
DOE Office of Scientific and Technical Information (OSTI.GOV)
Lasko, Loren M.; Jakob, Clarissa G.; Edalji, Rohinton P.
The dynamic and reversible acetylation of proteins, catalysed by histone acetyltransferases (HATs) and histone deacetylases (HDACs), is a major epigenetic regulatory mechanism of gene transcription1 and is associated with multiple diseases. Histone deacetylase inhibitors are currently approved to treat certain cancers, but progress on the development of drug-like histone actyltransferase inhibitors has lagged behind2. The histone acetyltransferase paralogues p300 and CREB-binding protein (CBP) are key transcriptional co-activators that are essential for a multitude of cellular processes, and have also been implicated in human pathological conditions (including cancer3). Current inhibitors of the p300 and CBP histone acetyltransferase domains, including natural products4,more » bi-substrate analogues5 and the widely used small molecule C6466,7, lack potency or selectivity. Here, we describe A-485, a potent, selective and drug-like catalytic inhibitor of p300 and CBP. We present a high resolution (1.95 Å) co-crystal structure of a small molecule bound to the catalytic active site of p300 and demonstrate that A-485 competes with acetyl coenzyme A (acetyl-CoA). A-485 selectively inhibited proliferation in lineage-specific tumour types, including several haematological malignancies and androgen receptor-positive prostate cancer. A-485 inhibited the androgen receptor transcriptional program in both androgen-sensitive and castration-resistant prostate cancer and inhibited tumour growth in a castration-resistant xenograft model. These results demonstrate the feasibility of using small molecule inhibitors to selectively target the catalytic activity of histone acetyltransferases, which may provide effective treatments for transcriptional activator-driven malignancies and diseases.« less
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Laccases as palladium oxidases.
Mekmouche, Yasmina; Schneider, Ludovic; Rousselot-Pailley, Pierre; Faure, Bruno; Simaan, A Jalila; Bochot, Constance; Réglier, Marius; Tron, Thierry
2015-02-01
The first example of a coupled catalytic system involving an enzyme and a palladium(ii) catalyst competent for the aerobic oxidation of alcohol in mild conditions is described. In the absence of dioxygen, the fungal laccase LAC3 is reduced by a palladium(0) species as evidenced by the UV/VIS and ESR spectra of the enzyme. During the oxidation of veratryl alcohol performed in water, at room temperature and atmospheric pressure, LAC3 regenerates the palladium catalyst, is reduced and catalyzes the four-electron reduction of dioxygen into water with no loss of enzyme activity. The association of a laccase with a water-soluble palladium complex results in a 7-fold increase in the catalytic efficiency of the complex. This is the first step in the design of a family of renewable palladium catalysts for aerobic oxidation.
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NASA Astrophysics Data System (ADS)
Reich, Jason; Wang, Linlin; Johnson, Duane
2013-03-01
We detail the results of a Density Functional Theory (DFT) based study of hydrogen desorption, including thermodynamics and kinetics with(out) catalytic dopants, on stepped (110) rutile and nanocluster MgH2. We investigate competing configurations (optimal surface and nanoparticle configurations) using simulated annealing with additional converged results at 0 K, necessary for finding the low-energy, doped MgH2 nanostructures. Thermodynamics of hydrogen desorption from unique dopant sites will be shown, as well as activation energies using the Nudged Elastic Band algorithm. To compare to experiment, both stepped structures and nanoclusters are required to understanding and predict the effects of ball milling. We demonstrate how these model systems relate to the intermediary sized structures typically seen in ball milling experiments.
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Mechanism of Oxidation of Ethane to Ethanol at Iron(IV)-Oxo Sites in Magnesium-Diluted Fe2(dobdc).
Verma, Pragya; Vogiatzis, Konstantinos D; Planas, Nora; Borycz, Joshua; Xiao, Dianne J; Long, Jeffrey R; Gagliardi, Laura; Truhlar, Donald G
2015-05-06
The catalytic properties of the metal-organic framework Fe2(dobdc), containing open Fe(II) sites, include hydroxylation of phenol by pure Fe2(dobdc) and hydroxylation of ethane by its magnesium-diluted analogue, Fe0.1Mg1.9(dobdc). In earlier work, the latter reaction was proposed to occur through a redox mechanism involving the generation of an iron(IV)-oxo species, which is an intermediate that is also observed or postulated (depending on the case) in some heme and nonheme enzymes and their model complexes. In the present work, we present a detailed mechanism by which the catalytic material, Fe0.1Mg1.9(dobdc), activates the strong C-H bonds of ethane. Kohn-Sham density functional and multireference wave function calculations have been performed to characterize the electronic structure of key species. We show that the catalytic nonheme-Fe hydroxylation of the strong C-H bond of ethane proceeds by a quintet single-state σ-attack pathway after the formation of highly reactive iron-oxo intermediate. The mechanistic pathway involves three key transition states, with the highest activation barrier for the transfer of oxygen from N2O to the Fe(II) center. The uncatalyzed reaction, where nitrous oxide directly oxidizes ethane to ethanol is found to have an activation barrier of 280 kJ/mol, in contrast to 82 kJ/mol for the slowest step in the iron(IV)-oxo catalytic mechanism. The energetics of the C-H bond activation steps of ethane and methane are also compared. Dehydrogenation and dissociation pathways that can compete with the formation of ethanol were shown to involve higher barriers than the hydroxylation pathway.
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Li, Qiuhong; Chang, Leifu; Aibara, Shintaro; Yang, Jing; Zhang, Ziguo; Barford, David
2016-09-20
The anaphase-promoting complex/cyclosome (APC/C) is a large multimeric cullin-RING E3 ubiquitin ligase that orchestrates cell-cycle progression by targeting cell-cycle regulatory proteins for destruction via the ubiquitin proteasome system. The APC/C assembly comprises two scaffolding subcomplexes: the platform and the TPR lobe that together coordinate the juxtaposition of the catalytic and substrate-recognition modules. The platform comprises APC/C subunits Apc1, Apc4, Apc5, and Apc15. Although the role of Apc1 as an APC/C scaffolding subunit has been characterized, its specific functions in contributing toward APC/C catalytic activity are not fully understood. Here, we report the crystal structure of the N-terminal domain of human Apc1 (Apc1N) determined at 2.2-Å resolution and provide an atomic-resolution description of the architecture of its WD40 (WD40 repeat) domain (Apc1(WD40)). To understand how Apc1(WD40) contributes to APC/C activity, a mutant form of the APC/C with Apc1(WD40) deleted was generated and evaluated biochemically and structurally. We found that the deletion of Apc1(WD40) abolished the UbcH10-dependent ubiquitination of APC/C substrates without impairing the Ube2S-dependent ubiquitin chain elongation activity. A cryo-EM structure of an APC/C-Cdh1 complex with Apc1(WD40) deleted showed that the mutant APC/C is locked into an inactive conformation in which the UbcH10-binding site of the catalytic module is inaccessible. Additionally, an EM density for Apc15 is not visible. Our data show that Apc1(WD40) is required to mediate the coactivator-induced conformational change of the APC/C that is responsible for stimulating APC/C catalytic activity by promoting UbcH10 binding. In contrast, Ube2S activity toward APC/C substrates is not dependent on the initiation-competent conformation of the APC/C.
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Li, Qiuhong; Chang, Leifu; Aibara, Shintaro; Yang, Jing; Zhang, Ziguo; Barford, David
2016-01-01
The anaphase-promoting complex/cyclosome (APC/C) is a large multimeric cullin–RING E3 ubiquitin ligase that orchestrates cell-cycle progression by targeting cell-cycle regulatory proteins for destruction via the ubiquitin proteasome system. The APC/C assembly comprises two scaffolding subcomplexes: the platform and the TPR lobe that together coordinate the juxtaposition of the catalytic and substrate-recognition modules. The platform comprises APC/C subunits Apc1, Apc4, Apc5, and Apc15. Although the role of Apc1 as an APC/C scaffolding subunit has been characterized, its specific functions in contributing toward APC/C catalytic activity are not fully understood. Here, we report the crystal structure of the N-terminal domain of human Apc1 (Apc1N) determined at 2.2-Å resolution and provide an atomic-resolution description of the architecture of its WD40 (WD40 repeat) domain (Apc1WD40). To understand how Apc1WD40 contributes to APC/C activity, a mutant form of the APC/C with Apc1WD40 deleted was generated and evaluated biochemically and structurally. We found that the deletion of Apc1WD40 abolished the UbcH10-dependent ubiquitination of APC/C substrates without impairing the Ube2S-dependent ubiquitin chain elongation activity. A cryo-EM structure of an APC/C–Cdh1 complex with Apc1WD40 deleted showed that the mutant APC/C is locked into an inactive conformation in which the UbcH10-binding site of the catalytic module is inaccessible. Additionally, an EM density for Apc15 is not visible. Our data show that Apc1WD40 is required to mediate the coactivator-induced conformational change of the APC/C that is responsible for stimulating APC/C catalytic activity by promoting UbcH10 binding. In contrast, Ube2S activity toward APC/C substrates is not dependent on the initiation-competent conformation of the APC/C. PMID:27601667
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Role of active site rigidity in activity: MD simulation and fluorescence study on a lipase mutant.
Kamal, Md Zahid; Mohammad, Tabrez Anwar Shamim; Krishnamoorthy, G; Rao, Nalam Madhusudhana
2012-01-01
Relationship between stability and activity of enzymes is maintained by underlying conformational flexibility. In thermophilic enzymes, a decrease in flexibility causes low enzyme activity while in less stable proteins such as mesophiles and psychrophiles, an increase in flexibility is associated with enhanced enzyme activity. Recently, we identified a mutant of a lipase whose stability and activity were enhanced simultaneously. In this work, we probed the conformational dynamics of the mutant and the wild type lipase, particularly flexibility of their active site using molecular dynamic simulations and time-resolved fluorescence techniques. In contrast to the earlier observations, our data show that active site of the mutant is more rigid than wild type enzyme. Further investigation suggests that this lipase needs minimal reorganization/flexibility of active site residues during its catalytic cycle. Molecular dynamic simulations suggest that catalytically competent active site geometry of the mutant is relatively more preserved than wild type lipase, which might have led to its higher enzyme activity. Our study implies that widely accepted positive correlation between conformation flexibility and enzyme activity need not be stringent and draws attention to the possibility that high enzyme activity can still be accomplished in a rigid active site and stable protein structures. This finding has a significant implication towards better understanding of involvement of dynamic motions in enzyme catalysis and enzyme engineering through mutations in active site.
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Single-molecule FRET unveils induced-fit mechanism for substrate selectivity in flap endonuclease 1
DOE Office of Scientific and Technical Information (OSTI.GOV)
Rashid, Fahad; Harris, Paul D.; Zaher, Manal S.
Human flap endonuclease 1 (FEN1) and related structure-specific 5’nucleases precisely identify and incise aberrant DNA structures during replication, repair and recombination to avoid genomic instability. Yet, it is unclear how the 5’nuclease mechanisms of DNA distortion and protein ordering robustly mediate efficient and accurate substrate recognition and catalytic selectivity. Here, single-molecule sub-millisecond and millisecond analyses of FEN1 reveal a protein-DNA induced-fit mechanism that efficiently verifies substrate and suppresses off-target cleavage. FEN1 sculpts DNA with diffusion-limited kinetics to test DNA substrate. This DNA distortion mutually ‘locks’ protein and DNA conformation and enables substrate verification with extreme precision. Strikingly, FEN1 never missesmore » cleavage of its cognate substrate while blocking probable formation of catalytically competent interactions with noncognate substrates and fostering their pre-incision dissociation. These findings establish FEN1 has practically perfect precision and that separate control of induced-fit substrate recognition sets up the catalytic selectivity of the nuclease active site for genome stability.« less
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Single-molecule FRET unveils induced-fit mechanism for substrate selectivity in flap endonuclease 1
Rashid, Fahad; Harris, Paul D.; Zaher, Manal S.; ...
2017-02-23
Human flap endonuclease 1 (FEN1) and related structure-specific 5’nucleases precisely identify and incise aberrant DNA structures during replication, repair and recombination to avoid genomic instability. Yet, it is unclear how the 5’nuclease mechanisms of DNA distortion and protein ordering robustly mediate efficient and accurate substrate recognition and catalytic selectivity. Here, single-molecule sub-millisecond and millisecond analyses of FEN1 reveal a protein-DNA induced-fit mechanism that efficiently verifies substrate and suppresses off-target cleavage. FEN1 sculpts DNA with diffusion-limited kinetics to test DNA substrate. This DNA distortion mutually ‘locks’ protein and DNA conformation and enables substrate verification with extreme precision. Strikingly, FEN1 never missesmore » cleavage of its cognate substrate while blocking probable formation of catalytically competent interactions with noncognate substrates and fostering their pre-incision dissociation. These findings establish FEN1 has practically perfect precision and that separate control of induced-fit substrate recognition sets up the catalytic selectivity of the nuclease active site for genome stability.« less
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Single-molecule FRET unveils induced-fit mechanism for substrate selectivity in flap endonuclease 1
Rashid, Fahad; Harris, Paul D; Zaher, Manal S; Sobhy, Mohamed A; Joudeh, Luay I; Yan, Chunli; Piwonski, Hubert; Tsutakawa, Susan E; Ivanov, Ivaylo; Tainer, John A; Habuchi, Satoshi; Hamdan, Samir M
2017-01-01
Human flap endonuclease 1 (FEN1) and related structure-specific 5’nucleases precisely identify and incise aberrant DNA structures during replication, repair and recombination to avoid genomic instability. Yet, it is unclear how the 5’nuclease mechanisms of DNA distortion and protein ordering robustly mediate efficient and accurate substrate recognition and catalytic selectivity. Here, single-molecule sub-millisecond and millisecond analyses of FEN1 reveal a protein-DNA induced-fit mechanism that efficiently verifies substrate and suppresses off-target cleavage. FEN1 sculpts DNA with diffusion-limited kinetics to test DNA substrate. This DNA distortion mutually ‘locks’ protein and DNA conformation and enables substrate verification with extreme precision. Strikingly, FEN1 never misses cleavage of its cognate substrate while blocking probable formation of catalytically competent interactions with noncognate substrates and fostering their pre-incision dissociation. These findings establish FEN1 has practically perfect precision and that separate control of induced-fit substrate recognition sets up the catalytic selectivity of the nuclease active site for genome stability. DOI: http://dx.doi.org/10.7554/eLife.21884.001 PMID:28230529
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Remote Exosites of the Catalytic Domain of Matrix Metalloproteinase-12 Enhance Elastin Degradation┼
Fulcher, Yan G.; Van Doren, Steven R.
2011-01-01
How does matrix metalloproteinase-12 (MMP-12 or metalloelastase) degrade elastin with high specific activity? NMR suggested soluble elastin to cover surfaces of MMP-12 far from its active site. Two of these surfaces have been found, by mutagenesis guided by the BINDSIght approach, to affect degradation and affinity for elastin substrates but not a small peptide substrate. Main exosite 1 has been extended out to Asp124 that binds calcium. Novel exosite 2 comprises residues from the II–III loop and β-strand I near the back of the catalytic domain. The high exposure of these distal exosites may make them accessible to elastin made more flexible by partial hydrolysis. Importantly, combination of a lesion at each of exosites 1 and 2 and active site decreased catalytic competence towards soluble elastin by 13- to 18-fold to the level of MMP-3, homologue and poor elastase. Double mutant cycle analysis of conservative mutations of Met156 (exosite 2) and either Asp124 (exosite 1) or Ile180 (active site) had additive effects. Compared to polar substitutions observed in other MMPs, Met156 enhanced affinity and Ile180 kcat for soluble elastin. Both residues detracted from the higher folding stability with polar mutations. This resembles the trend in enzymes of an inverse relationship between folding stability and activity. Restoring Asp124 from combination mutants enhanced kcat for soluble elastin. In elastin degradation, exosites 1 and 2 contributed independently of each other and Ile180 at the active site, but with partial coupling to Ala182 near the active site. The concept of weak, separated interactions coalescing somewhat independently can be extended to this proteolytic digestion of a protein from fibrils. PMID:21967233
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Delmonte Corrado, M U; Politi, H; Ognibene, M; Angelini, C; Trielli, F; Ballarini, P; Falugi, C
2001-06-01
We recently discovered, in mating-competent Paramecium primaurelia, the presence of functionally related molecules of the cholinergic system: the neurotransmitter acetylcholine (ACh), both its nicotinic and muscarinic receptors and its lytic enzyme acetylcholinesterase (AChE). Our results on the inhibition of mating-cell pairing in vivo in mating-competent cells treated with cholinomimetic drugs support the hypothesis that the cholinergic system plays a role in cell-to-cell adhesion. To investigate the possible function of the signal molecule ACh in conjugation in P. primaurelia, we attempted to detect the intracellular sites of ACh synthesis by localizing the ACh biosynthetic enzyme choline acetyltransferase (ChAT). Using immunocytochemical and histochemical methods, we have demonstrated the presence and activity of ChAT principally on the surface membrane of mating-competent cells and of mature but non-mating-competent cells. No evidence for ChAT activity was found in immature cells. Immunoblot analysis revealed the presence of immunoreactive bands, ranging in molecular mass from 42 to 133 kDa, as reported for ChAT isolated from higher organisms. In vivo experiments showed that inhibition of ChAT activity by Congo Red, known to be a potent competitive inhibitor of acetyl coenzyme A, did not affect mating-cell pairing. Conversely, inhibition of AChE with BW 284c51 or eserine, which block enzyme activity by reacting with a specific serine within the catalytic centre, significantly inhibited mating-cell pairing. Our results suggest that ACh has a negative modulating effect on conjugation in P. primaurelia.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Hazra, Saugata; Szewczak, Andrzej; Ort, Stephan
2012-03-26
Deoxycytidine kinase (dCK) uses either ATP or UTP as a phosphoryl donor to catalyze the phosphorylation of nucleoside acceptors. The kinetic properties of human dCK are modulated in vivo by phosphorylation of serine 74. This residue is a part of the insert region and is distant from the active site. Replacing the serine with a glutamic acid (S74E variant) can mimic phosphorylation of Ser74. To understand how phosphorylation affects the catalytic properties of dCK, we examined the S74E variant of dCK both structurally and kinetically. We observe that the presence of a glutamic acid at position 74 favors the adoptionmore » by the enzyme of the open conformation. Glu74 stabilizes the open conformation by directly interacting with the indole side chain of Trp58, a residue that is in the proximity of the base of the nucleoside substrate. The open dCK conformation is competent for the binding of nucleoside but not for phosphoryl transfer. In contrast, the closed conformation is competent for phosphoryl transfer but not for product release. Thus, dCK must make the transition between the open and closed states during the catalytic cycle. We propose a reaction scheme for dCK that incorporates the transition between the open and closed states, and this serves to rationalize the observed kinetic differences between wild-type dCK and the S74E variant.« less
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Induced Fit and the Catalytic Mechanism of Isocitrate Dehydrogenase†
Gonçalves, Susana; Miller, Stephen P.; Carrondo, Maria A.; Dean, Anthony M.; Matias, Pedro M.
2012-01-01
NADP+ dependent isocitrate dehydrogenase (IDH; EC 1.1.1.42) belongs to a large family of α-hydroxyacid oxidative β-decarboxylases that catalyze similar three-step reactions, with dehydrogenation to an oxaloacid intermediate preceding β-decarboxylation to an enol intermediate followed by tautomerization to the final α-ketone product. A comprehensive view of the induced fit needed for catalysis is revealed on comparing the first “fully closed” crystal structures of a pseudo-Michaelis complex of wild-type Escherichia coli IDH (EcoIDH) and the “fully closed” reaction product complex of the K100M mutant with previously obtained “quasi-closed” and “open” conformations. Conserved catalytic residues, binding the nicotinamide ring of NADP+ and the metal-bound substrate, move as rigid bodies during domain closure by a hinge motion that spans the central β-sheet in each monomer. Interactions established between Thr105 and Ser113, which flank the “phosphorylation loop”, and the nicotinamide mononucleotide moiety of NADP+ establish productive coenzyme binding. Electrostatic interactions of a Lys100-Leu103-Asn115-Glu336 tetrad play a pivotal role in assembling a catalytically competent active site. As predicted, Lys230* is positioned to deprotonate/reprotonate the α-hydroxyl in both reaction steps and Tyr160 moves into position to protonate C3 following β-decarboxylation. A proton relay from the catalytic triad Tyr160-Asp307-Lys230* connects the α-hydroxyl of isocitrate to the bulk solvent to complete the picture of the catalytic mechanism. PMID:22891681
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Stolley, Ryan M; Duong, Hung A; Thomas, David R; Louie, Janis
2012-09-12
The reaction of Ni(COD)(2), IPr, and nitrile affords dimeric [Ni(IPr)RCN](2) in high yields. X-ray analysis revealed these species display simultaneous η(1)- and η(2)-nitrile binding modes. These dimers are catalytically competent in the formation of pyridines from the cycloaddition of diynes and nitriles. Kinetic analysis showed the reaction to be first order in [Ni(IPr)RCN](2), zeroth order in added IPr, zeroth order in nitrile, and zeroth order in diyne. Extensive stoichiometric competition studies were performed, and selective incorporation of the exogenous, not dimer bound, nitrile was observed. Post cycloaddition, the dimeric state was found to be largely preserved. Nitrile and ligand exchange experiments were performed and found to be inoperative in the catalytic cycle. These observations suggest a mechanism whereby the catalyst is activated by partial dimer-opening followed by binding of exogenous nitrile and subsequent oxidative heterocoupling.
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Saathoff, Hinnerk; Brofelth, Mattias; Trinh, Anne; Parker, Benjamin L; Ryan, Daniel P; Low, Jason K K; Webb, Sarah R; Silva, Ana P G; Mackay, Joel P; Shepherd, Nicholas E
2015-03-01
We have developed an approach for directly isolating an intact multi-protein chromatin remodeling complex from mammalian cell extracts using synthetic peptide affinity reagent 4. FOG1(1-15), a short peptide sequence known to target subunits of the nucleosome remodeling and deacetylase (NuRD) complex, was joined via a 35-atom hydrophilic linker to the StreptagII peptide. Loading this peptide onto Streptactin beads enabled capture of the intact NuRD complex from MEL cell nuclear extract. Gentle biotin elution yielded the desired intact complex free of significant contaminants and in a form that was catalytically competent in a nucleosome remodeling assay. The efficiency of 4 in isolating the NuRD complex was comparable to other reported methods utilising recombinantly produced GST-FOG1(1-45). Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.
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de Vasconcellos, Adriano; Miller, Alex Henrique; Aranda, Donato A G; Nery, José Geraldo
2018-05-01
Nanozeolites with different crystallographic structures (Nano/TS1, Nano/GIS, Nano/LTA, Nano/BEA, Nano/X, and Nano-X/Ni), functionalized with (3-aminopropyl)trimethoxysilane (APTMS) and crosslinked with glutaraldehyde (GA), were studied as solid supports for Thermomyces lanuginosus lipase (TLL) immobilization. Physicochemical characterizations of the surface-functionalized nanozeolites and nanozeolite-enzyme complexes were performed using XRD, SEM, AFM, ATR-FTIR, and zeta potential measurements. The experimental enzymatic activity results indicated that the nanozeolitic supports functionalized with APTMS and GA immobilized larger amounts of enzymes and provided higher enzymatic activities, compared to unfunctionalized supports. Correlations were observed among the nanozeolite surface charges, the enzyme immobilization efficiencies, and the biocatalyst activities. The catalytic performance and reusability of these enzyme-nanozeolite complexes were evaluated in the ethanolysis transesterification of microalgae oil to fatty acid ethyl esters (FAEEs). TLL immobilized on the nanozeolite supports functionalized with APTMS and GA provided the most efficient biocatalysis, with FAEEs yields above 93% and stability during five reaction cycles. Lower FAEEs yields and poorer catalytic stability were found for nanozeolite-enzyme complexes prepared only by physical adsorption. The findings indicated the viability of designing highly efficient biocatalysts for biofuel production by means of chemical modulation of nanozeolite surfaces. The high biocatalyst catalytic efficiency observed in ethanolysis reactions using a lipid feedstock that does not compete with food production is an advantage that should encourage the industrial application of these biocatalysts. Copyright © 2018 Elsevier B.V. All rights reserved.
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Maihom, Thana; Sawangphruk, Montree; Probst, Michael; Limtrakul, Jumras
2018-02-28
The aerobic epoxidation of propylene over the metal-organic framework Fe 3 (btc) 2 (btc = 1,3,5-benzentricarboxylate) as catalyst has been investigated by means of density functional calculations. The mechanisms of the reaction towards propylene oxide, carbonylic products (acetone and propanal) and a pi-allyl radical were investigated to assess the efficiency of Fe 3 (btc) 2 for the selective formation of propylene oxide. Propylene oxide and carbonylic products are formed on Fe 3 (btc) 2 by proceeding via propyleneoxy intermediates in the first step. Subsequently, the intermediates can then either be transformed to propylene oxide by way of ring closure of the intermediate or to the carbonylic compounds of propanal and acetone via 1,2-hydride shift. The results show that the formation of propylene oxide is favored over the formation of carbonylic products mainly due to the activation barriers being 2-3 times smaller. The activation barriers for the formation of the propyleneoxy intermediates on the Fe 3 (btc) 2 catalyst for the first and second reaction cycle are also lower than the barriers obtained for the formation of the pi-allyl radical that acts as the precursor to combustion products. On the basis of these computational results, we therefore expect a high catalytic selectivity of the Fe 3 (btc) 2 catalyst with respect to the formation of propylene oxide. We also compared the catalytic activities of Fe 3 (btc) 2 and Cu 3 (btc) 2 . The activation energy of the rate-determining step is almost 2 times lower for Fe 3 (btc) 2 than that for Cu 3 (btc) 2 , due to a larger charge transfer from the catalytic site to the O 2 molecule in the case of Fe 3 (btc) 2 .
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Schneider, Ludovic; Rousselot-Pailley, Pierre; Faure, Bruno; Simaan, A. Jalila; Bochot, Constance; Réglier, Marius
2015-01-01
The first example of a coupled catalytic system involving an enzyme and a palladium(ii) catalyst competent for the aerobic oxidation of alcohol in mild conditions is described. In the absence of dioxygen, the fungal laccase LAC3 is reduced by a palladium(0) species as evidenced by the UV/VIS and ESR spectra of the enzyme. During the oxidation of veratryl alcohol performed in water, at room temperature and atmospheric pressure, LAC3 regenerates the palladium catalyst, is reduced and catalyzes the four-electron reduction of dioxygen into water with no loss of enzyme activity. The association of a laccase with a water-soluble palladium complex results in a 7-fold increase in the catalytic efficiency of the complex. This is the first step in the design of a family of renewable palladium catalysts for aerobic oxidation. PMID:29560210
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The agents of natural genome editing.
Witzany, Guenther
2011-06-01
The DNA serves as a stable information storage medium and every protein which is needed by the cell is produced from this blueprint via an RNA intermediate code. More recently it was found that an abundance of various RNA elements cooperate in a variety of steps and substeps as regulatory and catalytic units with multiple competencies to act on RNA transcripts. Natural genome editing on one side is the competent agent-driven generation and integration of meaningful DNA nucleotide sequences into pre-existing genomic content arrangements, and the ability to (re-)combine and (re-)regulate them according to context-dependent (i.e. adaptational) purposes of the host organism. Natural genome editing on the other side designates the integration of all RNA activities acting on RNA transcripts without altering DNA-encoded genes. If we take the genetic code seriously as a natural code, there must be agents that are competent to act on this code because no natural code codes itself as no natural language speaks itself. As code editing agents, viral and subviral agents have been suggested because there are several indicators that demonstrate viruses competent in both RNA and DNA natural genome editing.
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Migueleti, Deivid L. S.; Smetana, Juliana H. C.; Nunes, Hugo F.; Kobarg, Jörg; Zanchin, Nilson I. T.
2012-01-01
PP2A is the main serine/threonine-specific phosphatase in animal cells. The active phosphatase has been described as a holoenzyme consisting of a catalytic, a scaffolding, and a variable regulatory subunit, all encoded by multiple genes, allowing for the assembly of more than 70 different holoenzymes. The catalytic subunit can also interact with α4, TIPRL (TIP41, TOR signaling pathway regulator-like), the methyl-transferase LCMT-1, and the methyl-esterase PME-1. Here, we report that the gene encoding the catalytic subunit PP2Acα can generate two mRNA types, the standard mRNA and a shorter isoform, lacking exon 5, which we termed PP2Acα2. Higher levels of the PP2Acα2 mRNA, equivalent to the level of the longer PP2Acα mRNA, were detected in peripheral blood mononuclear cells that were left to rest for 24 h. After this time, the peripheral blood mononuclear cells are still viable and the PP2Acα2 mRNA decreases soon after they are transferred to culture medium, showing that generation of the shorter isoform depends on the incubation conditions. FLAG-tagged PP2Acα2 expressed in HEK293 is catalytically inactive. It displays a specific interaction profile with enhanced binding to the α4 regulatory subunit, but no binding to the scaffolding subunit and PME-1. Consistently, α4 out-competes PME-1 and LCMT-1 for binding to both PP2Acα isoforms in pulldown assays. Together with molecular modeling studies, this suggests that all three regulators share a common binding surface on the catalytic subunit. Our findings add important new insights into the complex mechanisms of PP2A regulation. PMID:22167190
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Competence in Streptococcus pneumoniae is regulated by the rate of ribosomal decoding errors.
Stevens, Kathleen E; Chang, Diana; Zwack, Erin E; Sebert, Michael E
2011-01-01
Competence for genetic transformation in Streptococcus pneumoniae develops in response to accumulation of a secreted peptide pheromone and was one of the initial examples of bacterial quorum sensing. Activation of this signaling system induces not only expression of the proteins required for transformation but also the production of cellular chaperones and proteases. We have shown here that activity of this pathway is sensitively responsive to changes in the accuracy of protein synthesis that are triggered by either mutations in ribosomal proteins or exposure to antibiotics. Increasing the error rate during ribosomal decoding promoted competence, while reducing the error rate below the baseline level repressed the development of both spontaneous and antibiotic-induced competence. This pattern of regulation was promoted by the bacterial HtrA serine protease. Analysis of strains with the htrA (S234A) catalytic site mutation showed that the proteolytic activity of HtrA selectively repressed competence when translational fidelity was high but not when accuracy was low. These findings redefine the pneumococcal competence pathway as a response to errors during protein synthesis. This response has the capacity to address the immediate challenge of misfolded proteins through production of chaperones and proteases and may also be able to address, through genetic exchange, upstream coding errors that cause intrinsic protein folding defects. The competence pathway may thereby represent a strategy for dealing with lesions that impair proper protein coding and for maintaining the coding integrity of the genome. The signaling pathway that governs competence in the human respiratory tract pathogen Streptococcus pneumoniae regulates both genetic transformation and the production of cellular chaperones and proteases. The current study shows that this pathway is sensitively controlled in response to changes in the accuracy of protein synthesis. Increasing the error rate during ribosomal decoding induced competence, while decreasing the error rate repressed competence. This pattern of regulation was promoted by the HtrA protease, which selectively repressed competence when translational fidelity was high but not when accuracy was low. Our findings demonstrate that this organism is able to monitor the accuracy of information used for protein biosynthesis and suggest that errors trigger a response addressing both the immediate challenge of misfolded proteins and, through genetic exchange, upstream coding errors that may underlie protein folding defects. This pathway may represent an evolutionary strategy for maintaining the coding integrity of the genome.
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Molecular Basis of Gain-of-Function LEOPARD Syndrome-Associated SHP2 Mutations
2015-01-01
The Src homology 2 (SH2) domain-containing protein tyrosine phosphatase 2 (SHP2) is a critical signal transducer downstream of growth factors that promotes the activation of the RAS-ERK1/2 cascade. In its basal state, SHP2 exists in an autoinhibited closed conformation because of an intramolecular interaction between its N-SH2 and protein tyrosine phosphatase (PTP) domains. Binding to pTyr ligands present on growth factor receptors and adaptor proteins with its N-SH2 domain localizes SHP2 to its substrates and frees the active site from allosteric inhibition. Germline mutations in SHP2 are known to cause both Noonan syndrome (NS) and LEOPARD syndrome (LS), two clinically similar autosomal dominant developmental disorders. NS-associated SHP2 mutants display elevated phosphatase activity, while LS-associated SHP2 mutants exhibit reduced catalytic activity. A conundrum in how clinically similar diseases result from mutations to SHP2 that have opposite effects on this enzyme’s catalytic functionality exists. Here we report a comprehensive investigation of the kinetic, structural, dynamic, and biochemical signaling properties of the wild type as well as all reported LS-associated SHP2 mutants. The results reveal that LS-causing mutations not only affect SHP2 phosphatase activity but also induce a weakening of the intramolecular interaction between the N-SH2 and PTP domains, leading to mutants that are more readily activated by competing pTyr ligands. Our data also indicate that the residual phosphatase activity associated with the LS SHP2 mutant is required for enhanced ERK1/2 activation. Consequently, catalytically impaired SHP2 mutants could display gain-of-function properties because of their ability to localize to the vicinity of substrates for longer periods of time, thereby affording the opportunity for prolonged substrate turnover and sustained RAS-ERK1/2 activation. PMID:24935154
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Inactive DNMT3B Splice Variants Modulate De Novo DNA Methylation
Gordon, Catherine A.; Hartono, Stella R.; Chédin, Frédéric
2013-01-01
Inactive DNA methyltransferase (DNMT) 3B splice isoforms are associated with changes in DNA methylation, yet the mechanisms by which they act remain largely unknown. Using biochemical and cell culture assays, we show here that the inactive DNMT3B3 and DNMT3B4 isoforms bind to and regulate the activity of catalytically competent DNMT3A or DNMT3B molecules. DNMT3B3 modestly stimulated the de novo methylation activity of DNMT3A and also counteracted the stimulatory effects of DNMT3L, therefore leading to subtle and contrasting effects on activity. DNMT3B4, by contrast, significantly inhibited de novo DNA methylation by active DNMT3 molecules, most likely due to its ability to reduce the DNA binding affinity of co-complexes, thereby sequestering them away from their substrate. Immunocytochemistry experiments revealed that in addition to their effects on the intrinsic catalytic function of active DNMT3 enzymes, DNMT3B3 and DNMT34 drive distinct types of chromatin compaction and patterns of histone 3 lysine 9 tri-methylation (H3K9me3) deposition. Our findings suggest that regulation of active DNMT3 members through the formation of co-complexes with inactive DNMT3 variants is a general mechanism by which DNMT3 variants function. This may account for some of the changes in DNA methylation patterns observed during development and disease. PMID:23894490
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Surface-immobilized DNAzyme-type biocatalysis
NASA Astrophysics Data System (ADS)
Stefan, Loic; Lavergne, Thomas; Spinelli, Nicolas; Defrancq, Eric; Monchaud, David
2014-02-01
The structure of the double helix of deoxyribonucleic acid (DNA, also called duplex-DNA) was elucidated sixty years ago by Watson, Crick, Wilkins and Franklin. Since then, DNA has continued to hold a fascination for researchers in diverse fields including medicine and nanobiotechnology. Nature has indeed excelled in diversifying the use of DNA: beyond its canonical role of repository of genetic information, DNA could also act as a nanofactory able to perform some complex catalytic tasks in an enzyme-mimicking manner. The catalytic capability of DNA was termed DNAzyme; in this context, a peculiar DNA structure, a quadruple helix also named quadruplex-DNA, has recently garnered considerable interest since its autonomous catalytic proficiency relies on its higher-order folding that makes it suitable to interact efficiently with hemin, a natural cofactor of many enzymes. Quadruplexes have thus been widely studied for their hemoprotein-like properties, chiefly peroxidase-like activity, i.e., their ability to perform hemin-mediated catalytic oxidation reactions. Recent literature is replete with applications of quadruplex-based peroxidase-mimicking DNAzyme systems. Herein, we take a further leap along the road to biochemical applications, assessing the actual efficiency of catalytic quadruplexes for the detection of picomolar levels of surface-bound analytes in an enzyme-linked immunosorbent (ELISA)-type assay. To this end, we exploit an innovative strategy based on the functionalization of DNA by a multitasking platform named RAFT (for regioselectivity addressable functionalized template), whose versatility enables the grafting of DNA whatever its nature (duplex-DNA, quadruplex-DNA, etc.). We demonstrate that the resulting biotinylated RAFT/quadruplex systems indeed acquire catalytic properties that allow for efficient luminescent detection of picomoles of surface-bound streptavidin. We also highlight some of the pitfalls that have to be faced during optimization, notably demonstrating that highly optimized experimental conditions can make DNA pre-catalysts catalytically competent whatever their secondary structures.
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Confinement of caspase-12 proteolytic activity to autoprocessing
Roy, Sophie; Sharom, Jeffrey R.; Houde, Caroline; Loisel, Thomas P.; Vaillancourt, John P.; Shao, Wei; Saleh, Maya; Nicholson, Donald W.
2008-01-01
Caspase-12 is a dominant-negative regulator of caspase-1 (IL-1β-converting enzyme) and an attenuator of cytokine responsiveness to septic infections. This molecular role for caspase-12 appears to be akin to the role of cFLIP in regulating caspase-8 in the extrinsic cell death pathway; however, unlike cFLIP/Usurpin, we demonstrate here that caspase-12 is catalytically competent. To examine these catalytic properties, rat caspase-12 was cloned, and the recombinant enzyme was used to examine the cleavage of macromolecular and synthetic fluorogenic substrates. Although caspase-12 could mediate autoproteolytic maturation of its own proenzyme, in both cis and trans, it was not able to cleave any other polypeptide substrate, including other caspase proenzymes, apoptotic substrates, cytokine precursors, or proteins in the endoplasmic reticulum that normally undergo caspase-mediated proteolysis. The dearth of potential substrates for caspase-12 also was confirmed by whole-cell diagonal-gel analysis. Autolytic cleavage within the caspase-12 proenzyme was mapped to a single site at the large–small subunit junction, ATAD319, and this motif was recognized by caspase-12 when incorporated into synthetic fluorogenic substrates. The specific activity of caspase-12 with these substates was several orders of magnitude lower than caspases-1 and -3, highlighting its relative catalytic paucity. In intact cells, caspase-12 autoproteolysis occurred in the inhibitory complex containing caspase-1. We propose that the proteolytic activity of caspase-12 is confined to its own proenzyme and that autocleavage within the caspase-1 complex may be a means for temporal limitation of the inhibitory effects of caspase-12 on proinflammatory cytokine maturation. PMID:18332441
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Patched bimetallic surfaces are active catalysts for ammonia decomposition.
Guo, Wei; Vlachos, Dionisios G
2015-10-07
Ammonia decomposition is often used as an archetypical reaction for predicting new catalytic materials and understanding the very reason of why some reactions are sensitive on material's structure. Core-shell or surface-segregated bimetallic nanoparticles expose outstanding activity for many heterogeneously catalysed reactions but the reasons remain elusive owing to the difficulties in experimentally characterizing active sites. Here by performing multiscale simulations in ammonia decomposition on various nickel loadings on platinum (111), we show that the very high activity of core-shell structures requires patches of the guest metal to create and sustain dual active sites: nickel terraces catalyse N-H bond breaking and nickel edge sites drive atomic nitrogen association. The structure sensitivity on these active catalysts depends profoundly on reaction conditions due to kinetically competing relevant elementary reaction steps. We expose a remarkable difference in active sites between transient and steady-state studies and provide insights into optimal material design.
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Patched bimetallic surfaces are active catalysts for ammonia decomposition
NASA Astrophysics Data System (ADS)
Guo, Wei; Vlachos, Dionisios G.
2015-10-01
Ammonia decomposition is often used as an archetypical reaction for predicting new catalytic materials and understanding the very reason of why some reactions are sensitive on material's structure. Core-shell or surface-segregated bimetallic nanoparticles expose outstanding activity for many heterogeneously catalysed reactions but the reasons remain elusive owing to the difficulties in experimentally characterizing active sites. Here by performing multiscale simulations in ammonia decomposition on various nickel loadings on platinum (111), we show that the very high activity of core-shell structures requires patches of the guest metal to create and sustain dual active sites: nickel terraces catalyse N-H bond breaking and nickel edge sites drive atomic nitrogen association. The structure sensitivity on these active catalysts depends profoundly on reaction conditions due to kinetically competing relevant elementary reaction steps. We expose a remarkable difference in active sites between transient and steady-state studies and provide insights into optimal material design.
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Ohashi, Masato; Ishida, Naoyoshi; Ando, Kota; Hashimoto, Yu; Shigaki, Anna; Kikushima, Kotaro; Ogoshi, Sensuke
2018-05-16
The Cu(I)-catalyzed pentafluoroethylation of iodoarenes via the fluorocupration of tetrafluoroethylene (TFE) is disclosed. The active species, (phen)CuC₂F₅, was isolated and its molecular structure confirmed by a single-crystal X-ray diffraction analysis. The key to the successful suppression of the competing oligomerization of TFE is to refrain from stirring the reaction mixture. A mechanistic study clearly discarded the possibility that the catalytic reaction proceeds via a radical pathway. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
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Active site loop dynamics of a class IIa fructose 1,6-bisphosphate aldolase from M. tuberculosis
Pegan, Scott D.; Rukseree, Kamolchanok; Capodagli, Glenn C.; Baker, Erica A; Krasnykh, Olga; Franzblau, Scott G; Mesecar, Andrew D
2014-01-01
Class II fructose 1,6-bisphosphate aldolases (FBA; E.C. 4.1.2.13) comprise one of two families of aldolases. Instead of forming a Schiff-base intermediate using an ε-amino group of a lysine side chain, class II FBAs utilize Zn(II) to stabilize a proposed hydroxyenolate intermediate (HEI) in the reversible cleavage of fructose 1,6-bisphosphate forming glyceraldehyde 3-phosphate and dihydroxyacetone phosphate (DHAP). As class II FBAs has been shown to be essential in pathogenic bacteria, focus has been placed on these enzymes as potential antibacterial targets. Although structural studies on class II FBAs from Mycobacterium tuberculosis (MtFBA), other bacteria and protozoa have been reported, the structure of the active site loop responsible for catalyzing the protonation/deprotonation steps of the reaction for class II FBAs has not yet been observed. We therefore utilized the potent class II FBA inhibitor phosphoglycolohydroxamate (PGH) as a mimic of the HEI/DHAP bound form of the enzyme and determined the X-ray structure of MtFBA-PGH complex to 1.58 Å. Remarkably, we are able to observe well-defined electron density for the previously elusive active site loop of MtFBA trapped in a catalytically competent orientation. Utilization of this structural information plus site-directed mutagenesis and kinetic studies conducted on a series of residues within the active-site loop revealed that E169 facilitates a water mediated deprotonation/protonation step of the MtFBA reaction mechanism. Also, secondary isotope effects on MtFBA and catalytically relevant mutants were used to probe the effect of loop flexibility on catalytic efficiency. Additionally, we also reveal the structure of MtFBA in its holoenzyme form. PMID:23298222
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Ramezanpour, Mohsen; Lee, Jaeyong; Taneva, Svetla G.; Tieleman, D. Peter; Cornell, Rosemary B.
2018-01-01
The activity of CTP:phosphocholine cytidylyltransferase (CCT), a key enzyme in phosphatidylcholine synthesis, is regulated by reversible interactions of a lipid-inducible amphipathic helix (domain M) with membrane phospholipids. When dissociated from membranes, a portion of the M domain functions as an auto-inhibitory (AI) element to suppress catalysis. The AI helix from each subunit binds to a pair of α helices (αE) that extend from the base of the catalytic dimer to create a four-helix bundle. The bound AI helices make intimate contact with loop L2, housing a key catalytic residue, Lys122. The impacts of the AI helix on active-site dynamics and positioning of Lys122 are unknown. Extensive MD simulations with and without the AI helix revealed that backbone carbonyl oxygens at the point of contact between the AI helix and loop L2 can entrap the Lys122 side chain, effectively competing with the substrate, CTP. In silico, removal of the AI helices dramatically increased αE dynamics at a predicted break in the middle of these helices, enabling them to splay apart and forge new contacts with loop L2. In vitro cross-linking confirmed the reorganization of the αE element upon membrane binding of the AI helix. Moreover, when αE bending was prevented by disulfide engineering, CCT activation by membrane binding was thwarted. These findings suggest a novel two-part auto-inhibitory mechanism for CCT involving capture of Lys122 and restraint of the pliable αE helices. We propose that membrane binding enables bending of the αE helices, bringing the active site closer to the membrane surface. PMID:29519816
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D’Antonio, Jennifer; Ghiladi, Reza A.
2011-01-01
Dehaloperoxidase (DHP) from the terebellid polychaete Amphitrite ornata is a bifunctional enzyme that possesses both hemoglobin and peroxidase activities. The bifunctional nature of DHP as a globin-peroxidase appears to be at odds with the traditional starting oxidation state for each individual activity. Namely, reversible oxygen-binding is only mediated via a ferrous heme in globins, and peroxidase activity is initiated from ferric centers and to the exclusion of the oxyferrous oxidation state from the peroxidase cycle. Thus, to address what appears to be a paradox, herein we report the details of our investigations into the DHP catalytic cycle when initiated from the deoxy- and oxyferrous states using biochemical assays, stopped-flow UV-visible and rapid-freeze-quench electron paramagnetic resonance spectroscopies, and anaerobic methods. We demonstrate the formation of Compound II directly from deoxyferrous DHP B upon its reaction with hydrogen peroxide, and show that this occurs both in the presence and absence of trihalophenol. Prior to Compound II formation, we have identified a new species which we have preliminarily attributed to a ferrous-hydroperoxide precursor that undergoes heterolysis to generate the aforementioned ferryl intermediate. Taken together, the results demonstrate that the oxyferrous state in DHP is a peroxidase competent starting species, and an updated catalytic cycle for DHP is proposed in which the ferric oxidation state is not an obligatory starting point for the peroxidase catalytic cycle of dehaloperoxidase. The data presented herein provide a link between the peroxidase and oxygen transport activities which furthers our understanding of how this bifunctional enzyme is able to unite its two inherent functions in one system. PMID:21619067
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Schafer, Christopher M; Sheikh, M Osman; Zhang, Dongmei; West, Christopher M
2014-03-28
The role of Skp1 as an adaptor protein that links Cullin-1 to F-box proteins in E3 Skp1/Cullin-1/F-box protein (SCF) ubiquitin ligases is well characterized. In the social amoeba Dictyostelium and probably many other unicellular eukaryotes, Skp1 is modified by a pentasaccharide attached to a hydroxyproline near its C terminus. This modification is important for oxygen-sensing during Dictyostelium development and is mediated by a HIF-α type prolyl 4-hydroxylase and five sequentially acting cytoplasmic glycosyltransferase activities. Gene disruption studies show that AgtA, the enzyme responsible for addition of the final two galactose residues, in α-linkages to the Skp1 core trisaccharide, is unexpectedly critical for oxygen-dependent terminal development. AgtA possesses a WD40 repeat domain C-terminal to its single catalytic domain and, by use of domain deletions, binding studies, and enzyme assays, we find that the WD40 repeats confer a salt-sensitive second-site binding interaction with Skp1 that mediates novel catalytic activation in addition to simple substrate recognition. In addition, AgtA binds similarly well to precursor isoforms of Skp1 by a salt-sensitive mechanism that competes with binding to an F-box protein and recognition by early modification enzymes, and the effect of binding is diminished when AgtA modifies Skp1. Genetic studies show that loss of AgtA is more severe when an earlier glycosylation step is blocked, and overexpressed AgtA is deleterious if catalytically inactivated. Together, the findings suggest that AgtA mediates non-enzymatic control of unmodified and substrate precursor forms of Skp1 by a binding mechanism that is normally relieved by switch-like activation of its glycosylation function.
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Pegan, Scott D; Rukseree, Kamolchanok; Capodagli, Glenn C; Baker, Erica A; Krasnykh, Olga; Franzblau, Scott G; Mesecar, Andrew D
2013-02-05
Class II fructose 1,6-bisphosphate aldolases (FBAs, EC 4.1.2.13) comprise one of two families of aldolases. Instead of forming a Schiff base intermediate using an ε-amino group of a lysine side chain, class II FBAs utilize Zn(II) to stabilize a proposed hydroxyenolate intermediate (HEI) in the reversible cleavage of fructose 1,6-bisphosphate, forming glyceraldehyde 3-phosphate and dihydroxyacetone phosphate (DHAP). As class II FBAs have been shown to be essential in pathogenic bacteria, focus has been placed on these enzymes as potential antibacterial targets. Although structural studies of class II FBAs from Mycobacterium tuberculosis (MtFBA), other bacteria, and protozoa have been reported, the structure of the active site loop responsible for catalyzing the protonation-deprotonation steps of the reaction for class II FBAs has not yet been observed. We therefore utilized the potent class II FBA inhibitor phosphoglycolohydroxamate (PGH) as a mimic of the HEI- and DHAP-bound form of the enzyme and determined the X-ray structure of the MtFBA-PGH complex to 1.58 Å. Remarkably, we are able to observe well-defined electron density for the previously elusive active site loop of MtFBA trapped in a catalytically competent orientation. Utilization of this structural information and site-directed mutagenesis and kinetic studies conducted on a series of residues within the active site loop revealed that E169 facilitates a water-mediated deprotonation-protonation step of the MtFBA reaction mechanism. Also, solvent isotope effects on MtFBA and catalytically relevant mutants were used to probe the effect of loop flexibility on catalytic efficiency. Additionally, we also reveal the structure of MtFBA in its holoenzyme form.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Pegan, Scott D.; Rukseree, Kamolchanok; Capodagli, Glenn C.
The class II fructose 1,6-bisphosphate aldolases (FBAs, EC 4.1.2.13) comprises one of two families of aldolases. Instead of forming a Schiff base intermediate using an ε-amino group of a lysine side chain, class II FBAs utilize Zn(II) to stabilize a proposed hydroxyenolate intermediate (HEI) in the reversible cleavage of fructose 1,6-bisphosphate, forming glyceraldehyde 3-phosphate and dihydroxyacetone phosphate (DHAP). As class II FBAs have been shown to be essential in pathogenic bacteria, focus has been placed on these enzymes as potential antibacterial targets. Although structural studies of class II FBAs from Mycobacterium tuberculosis (MtFBA), other bacteria, and protozoa have been reported,more » the structure of the active site loop responsible for catalyzing the protonation–deprotonation steps of the reaction for class II FBAs has not yet been observed. We therefore utilized the potent class II FBA inhibitor phosphoglycolohydroxamate (PGH) as a mimic of the HEI- and DHAP-bound form of the enzyme and determined the X-ray structure of the MtFBA–PGH complex to 1.58 Å. Remarkably, we are able to observe well-defined electron density for the previously elusive active site loop of MtFBA trapped in a catalytically competent orientation. Utilization of this structural information and site-directed mutagenesis and kinetic studies conducted on a series of residues within the active site loop revealed that E169 facilitates a water-mediated deprotonation–protonation step of the MtFBA reaction mechanism. Furthermore, solvent isotope effects on MtFBA and catalytically relevant mutants were used to probe the effect of loop flexibility on catalytic efficiency. Additionally, we also reveal the structure of MtFBA in its holoenzyme form.« less
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Smith, Andrew T; Doyle, Wendy A; Dorlet, Pierre; Ivancich, Anabella
2009-09-22
The surface oxidation site (Trp-171) in lignin peroxidase (LiP) required for the reaction with veratryl alcohol a high-redox-potential (1.4 V) substrate, was engineered into Coprinus cinereus peroxidase (CiP) by introducing a Trp residue into a heme peroxidase that has similar protein fold but lacks this activity. To create the catalytic activity toward veratryl alcohol in CiP, it was necessary to reproduce the Trp site and its negatively charged microenvironment by means of a triple mutation. The resulting D179W+R258E+R272D variant was characterized by multifrequency EPR spectroscopy. The spectra unequivocally showed that a new Trp radical [g values of g(x) = 2.0035(5), g(y) = 2.0027(5), and g(z) = 2.0022(1)] was formed after the [Fe(IV)=O Por(*+)] intermediate, as a result of intramolecular electron transfer between Trp-179 and the porphyrin. Also, the EPR characterization crucially showed that [Fe(IV)=O Trp-179(*)] was the reactive intermediate with veratryl alcohol. Accordingly, our work shows that it is necessary to take into account the physicochemical properties of the radical, fine-tuned by the microenvironment, as well as those of the preceding [Fe(IV)=O Por(*+)] intermediate to engineer a catalytically competent Trp site for a given substrate. Manipulation of the microenvironment of the Trp-171 site in LiP allowed the detection by EPR spectroscopy of the Trp-171(*), for which direct evidence has been missing so far. Our work also highlights the role of Trp residues as tunable redox-active cofactors for enzyme catalysis in the context of peroxidases with a unique reactivity toward recalcitrant substrates that require oxidation potentials not realized at the heme site.
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Dell'Acqua, Simone; Pauleta, Sofia R.; Moura, José J. G.; Moura, Isabel
2012-01-01
Nitrous oxide reductase (N2OR) catalyses the final step of the denitrification pathway—the reduction of nitrous oxide to nitrogen. The catalytic centre (CuZ) is a unique tetranuclear copper centre bridged by inorganic sulphur in a tetrahedron arrangement that can have different oxidation states. Previously, Marinobacter hydrocarbonoclasticus N2OR was isolated with the CuZ centre as CuZ*, in the [1Cu2+ : 3Cu+] redox state, which is redox inert and requires prolonged incubation under reductive conditions to be activated. In this work, we report, for the first time, the isolation of N2OR from M. hydrocarbonoclasticus in the ‘purple’ form, in which the CuZ centre is in the oxidized [2Cu2+ : 2Cu+] redox state and is redox active. This form of the enzyme was isolated in the presence of oxygen from a microaerobic culture in the presence of nitrate and also from a strictly anaerobic culture. The purple form of the enzyme was biochemically characterized and was shown to be a redox active species, although it is still catalytically non-competent, as its specific activity is lower than that of the activated fully reduced enzyme and comparable with that of the enzyme with the CuZ centre in either the [1Cu2+ : 3Cu+] redox state or in the redox inactive CuZ* state. PMID:22451106
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Stolley, Ryan M.; Duong, Hung A.; Thomas, David R.; Louie, Janis
2012-01-01
The reaction of Ni(COD)2, IPr, and nitrile affords dimeric [Ni(IPr)RCN]2 in high yields. X-ray analysis revealed these species display simultaneous η1- and η2-nitrile binding modes. These dimers are catalytically competent in the formation of pyridines from the cycloaddition of diynes and nitriles. Kinetic analysis showed the reaction to be first order in [Ni(IPr)RCN]2, zeroth order in added IPr, zeroth order in nitrile, and zeroth order in diyne. Extensive stoichiometric competition studies were performed, and selective incorporation of the exogenous, not dimer bound, nitrile was observed. Post cycloaddition, the dimeric state was found to be largely preserved. Nitrile and ligand exchange experiments were performed and found to be inoperative in the catalytic cycle. These observations suggest a mechanism whereby the catalyst is activated by partial dimer-opening followed by binding of exogenous nitrile and subsequent oxidative heterocoupling. PMID:22917161
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Structural Basis of Wee Kinases Functionality and Inactivation by Diverse Small Molecule Inhibitors.
Zhu, Jin-Yi; Cuellar, Rebecca A; Berndt, Norbert; Lee, Hee Eun; Olesen, Sanne H; Martin, Mathew P; Jensen, Jeffrey T; Georg, Gunda I; Schönbrunn, Ernst
2017-09-28
Members of the Wee family of kinases negatively regulate the cell cycle via phosphorylation of CDK1 and are considered potential drug targets. Herein, we investigated the structure-function relationship of human Wee1, Wee2, and Myt1 (PKMYT1). Purified recombinant full-length proteins and kinase domain constructs differed substantially in phosphorylation states and catalytic competency, suggesting complex mechanisms of activation. A series of crystal structures reveal unique features that distinguish Wee1 and Wee2 from Myt1 and establish the structural basis of differential inhibition by the widely used Wee1 inhibitor MK-1775. Kinome profiling and cellular studies demonstrate that, in addition to Wee1 and Wee2, MK-1775 is an equally potent inhibitor of the polo-like kinase PLK1. Several previously unrecognized inhibitors of Wee kinases were discovered and characterized. Combined, the data provide a comprehensive view on the catalytic and structural properties of Wee kinases and a framework for the rational design of novel inhibitors thereof.
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Optimization of Cholinesterase-Based Catalytic Bioscavengers Against Organophosphorus Agents.
Lushchekina, Sofya V; Schopfer, Lawrence M; Grigorenko, Bella L; Nemukhin, Alexander V; Varfolomeev, Sergei D; Lockridge, Oksana; Masson, Patrick
2018-01-01
Organophosphorus agents (OPs) are irreversible inhibitors of acetylcholinesterase (AChE). OP poisoning causes major cholinergic syndrome. Current medical counter-measures mitigate the acute effects but have limited action against OP-induced brain damage. Bioscavengers are appealing alternative therapeutic approach because they neutralize OPs in bloodstream before they reach physiological targets. First generation bioscavengers are stoichiometric bioscavengers. However, stoichiometric neutralization requires administration of huge doses of enzyme. Second generation bioscavengers are catalytic bioscavengers capable of detoxifying OPs with a turnover. High bimolecular rate constants ( k cat / K m > 10 6 M -1 min -1 ) are required, so that low enzyme doses can be administered. Cholinesterases (ChE) are attractive candidates because OPs are hemi-substrates. Moderate OP hydrolase (OPase) activity has been observed for certain natural ChEs and for G117H-based human BChE mutants made by site-directed mutagenesis. However, before mutated ChEs can become operational catalytic bioscavengers their dephosphylation rate constant must be increased by several orders of magnitude. New strategies for converting ChEs into fast OPase are based either on combinational approaches or on computer redesign of enzyme. The keystone for rational conversion of ChEs into OPases is to understand the reaction mechanisms with OPs. In the present work we propose that efficient OP hydrolysis can be achieved by re-designing the configuration of enzyme active center residues and by creating specific routes for attack of water molecules and proton transfer. Four directions for nucleophilic attack of water on phosphorus atom were defined. Changes must lead to a novel enzyme, wherein OP hydrolysis wins over competing aging reactions. Kinetic, crystallographic, and computational data have been accumulated that describe mechanisms of reactions involving ChEs. From these studies, it appears that introducing new groups that create a stable H-bonded network susceptible to activate and orient water molecule, stabilize transition states (TS), and intermediates may determine whether dephosphylation is favored over aging. Mutations on key residues (L286, F329, F398) were considered. QM/MM calculations suggest that mutation L286H combined to other mutations favors water attack from apical position. However, the aging reaction is competing. Axial direction of water attack is not favorable to aging. QM/MM calculation shows that F329H+F398H-based multiple mutants display favorable energy barrier for fast reactivation without aging.
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Lucas, María; Gaspar, Andrew H.; Pallara, Chiara; Rojas, Adriana Lucely; Fernández-Recio, Juan; Machner, Matthias P.; Hierro, Aitor
2014-01-01
A challenge for microbial pathogens is to assure that their translocated effector proteins target only the correct host cell compartment during infection. The Legionella pneumophila effector vacuolar protein sorting inhibitor protein D (VipD) localizes to early endosomal membranes and alters their lipid and protein composition, thereby protecting the pathogen from endosomal fusion. This process requires the phospholipase A1 (PLA1) activity of VipD that is triggered specifically on VipD binding to the host cell GTPase Rab5, a key regulator of endosomes. Here, we present the crystal structure of VipD in complex with constitutively active Rab5 and reveal the molecular mechanism underlying PLA1 activation. An active site-obstructing loop that originates from the C-terminal domain of VipD is repositioned on Rab5 binding, thereby exposing the catalytic pocket within the N-terminal PLA1 domain. Substitution of amino acid residues located within the VipD–Rab5 interface prevented Rab5 binding and PLA1 activation and caused a failure of VipD mutant proteins to target to Rab5-enriched endosomal structures within cells. Experimental and computational analyses confirmed an extended VipD-binding interface on Rab5, explaining why this L. pneumophila effector can compete with cellular ligands for Rab5 binding. Together, our data explain how the catalytic activity of a microbial effector can be precisely linked to its subcellular localization. PMID:25114243
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A Novel Mechanism of Latency in Matrix Metalloproteinases*
López-Pelegrín, Mar; Ksiazek, Miroslaw; Karim, Abdulkarim Y.; Guevara, Tibisay; Arolas, Joan L.; Potempa, Jan; Gomis-Rüth, F. Xavier
2015-01-01
The matrix metalloproteinases (MMPs) are a family of secreted soluble or membrane-anchored multimodular peptidases regularly found in several paralogous copies in animals and plants, where they have multiple functions. The minimal consensus domain architecture comprises a signal peptide, a 60–90-residue globular prodomain with a conserved sequence motif including a cysteine engaged in “cysteine-switch” or “Velcro” mediated latency, and a catalytic domain. Karilysin, from the human periodontopathogen Tannerella forsythia, is the only bacterial MMP to have been characterized biochemically to date. It shares with eukaryotic forms the catalytic domain but none of the flanking domains. Instead of the consensus MMP prodomain, it features a 14-residue propeptide, the shortest reported for a metallopeptidase, which lacks cysteines. Here we determined the structure of a prokarilysin fragment encompassing the propeptide and the catalytic domain, and found that the former runs across the cleft in the opposite direction to a bound substrate and inhibits the latter through an “aspartate-switch” mechanism. This finding is reminiscent of latency maintenance in the otherwise unrelated astacin and fragilysin metallopeptidase families. In addition, in vivo and biochemical assays showed that the propeptide contributes to protein folding and stability. Our analysis of prokarilysin reveals a novel mechanism of latency and activation in MMPs. Finally, our findings support the view that the karilysin catalytic domain was co-opted by competent bacteria through horizontal gene transfer from a eukaryotic source, and later evolved in a specific bacterial environment. PMID:25555916
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Hod, Idan; Sampson, Matthew D.; Deria, Pravas; ...
2015-09-18
Realization of heterogeneous electrochemical CO 2-to-fuel conversion via molecular catalysis under high-flux conditions requires the assembly of large quantities of reactant-accessible catalysts on conductive surfaces. As a proof of principle, we demonstrate that electrophoretic deposition of thin films of an appropriately chosen metal–organic framework (MOF) material is an effective method for immobilizing the needed quantity of catalyst. For electrocatalytic CO 2 reduction, we used a material that contains functionalized Fe-porphyrins as catalytically competent, redox-conductive linkers. The approach yields a high effective surface coverage of electrochemically addressable catalytic sites (~10 15 sites/cm 2). The chemical products of the reduction, obtained withmore » ~100% Faradaic efficiency, are mixtures of CO and H 2. The results validate the strategy of using MOF chemistry to obtain porous, electrode-immobilized, networks of molecular catalysts having competency for energy-relevant electrochemical reactions.« less
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Willenbrock, F; Brocklehurst, K
1984-01-01
Cathepsin B (EC 3.4.22.1) from bovine spleen and the analogous enzyme from rat liver were investigated at 25 degrees C at I0.1 in acidic media by kinetic study of (a) the reactions of their catalytic-site thiol groups towards the two-protonic-state reactivity probe 2,2'-dipyridyl disulphide and (b) their catalysis of the hydrolysis of N-alpha-benzyloxycarbonyl-L-arginyl-L-arginine 2-naphthylamide. Reactivity-probe kinetics showed that nucleophilic character is generated in the sulphur atom of cathepsin B by protonic dissociation with pKa 3.4, presumably to form an S-/ImH+ ion-pair. Substrate-catalysis kinetics showed that ion-pair formation is not sufficient to generate catalytic competence in cathepsin B, because catalytic activity is not generated as the pH is raised across pKa 3.4 but rather as it is raised across pKa 5-6 (5.1 for kcat; 5.6 for kcat./Km for the bovine spleen enzyme and 5.8 for kcat./Km for the rat liver enzyme). The implications of these results and of known structural differences between the catalytic sites of the rat liver enzyme and papain (EC 3.4.22.2) for the mechanism of cysteine-proteinase-catalysed hydrolysis are discussed. PMID:6534384
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Blayney, Michelle J; Whitney, Spencer M; Beck, Jennifer L
2011-09-01
Ribulose bisphosphate carboxylase/oxygenase (Rubisco) is the protein that is responsible for the fixation of carbon dioxide in photosynthesis. Inhibitory sugar phosphate molecules, which can include its substrate ribulose-1,5-bisphosphate (RuBP), can bind to Rubisco catalytic sites and inhibit catalysis. These are removed by interaction with Rubisco activase (RA) via an ATP hydrolytic reaction. Here we show the first nanoESI mass spectra of the hexadecameric Rubisco and of RA from a higher plant (tobacco). The spectra of recombinant, purified RA revealed polydispersity in its oligomeric forms (up to hexamer) and that ADP was bound. ADP was removed by dialysis against a high ionic strength solution and nucleotide binding experiments showed that ADP bound more tightly to RA than AMP-PNP (a non-hydrolysable ATP analog). There was evidence that there may be two nucleotide binding sites per RA monomer. The oligomerization capacity of mutant and wild-type tobacco RA up to hexamers is analogous to the subunit stoichiometry for other AAA+ enzymes. This suggests assembly of RA into hexamers is likely the most active conformation for removing inhibitory sugar phosphate molecules from Rubisco to enable its catalytic competency. Stoichiometric binding of RuBP or carboxyarabinitol bisphosphate (CABP) to each of the eight catalytic sites of Rubisco was observed.
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Huang, Kezhen; Wang, Yue-Hao; Brown, Alex; Sun, Gongqin
2009-01-01
Csk and Src protein tyrosine kinases are structurally homologous, but use opposite regulatory strategies. The isolated catalytic domain of Csk is intrinsically inactive and is activated by interactions with the regulatory SH3 and SH2 domains, while the isolated catalytic domain of Src is intrinsically active and is suppressed by interactions with the regulatory SH3 and SH2 domains. The structural basis for why one isolated catalytic domain is intrinsically active while the other is inactive is not clear. In this current study, we identify the structural elements in the N-terminal lobe of the catalytic domain that render the Src catalytic domain active. These structural elements include the α-helix C region, a β-turn between the β-4 and β-5 strands, and an Arg residue at the beginning of the catalytic domain. These three motifs interact with each other to activate the Src catalytic domain, but the equivalent motifs in Csk directly interact with the regulatory domains that are important for Csk activation. The Src motifs can be grafted to the Csk catalytic domain to obtain an active Csk catalytic domain. These results, together with available Src and Csk tertiary structures, reveal an important structural switch that determines the kinase activity of a catalytic domain and dictates the regulatory strategy of a kinase. PMID:19244618
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Aconitase couples metabolic regulation to mitochondrial DNA maintenance.
Chen, Xin Jie; Wang, Xiaowen; Kaufman, Brett A; Butow, Ronald A
2005-02-04
Mitochondrial DNA (mtDNA) is essential for cells to maintain respiratory competency and is inherited as a protein-DNA complex called the nucleoid. We have identified 22 mtDNA-associated proteins in yeast, among which is mitochondrial aconitase (Aco1p). We show that this Krebs-cycle enzyme is essential for mtDNA maintenance independent of its catalytic activity. Regulation of ACO1 expression by the HAP and retrograde metabolic signaling pathways directly affects mtDNA maintenance. When constitutively expressed, Aco1p can replace the mtDNA packaging function of the high-mobility-group protein Abf2p. Thus, Aco1p may integrate metabolic signals and mtDNA maintenance.
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Expression, Purification, and Analysis of G-Protein-Coupled Receptor Kinases
Sterne-Marr, Rachel; Baillargeon, Alison I.; Michalski, Kevin R.; Tesmer, John J.G.
2015-01-01
G-protein-coupled receptor (GPCR) kinases (GRKs) were first identified based on their ability to specifically phosphorylate activated GPCRs. Although many soluble substrates have since been identified, the chief physiological role of GRKs still remains the uncoupling of GPCRs from heterotrimeric G-proteins by promoting β-arrestin binding through the phosphorylation of the receptor. It is expected that GRKs recognize activated GPCRs through a docking site that not only recognizes the active conformation of the transmembrane domain of the receptor but also stabilizes a more catalytically competent state of the kinase domain. Many of the recent gains in understanding GRK-receptor interactions have been gleaned through biochemical and structural analysis of recombinantly expressed GRKs. Described herein are current techniques and procedures being used to express, purify, and assay GRKs in both in vitro and living cells. PMID:23351749
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Denmark, Scott E; Beutner, Gregory L; Wynn, Thomas; Eastgate, Martin D
2005-03-23
The concept of Lewis base activation of Lewis acids has been reduced to practice for catalysis of the aldol reaction of silyl ketene acetals and silyl dienol ethers with aldehydes. The weakly acidic species, silicon tetrachloride (SiCl4), can be activated by binding of a strongly Lewis basic chiral phosphoramide, leading to in situ formation of a chiral Lewis acid. This species has proven to be a competent catalyst for the aldol addition of acetate-, propanoate-, and isobutyrate-derived silyl ketene acetals to conjugated and nonconjugated aldehydes. Furthermore, vinylogous aldol reactions of silyl dienol ethers are also demonstrated. The high levels of regio-, anti diastereo-, and enantioselectivity observed in these reactions can be rationalized through consideration of an open transition structure where steric interactions between the silyl cation complex and the approaching nucleophile are dominant.
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Structural Dynamics as a Contributor to Error-prone Replication by an RNA-dependent RNA Polymerase*
Moustafa, Ibrahim M.; Korboukh, Victoria K.; Arnold, Jamie J.; Smidansky, Eric D.; Marcotte, Laura L.; Gohara, David W.; Yang, Xiaorong; Sánchez-Farrán, María Antonieta; Filman, David; Maranas, Janna K.; Boehr, David D.; Hogle, James M.; Colina, Coray M.; Cameron, Craig E.
2014-01-01
RNA viruses encoding high- or low-fidelity RNA-dependent RNA polymerases (RdRp) are attenuated. The ability to predict residues of the RdRp required for faithful incorporation of nucleotides represents an essential step in any pipeline intended to exploit perturbed fidelity as the basis for rational design of vaccine candidates. We used x-ray crystallography, molecular dynamics simulations, NMR spectroscopy, and pre-steady-state kinetics to compare a mutator (H273R) RdRp from poliovirus to the wild-type (WT) enzyme. We show that the nucleotide-binding site toggles between the nucleotide binding-occluded and nucleotide binding-competent states. The conformational dynamics between these states were enhanced by binding to primed template RNA. For the WT, the occluded conformation was favored; for H273R, the competent conformation was favored. The resonance for Met-187 in our NMR spectra reported on the ability of the enzyme to check the correctness of the bound nucleotide. Kinetic experiments were consistent with the conformational dynamics contributing to the established pre-incorporation conformational change and fidelity checkpoint. For H273R, residues comprising the active site spent more time in the catalytically competent conformation and were more positively correlated than the WT. We propose that by linking the equilibrium between the binding-occluded and binding-competent conformations of the nucleotide-binding pocket and other active-site dynamics to the correctness of the bound nucleotide, faithful nucleotide incorporation is achieved. These studies underscore the need to apply multiple biophysical and biochemical approaches to the elucidation of the physical basis for polymerase fidelity. PMID:25378410
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Catalyst material and method of making
Matson, Dean W.; Fulton, John L.; Linehan, John C.; Bean, Roger M.; Brewer, Thomas D.; Werpy, Todd A.; Darab, John G.
1997-01-01
The material of the present invention is a mixture of catalytically active material and carrier materials, which may be catalytically active themselves. Hence, the material of the present invention provides a catalyst particle that has catalytically active material throughout its bulk volume as well as on its surface. The presence of the catalytically active material throughout the bulk volume is achieved by chemical combination of catalytically active materials with carrier materials prior to or simultaneously with crystallite formation.
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Catalyst material and method of making
Matson, D.W.; Fulton, J.L.; Linehan, J.C.; Bean, R.M.; Brewer, T.D.; Werpy, T.A.; Darab, J.G.
1997-07-29
The material of the present invention is a mixture of catalytically active material and carrier materials, which may be catalytically active themselves. Hence, the material of the present invention provides a catalyst particle that has catalytically active material throughout its bulk volume as well as on its surface. The presence of the catalytically active material throughout the bulk volume is achieved by chemical combination of catalytically active materials with carrier materials prior to or simultaneously with crystallite formation. 7 figs.
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Naing, Swe-Htet; Kalyoncu, Sibel; Smalley, David M.; Kim, Hyojung; Tao, Xingjian; George, Josh B.; Jonke, Alex P.; Oliver, Ryan C.; Urban, Volker S.; Torres, Matthew P.; Lieberman, Raquel L.
2018-01-01
Mechanistic details of intramembrane aspartyl protease (IAP) chemistry, which is central to many biological and pathogenic processes, remain largely obscure. Here, we investigated the in vitro kinetics of a microbial intramembrane aspartyl protease (mIAP) fortuitously acting on the renin substrate angiotensinogen and the C-terminal transmembrane segment of amyloid precursor protein (C100), which is cleaved by the presenilin subunit of γ-secretase, an Alzheimer disease (AD)-associated IAP. mIAP variants with substitutions in active-site and putative substrate-gating residues generally exhibit impaired, but not abolished, activity toward angiotensinogen and retain the predominant cleavage site (His–Thr). The aromatic ring, but not the hydroxyl substituent, within Tyr of the catalytic Tyr–Asp (YD) motif plays a catalytic role, and the hydrolysis reaction incorporates bulk water as in soluble aspartyl proteases. mIAP hydrolyzes the transmembrane region of C100 at two major presenilin cleavage sites, one corresponding to the AD-associated Aβ42 peptide (Ala–Thr) and the other to the non-pathogenic Aβ48 (Thr–Leu). For the former site, we observed more favorable kinetics in lipid bilayer–mimicking bicelles than in detergent solution, indicating that substrate–lipid and substrate–enzyme interactions both contribute to catalytic rates. High-resolution MS analyses across four substrates support a preference for threonine at the scissile bond. However, results from threonine-scanning mutagenesis of angiotensinogen demonstrate a competing positional preference for cleavage. Our results indicate that IAP cleavage is controlled by both positional and chemical factors, opening up new avenues for selective IAP inhibition for therapeutic interventions. PMID:29382721
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Evidence for Loss of a Partial Flagellar Glycolytic Pathway during Trypanosomatid Evolution
Brown, Robert W. B.; Collingridge, Peter W.; Gull, Keith; Rigden, Daniel J.; Ginger, Michael L.
2014-01-01
Classically viewed as a cytosolic pathway, glycolysis is increasingly recognized as a metabolic pathway exhibiting surprisingly wide-ranging variations in compartmentalization within eukaryotic cells. Trypanosomatid parasites provide an extreme view of glycolytic enzyme compartmentalization as several glycolytic enzymes are found exclusively in peroxisomes. Here, we characterize Trypanosoma brucei flagellar proteins resembling glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and phosphoglycerate kinase (PGK): we show the latter associates with the axoneme and the former is a novel paraflagellar rod component. The paraflagellar rod is an essential extra-axonemal structure in trypanosomes and related protists, providing a platform into which metabolic activities can be built. Yet, bioinformatics interrogation and structural modelling indicate neither the trypanosome PGK-like nor the GAPDH-like protein is catalytically active. Orthologs are present in a free-living ancestor of the trypanosomatids, Bodo saltans: the PGK-like protein from B. saltans also lacks key catalytic residues, but its GAPDH-like protein is predicted to be catalytically competent. We discuss the likelihood that the trypanosome GAPDH-like and PGK-like proteins constitute molecular evidence for evolutionary loss of a flagellar glycolytic pathway, either as a consequence of niche adaptation or the re-localization of glycolytic enzymes to peroxisomes and the extensive changes to glycolytic flux regulation that accompanied this re-localization. Evidence indicating loss of localized ATP provision via glycolytic enzymes therefore provides a novel contribution to an emerging theme of hidden diversity with respect to compartmentalization of the ubiquitous glycolytic pathway in eukaryotes. A possibility that trypanosome GAPDH-like protein additionally represents a degenerate example of a moonlighting protein is also discussed. PMID:25050549
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Butler, Georgina S; Tam, Eric M; Overall, Christopher M
2004-04-09
Matrix metalloproteinases (MMPs) are an important family of extracellular proteases that process a variety of biologically significant molecules. MMPs are members of the metzincin superfamily of >770 zinc endopeptidases, which includes astacins, serralysins, adamalysins, leishmanolysins, and snapalysins. Metzincins are characterized by an absolutely conserved methionine residue COOH-terminal to the third histidine in the consensus sequence HEXXHXXGXX(H/D), where the histidine residues chelate a catalytic zinc ion. The canonical methionine is part of a tight 1,4-beta-turn that loops the polypeptide chain beneath the catalytic zinc ion, forming a hydrophobic floor to the Zn(2+) ion binding site. The role of this methionine is uncertain, but its absolute conservation indicates an essential catalytic or structural function. To investigate this hypothesis, we replaced Met-392 that forms the Met-turn of human MMP-2 (gelatinase A) by site-directed mutagenesis. The catalytic competence of leucine and serine mutants was assessed. (M392L)MMP-2 and (M392S)MMP-2 cleaved the physiological substrates gelatin, native type I collagen, and the chemokine monocyte chemoattractant protein-3 with similar efficiency to wild-type MMP-2. These mutants also cleaved two quenched fluorescent peptide substrates with a k(cat)/K(m) comparable to wild-type MMP-2 and underwent 4-aminophenylmercuric acetate-induced autoactivation with similar kinetics. (M392L)MMP-2 and (M392S)MMP-2 were inhibited by tissue inhibitor of metalloproteinases (TIMP)-1, -2, and -4 and by the zinc chelators 1,10-phenanthroline and a synthetic hydroxamate inhibitor, Batimastat, similar to the wild-type protein, indicating an unaltered active site topography. A tryptic susceptibility assay also suggested that (M392L)MMP-2 and (M392S)MMP-2 were correctly folded. These results challenge the dogma that this methionine residue and the Met-turn, which are absolutely conserved in all of the subfamilies of the metzincins, play an essential role in catalysis or active site structure.
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Patched bimetallic surfaces are active catalysts for ammonia decomposition
DOE Office of Scientific and Technical Information (OSTI.GOV)
Guo, Wei; Vlachos, Dionisios G.
In this study, ammonia decomposition is often used as an archetypical reaction for predicting new catalytic materials and understanding the very reason of why some reactions are sensitive on material’s structure. Core–shell or surface-segregated bimetallic nanoparticles expose outstanding activity for many heterogeneously catalysed reactions but the reasons remain elusive owing to the difficulties in experimentally characterizing active sites. Here by performing multiscale simulations in ammonia decomposition on various nickel loadings on platinum (111), we show that the very high activity of core–shell structures requires patches of the guest metal to create and sustain dual active sites: nickel terraces catalyse N-Hmore » bond breaking and nickel edge sites drive atomic nitrogen association. The structure sensitivity on these active catalysts depends profoundly on reaction conditions due to kinetically competing relevant elementary reaction steps. We expose a remarkable difference in active sites between transient and steady-state studies and provide insights into optimal material design.« less
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Patched bimetallic surfaces are active catalysts for ammonia decomposition
Guo, Wei; Vlachos, Dionisios G.
2015-10-07
In this study, ammonia decomposition is often used as an archetypical reaction for predicting new catalytic materials and understanding the very reason of why some reactions are sensitive on material’s structure. Core–shell or surface-segregated bimetallic nanoparticles expose outstanding activity for many heterogeneously catalysed reactions but the reasons remain elusive owing to the difficulties in experimentally characterizing active sites. Here by performing multiscale simulations in ammonia decomposition on various nickel loadings on platinum (111), we show that the very high activity of core–shell structures requires patches of the guest metal to create and sustain dual active sites: nickel terraces catalyse N-Hmore » bond breaking and nickel edge sites drive atomic nitrogen association. The structure sensitivity on these active catalysts depends profoundly on reaction conditions due to kinetically competing relevant elementary reaction steps. We expose a remarkable difference in active sites between transient and steady-state studies and provide insights into optimal material design.« less
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Self-assembly Controls Self-cleavage of HHR from ASBVd (-): a Combined SANS and Modeling Study
NASA Astrophysics Data System (ADS)
Leclerc, Fabrice; Zaccai, Giuseppe; Vergne, Jacques; Řìhovà, Martina; Martel, Anne; Maurel, Marie-Christine
2016-07-01
In the Avocado Sunblotch Viroid (ASBVd: 249-nt) from the Avsunviroidae family, a symmetric rolling-circle replication operates through an autocatalytic mechanism mediated by hammerhead ribozymes (HHR) embedded in both polarity strands. The concatenated multimeric ASBVd (+) and ASBVd (-) RNAs thus generated are processed by cleavage to unit-length where ASBVd (-) self-cleaves with more efficiency. Absolute scale small angle neutron scattering (SANS) revealed a temperature-dependent dimer association in both ASBVd (-) and its derived 79-nt HHR (-). A joint thermodynamic analysis of SANS and catalytic data indicates the rate-determining step corresponds to the dimer/monomer transition. 2D and 3D models of monomeric and dimeric HHR (-) suggest that the inter-molecular contacts stabilizing the dimer (between HI and HII domains) compete with the intra-molecular ones stabilizing the active conformation of the full-length HHR required for an efficient self-cleavage. Similar competing intra- and inter-molecular contacts are proposed in ASBVd (-) though with a remoter region from an extension of the HI domain.
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Catalytic bioreactors and methods of using same
Worden, Robert Mark; Liu, Yangmu Chloe
2017-07-25
Various embodiments provide a bioreactor for producing a bioproduct comprising one or more catalytically active zones located in a housing and adapted to keep two incompatible gaseous reactants separated when in a gas phase, wherein each of the one or more catalytically active zones may comprise a catalytic component retainer and a catalytic component retained within and/or thereon. Each of the catalytically active zones may additionally or alternatively comprise a liquid medium located on either side of the catalytic component retainer. Catalytic component may include a microbial cell culture located within and/or on the catalytic component retainer, a suspended catalytic component suspended in the liquid medium, or a combination thereof. Methods of using various embodiments of the bioreactor to produce a bioproduct, such as isobutanol, are also provided.
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Competing reaction processes on a lattice as a paradigm for catalyst deactivation
NASA Astrophysics Data System (ADS)
Abad, E.; Kozak, J. J.
2015-02-01
We mobilize both a generating function approach and the theory of finite Markov processes to compute the probability of irreversible absorption of a randomly diffusing species on a lattice with competing reaction centers. We consider an N-site lattice populated by a single deep trap, and N -1 partially absorbing traps (absorption probability 0
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Particle size and support effects in electrocatalysis.
Hayden, Brian E
2013-08-20
Researchers increasingly recognize that, as with standard supported heterogeneous catalysts, the activity and selectivity of supported metal electrocatalysts are influenced by particle size, particle structure, and catalyst support. Studies using model supported heterogeneous catalysts have provided information about these effects. Similarly, model electrochemical studies on supported metal electrocatalysts can provide insight into the factors determining catalytic activity. High-throughput methods for catalyst synthesis and screening can determine systematic trends in activity as a function of support and particle size with excellent statistical certainty. In this Account, we describe several such studies investigating methods for dispersing precious metals on both carbon and oxide supports, with particular emphasis on the prospects for the development of low-temperature fuel-cell electrocatalysts. One key finding is a decrease in catalytic activity with decreasing particle size independent of the support for both oxygen reduction and CO oxidation on supported gold and platinum. For these reactions, there appears to be an intrinsic particle size effect that results in a loss of activity at particle sizes below 2-3 nm. A titania support, however, also increases activity of gold particles in the electrooxidation of CO and in the reduction of oxygen, with an optimum at 3 nm particle size. This optimum may represent the superposition of competing effects: a titania-induced enhanced activity versus deactivation at small particle sizes. The titania support shows catalytic activity at potentials where carbon-supported and bulk-gold surfaces are normally oxidized and CO electrooxidation is poisoned. On the other hand, platinum on amorphous titania shows a different effect: the oxidation reduction reaction is strongly poisoned in the same particle size range. We correlated the influence of the titania support with titania-induced changes in the surface redox behavior of the platinum particles. For both supported gold and platinum particles in electrocatalysis, we observe parallels to the effects of particle size and support in the equivalent heterogeneous catalysts. Studies of model supported-metal electrocatalysts, performs efficiently using high throughput synthetic and screening methodologies, will lead to a better understanding of the mechanisms responsible for support and particle size effects in electrocatalysis, and will drive the development of more effective and robust catalysts in the future.
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Sun, Zhuohua; Barta, Katalin
2018-06-21
The structural complexity of lignocellulose offers unique opportunities for the development of entirely new, energy efficient and waste-free pathways in order to obtain valuable bio-based building blocks. Such sustainable catalytic methods - specifically tailored to address the efficient conversion of abundant renewable starting materials - are necessary to successfully compete, in the future, with fossil-based multi-step processes. In this contribution we give a summary of recent developments in this field and describe our "cleave and couple" strategy, where "cleave" refers to the catalytic deconstruction of lignocellulose to aromatic and aliphatic alcohol intermediates, and "couple" involves the development of novel, sustainable transformations for the formation of C-C and C-N bonds in order to obtain a range of attractive products from lignocellulose.
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Ionizable side chains at catalytic active sites of enzymes.
Jimenez-Morales, David; Liang, Jie; Eisenberg, Bob
2012-05-01
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 1,072 Å(3). 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.
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Ionizable Side Chains at Catalytic Active Sites of Enzymes
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
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Insights into the Functional Architecture of the Catalytic Center of a Maize β-Glucosidase Zm-p60.11
Zouhar, Jan; Vévodová, Jitka; Marek, Jaromír; Damborský, Jir̆í; Su, Xiao-Dong; Brzobohatý, Br̆etislav
2001-01-01
The maize (Zea mays) β-glucosidase Zm-p60.1 has been implicated in regulation of plant development by the targeted release of free cytokinins from cytokinin-O-glucosides, their inactive storage forms. The crystal structure of the wild-type enzyme was solved at 2.05-Å resolution, allowing molecular docking analysis to be conducted. This indicated that the enzyme specificity toward substrates with aryl aglycones is determined by aglycone aromatic system stacking with W373, and interactions with edges of F193, F200, and F461 located opposite W373 in a slot-like aglycone-binding site. These aglycone-active site interactions recently were hypothesized to determine substrate specificity in inactive enzyme substrate complexes of ZM-Glu1, an allozyme of Zm-p60.1. Here, we test this hypothesis by kinetic analysis of F193I/Y/W mutants. The decreased Km of all mutants confirmed the involvement of F193 in determining enzyme affinity toward substrates with an aromatic aglycone. It was unexpected that a 30-fold decrease in kcat was found in F193I mutant compared with the wild type. Kinetic analysis and computer modeling demonstrated that the F193-aglycone-W373 interaction not only contributes to aglycone recognition as hypothesized previously but also codetermines catalytic rate by fixing the glucosidic bond in an orientation favorable for attack by the catalytic pair, E186 and E401. The catalytic pair, assigned initially by their location in the structure, was confirmed by kinetic analysis of E186D/Q and E401D/Q mutants. It was unexpected that the E401D as well as C205S and C211S mutations dramatically impaired the assembly of a catalysis-competent homodimer, suggesting novel links between the active site structure and dimer formation. PMID:11706179
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Can, Mehmet; Giles, Logan J.; Ragsdale, Stephen W.
Acetyl-CoA synthase (ACS) is a key enzyme in the Wood–Ljungdahl pathway of anaerobic CO 2 fixation, which has long been proposed to operate by a novel mechanism involving a series of protein-bound organometallic (Ni–CO, methyl–Ni, and acetyl–Ni) intermediates. Here we report the first direct structural evidence of the proposed metal–carbon bond. We describe the preparation of the highly active metal-replete enzyme and near-quantitative generation of the kinetically competent carbonylated intermediate. This advance has allowed a combination of Ni and Fe K-edge X-ray absorption spectroscopy and extended X-ray absorption fine structure experiments along with density functional theory calculations. The data revealmore » that CO binds to the proximal Ni of the six-metal metallocenter at the active site and undergoes dramatic structural and electronic perturbation in forming this organometallic Ni–CO intermediate. This direct identification of a Ni–carbon bond in the catalytically competent CO-bound form of the In conclusion, a cluster of ACS provides definitive experimental structural evidence supporting the proposed organometallic mechanism of anaerobic acetyl-CoA synthesis.« less
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Can, Mehmet; Giles, Logan J.; Ragsdale, Stephen W.; ...
2017-02-10
Acetyl-CoA synthase (ACS) is a key enzyme in the Wood–Ljungdahl pathway of anaerobic CO 2 fixation, which has long been proposed to operate by a novel mechanism involving a series of protein-bound organometallic (Ni–CO, methyl–Ni, and acetyl–Ni) intermediates. Here we report the first direct structural evidence of the proposed metal–carbon bond. We describe the preparation of the highly active metal-replete enzyme and near-quantitative generation of the kinetically competent carbonylated intermediate. This advance has allowed a combination of Ni and Fe K-edge X-ray absorption spectroscopy and extended X-ray absorption fine structure experiments along with density functional theory calculations. The data revealmore » that CO binds to the proximal Ni of the six-metal metallocenter at the active site and undergoes dramatic structural and electronic perturbation in forming this organometallic Ni–CO intermediate. This direct identification of a Ni–carbon bond in the catalytically competent CO-bound form of the In conclusion, a cluster of ACS provides definitive experimental structural evidence supporting the proposed organometallic mechanism of anaerobic acetyl-CoA synthesis.« less
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Zhang, Chunqiu; Shafi, Ramim; Lampel, Ayala; MacPherson, Douglas; Pappas, Charalampos G; Narang, Vishal; Wang, Tong; Maldarelli, Charles; Ulijn, Rein V
2017-11-13
The reversible regulation of catalytic activity is a feature found in natural enzymes which is not commonly observed in artificial catalytic systems. Here, we fabricate an artificial hydrolase with pH-switchable activity, achieved by introducing a catalytic histidine residue at the terminus of a pH-responsive peptide. The peptide exhibits a conformational transition from random coil to β-sheet by changing the pH from acidic to alkaline. The β-sheet self-assembles to form long fibrils with the hydrophobic edge and histidine residues extending in an ordered array as the catalytic microenvironment, which shows significant esterase activity. Catalytic activity can be reversible switched by pH-induced assembly/disassembly of the fibrils into random coils. At higher concentrations, the peptide forms a hydrogel which is also catalytically active and maintains its reversible (de-)activation. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
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Surface Chemistry and Nano-/Microstructure Engineering on Photocatalytic In2S3 Nanocrystals.
Berestok, Taisiia; Guardia, Pablo; Portals, Javier Blanco; Estradé, Sònia; Llorca, Jordi; Peiró, Francesca; Cabot, Andreu; Brock, Stephanie L
2018-06-05
Colloidal nanocrystals (NCs) compete with molecular catalysts in the field of homogenous catalysis, offering easier recyclability and a number of potentially advantageous functionalities, such as tunable band gaps, plasmonic properties, or a magnetic moment. Using high-throughput printing technologies, colloidal NCs can also be supported onto substrates to produce cost-effective electronic, optoelectronic, electrocatalytic, and sensing devices. For both catalytic and technological application, NC surface chemistry and supracrystal organization are key parameters determining final performance. Here, we study the influence of the surface ligands and the NC organization on the catalytic properties of In 2 S 3 , both as a colloid and as a supported layer. As a colloid, NCs stabilized by inorganic ligands show the highest photocatalytic activities, which we associate with their large and more accessible surfaces. On the other hand, when NCs are supported on a substrate, their organization becomes an essential parameter determining performance. For instance, NC-based films produced through a gelation process provided five-fold higher photocurrent densities than those obtained from dense films produced by the direct printing of NCs.
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Schafer, Christopher M.; Sheikh, M. Osman; Zhang, Dongmei; West, Christopher M.
2014-01-01
The role of Skp1 as an adaptor protein that links Cullin-1 to F-box proteins in E3 Skp1/Cullin-1/F-box protein (SCF) ubiquitin ligases is well characterized. In the social amoeba Dictyostelium and probably many other unicellular eukaryotes, Skp1 is modified by a pentasaccharide attached to a hydroxyproline near its C terminus. This modification is important for oxygen-sensing during Dictyostelium development and is mediated by a HIF-α type prolyl 4-hydroxylase and five sequentially acting cytoplasmic glycosyltransferase activities. Gene disruption studies show that AgtA, the enzyme responsible for addition of the final two galactose residues, in α-linkages to the Skp1 core trisaccharide, is unexpectedly critical for oxygen-dependent terminal development. AgtA possesses a WD40 repeat domain C-terminal to its single catalytic domain and, by use of domain deletions, binding studies, and enzyme assays, we find that the WD40 repeats confer a salt-sensitive second-site binding interaction with Skp1 that mediates novel catalytic activation in addition to simple substrate recognition. In addition, AgtA binds similarly well to precursor isoforms of Skp1 by a salt-sensitive mechanism that competes with binding to an F-box protein and recognition by early modification enzymes, and the effect of binding is diminished when AgtA modifies Skp1. Genetic studies show that loss of AgtA is more severe when an earlier glycosylation step is blocked, and overexpressed AgtA is deleterious if catalytically inactivated. Together, the findings suggest that AgtA mediates non-enzymatic control of unmodified and substrate precursor forms of Skp1 by a binding mechanism that is normally relieved by switch-like activation of its glycosylation function. PMID:24550398
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Diverse Functional Properties of Wilson Disease ATP7B Variants
Huster, Dominik; Kühne, Angelika; Bhattacharjee, Ashima; Raines, Lily; Jantsch, Vanessa; Noe, Johannes; Schirrmeister, Wiebke; Sommerer, Ines; Sabri, Osama; Berr, Frieder; Mössner, Joachim; Stieger, Bruno; Caca, Karel; Lutsenko, Svetlana
2012-01-01
BACKGROUND & AIMS Wilson disease is a severe disorder of copper metabolism caused by mutations in ATP7B, which encodes a copper-transporting adenosine triphosphatase. The disease presents with a variable phenotype that complicates the diagnostic process and treatment. Little is known about the mechanisms that contribute to the different phenotypes of the disease. METHODS We analyzed 28 variants of ATP7B from patients with Wilson disease that affected different functional domains; the gene products were expressed using the baculovirus expression system in Sf9 cells. Protein function was analyzed by measuring catalytic activity and copper (64Cu) transport into vesicles. We studied intracellular localization of variants of ATP7B that had measurable transport activities and were tagged with green fluorescent protein in mammalian cells using confocal laser scanning microscopy. RESULTS Properties of ATP7B variants with pathogenic amino-acid substitution varied greatly even if substitutions were in the same functional domain. Some variants had complete loss of catalytic and transport activity, whereas others lost transport activity but retained phosphor-intermediate formation or had partial losses of activity. In mammalian cells, transport-competent variants differed in stability and subcellular localization. CONCLUSIONS Variants in ATP7B associated with Wilson disease disrupt the protein’s transport activity, result in its mislocalization, and reduce its stability. Single assays are insufficient to accurately predict the effects of ATP7B variants the function of its product and development of Wilson disease. These findings will contribute to our understanding of genotype–phenotype correlation and mechanisms of disease pathogenesis. PMID:22240481
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STD-NMR-Based Protein Engineering of the Unique Arylpropionate-Racemase AMDase G74C.
Gaßmeyer, Sarah Katharina; Yoshikawa, Hiroyuki; Enoki, Junichi; Hülsemann, Nadine; Stoll, Raphael; Miyamoto, Kenji; Kourist, Robert
2015-06-23
Structure-guided protein engineering achieved a variant of the unique racemase AMDase G74C, with 40-fold increased activity in the racemisation of several arylaliphatic carboxylic acids. Substrate binding during catalysis was investigated by saturation-transfer-difference NMR (STD-NMR) spectroscopy. All atoms of the substrate showed interactions with the enzyme. STD-NMR measurements revealed distinct nuclear Overhauser effects in experiments with and without molecular conversion. The spectroscopic analysis led to the identification of several amino acid residues whose substitutions increased the activity of G74C. Single amino acid exchanges increased the activity moderately; structure-guided saturation mutagenesis yielded a quadruple mutant with a 40 times higher reaction rate. This study presents STD-NMR as versatile tool for the analysis of enzyme-substrate interactions in catalytically competent systems and for the guidance of protein engineering. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
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Catalytic oxidation of Hg(0) by MnOx-CeO2/γ-Al2O3 catalyst at low temperatures.
Wang, Pengying; Su, Sheng; Xiang, Jun; You, Huawei; Cao, Fan; Sun, Lushi; Hu, Song; Zhang, Yun
2014-04-01
MnOx-CeO2/γ-Al2O3 (MnCe) selective catalytic reduction (SCR) catalysts prepared by sol-gel method were employed for low-temperature Hg(0) oxidation on a fixed-bed experimental setup. BET, XRD and XPS were used to characterize the catalysts. MnCe catalysts exhibited high Hg(0) oxidation activity at low temperatures (100-250 °C) under the simulated flue gas (O2, CO2, NO, SO2, HCl, H2O and balanced with N2). Only a small decrease in mercury oxidation was observed in the presence of 1200 ppm SO2, which proved that the addition of Ce helped resist SO2 poisoning. An enhancing effect of NO was observed due to the formation of multi-activity NOx species. The presence of HCl alone had excellent Hg(0) oxidation ability, while 10 ppm HCl plus 5% O2 further increased Hg(0) oxidation efficiency to 100%. Hg(0) oxidation on the MnCe catalyst surface followed the Langmiur-Hinshelwood mechanism, where reactions took place between the adsorbed active species and adsorbed Hg(0) to form Hg(2+). NH3 competed with Hg(0) for active sites on the catalyst surface, hence inhibiting Hg(0) oxidation. This study shows the feasibility of a single-step process integrating low-temperature SCR and Hg(0) oxidation from the coal combustion flue gas. Copyright © 2013 Elsevier Ltd. All rights reserved.
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Kim, Sang Chai; Shim, Wang Geun
2008-06-15
The catalytic oxidation of toluene was studied over an iron-based spent and regenerated catalysts. Air, hydrogen, or four different acid solutions (oxalic acid (C2H2O4), citric acid (C6H8O7), acetic acid (CH3COOH), and nitric acid (HNO3)) were employed to regenerate the spent catalyst. The properties of pretreated spent catalyst were characterized by the Brunauer Emmett Teller (BET), inductively coupled plasma (ICP), temperature programmed reduction (TPR), and X-ray diffraction (XRD) analyses. The air pretreatment significantly enhanced the catalytic activity of the spent catalyst in the pretreatment temperature range of 200-400 degrees C, but its catalytic activity diminished at the pretreatment temperature of 600 degrees C. The catalytic activity sequence with respect to the air pretreatment temperatures was 400 degrees C>200 degrees C>parent>600 degrees C. The TPR results indicated that the catalytic activity was correlated with both the oxygen mobility and the amount of available oxygen on the catalyst. In contrast, the hydrogen pretreatment had a negative effect on the catalytic activity, and toluene conversion decreased with increasing pretreatment temperatures (200-600 degrees C). The XRD and TPR results confirmed the formation of metallic iron which had a negative effect on the catalytic activity with increasing pretreatment temperature. The acid pretreatment improved the catalytic activity of the spent catalyst. The catalytic activity sequence with respect to different acids pretreatment was found to be oxalic acid>citric acid>acetic acid>or=nitric acid>parent. The TPR results of acid pretreated samples showed an increased amount of available oxygen which gave a positive effect on the catalytic activity. Accordingly, air or acid pretreatments were more promising methods of regenerating the iron-based spent catalyst. In particular, the oxalic acid pretreatment was found to be most effective in the formation of FeC2O4 species which contributed highly to the catalytic combustion of toluene.
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Vilella, Laia; Conde, Ana; Balcells, David; Díaz-Requejo, M Mar; Lledós, Agustí; Pérez, Pedro J
2017-12-01
A dual mechanism for direct benzene catalytic hydroxylation is described. Experimental studies and DFT calculations have provided a mechanistic explanation for the acid-free, Tp x Cu-catalyzed hydroxylation of benzene with hydrogen peroxide (Tp x = hydrotrispyrazolylborate ligand). In contrast with other catalytic systems that promote this transformation through Fenton-like pathways, this system operates through a copper-oxyl intermediate that may interact with the arene ring following two different, competitive routes: (a) electrophilic aromatic substitution, with the copper-oxyl species acting as the formal electrophile, and (b) the so-called rebound mechanism, in which the hydrogen is abstracted by the Cu-O moiety prior to the C-O bond formation. Both pathways contribute to the global transformation albeit to different extents, the electrophilic substitution route seeming to be largely favoured.
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Rivalta, Ivan; Lisi, George P; Snoeberger, Ning-Shiuan; Manley, Gregory; Loria, J Patrick; Batista, Victor S
2016-11-29
Allosteric enzymes regulate a wide range of catalytic transformations, including biosynthetic mechanisms of important human pathogens, upon binding of substrate molecules to an orthosteric (or active) site and effector ligands at distant (allosteric) sites. We find that enzymatic activity can be impaired by small molecules that bind along the allosteric pathway connecting the orthosteric and allosteric sites, without competing with endogenous ligands. Noncompetitive allosteric inhibitors disrupted allostery in the imidazole glycerol phosphate synthase (IGPS) enzyme from Thermotoga maritima as evidenced by nuclear magnetic resonance, microsecond time-scale molecular dynamics simulations, isothermal titration calorimetry, and kinetic assays. The findings are particularly relevant for the development of allosteric antibiotics, herbicides, and antifungal compounds because IGPS is absent in mammals but provides an entry point to fundamental biosynthetic pathways in plants, fungi, and bacteria.
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Uncoupling binding of substrate CO from turnover by vanadium nitrogenase.
Lee, Chi Chung; Fay, Aaron W; Weng, Tsu-Chien; Krest, Courtney M; Hedman, Britt; Hodgson, Keith O; Hu, Yilin; Ribbe, Markus W
2015-11-10
Biocatalysis by nitrogenase, particularly the reduction of N2 and CO by this enzyme, has tremendous significance in environment- and energy-related areas. Elucidation of the detailed mechanism of nitrogenase has been hampered by the inability to trap substrates or intermediates in a well-defined state. Here, we report the capture of substrate CO on the resting-state vanadium-nitrogenase in a catalytically competent conformation. The close resemblance of this active CO-bound conformation to the recently described structure of CO-inhibited molybdenum-nitrogenase points to the mechanistic relevance of sulfur displacement to the activation of iron sites in the cofactor for CO binding. Moreover, the ability of vanadium-nitrogenase to bind substrate in the resting-state uncouples substrate binding from subsequent turnover, providing a platform for generation of defined intermediate(s) of both CO and N2 reduction.
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Tobisch, Sven
2012-06-04
The present study comprehensively explores diverse mechanistic pathways for intramolecular hydroamination of prototype 2,2-dimethyl-4-penten-1-amine by Cp*Ir chloropyrazole (1; Cp*=pentamethylcyclopentadienyl) in the presence of KOtBu base with the aid of density functional theory (DFT) calculations. The most accessible mechanistic pathway for catalytic turnover commences from Cp*Ir pyrazolato (Pz) substrate adduct 2⋅S, representing the catalytically competent compound and proceeds via initial electrophilic activation of the olefin C=C bond by the metal centre. It entails 1) facile and reversible anti nucleophilic amine attack on the iridium-olefin linkage; 2) Ir-C bond protonolysis via stepwise transfer of the ammonium N-H proton at the zwitterionic [Cp*IrPz-alkyl] intermediate onto the metal that is linked to turnover-limiting, reductive, cycloamine elimination commencing from a high-energy, metastable [Cp*IrPz-hydrido-alkyl] species; and 3) subsequent facile cycloamine liberation to regenerate the active catalyst species. The amine-iridium bound 2 a⋅S likely corresponds to the catalyst resting state and the catalytic reaction is expected to proceed with a significant primary kinetic isotope. This study unveils the vital role of a supportive hydrogen-bonded network involving suitably aligned β-basic pyrazolato and cycloamido moieties together with an external amine molecule in facilitating metal protonation and reductive elimination. Cooperative hydrogen bonding thus appears pivotal for effective catalysis. The mechanistic scenario is consonant with catalyst performance data and furthermore accounts for the variation in performance for [Cp*IrPz] compounds featuring a β- or γ-basic pyrazolato unit. As far as the route that involves amine N-H bond activation is concerned, a thus far undocumented pathway for concerted amidoalkene → cycloamine conversion through olefin protonation by the pyrazole N-H concurrent with N-C ring closure is disclosed as a favourable scenario. Although not practicable in the present system, this pathway describes a novel mechanistic variant in late transition metal-ligand bifunctional hydroamination catalysis that can perhaps be viable for tailored catalyst designs. The insights revealed herein concerning the operative mechanism and the structure-reactivity relationships will likely govern the rational design of late transition metal-ligand bifunctional catalysts and facilitate further conceptual advances in the area. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
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Characterization of the catalytic center of the Ebola virus L polymerase.
Schmidt, Marie Luisa; Hoenen, Thomas
2017-10-01
Ebola virus (EBOV) causes a severe hemorrhagic fever in humans and non-human primates. While no licensed therapeutics are available, recently there has been tremendous progress in developing antivirals. Targeting the ribonucleoprotein complex (RNP) proteins, which facilitate genome replication and transcription, and particularly the polymerase L, is a promising antiviral approach since these processes are essential for the virus life cycle. However, until now little is known about L in terms of its structure and function, and in particular the catalytic center of the RNA-dependent RNA polymerase (RdRp) of L, which is one of the most promising molecular targets, has never been experimentally characterized. Using multiple sequence alignments with other negative sense single-stranded RNA viruses we identified the putative catalytic center of the EBOV RdRp. An L protein with mutations in this center was then generated and characterized using various life cycle modelling systems. These systems are based on minigenomes, i.e. miniature versions of the viral genome, in which the viral genes are exchanged against a reporter gene. When such minigenomes are coexpressed with RNP proteins in mammalian cells, the RNP proteins recognize them as authentic templates for replication and transcription, resulting in reporter activity reflecting these processes. Replication-competent minigenome systems indicated that our L catalytic domain mutant was impaired in genome replication and/or transcription, and by using replication-deficient minigenome systems, as well as a novel RT-qPCR-based genome replication assay, we showed that it indeed no longer supported either of these processes. However, it still showed similar expression to wild-type L, and retained its ability to be incorporated into inclusion bodies, which are the sites of EBOV genome replication. We have experimentally defined the catalytic center of the EBOV RdRp, and thus a promising antiviral target regulating an essential aspect of the EBOV life cycle.
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NASA Astrophysics Data System (ADS)
Li, Jingying; Tang, Xiaolong; Yi, Honghong; Yu, Qingjun; Gao, Fengyu; Zhang, Runcao; Li, Chenlu; Chu, Chao
2017-08-01
Different copper-precursors were used to prepare Cu/graphene catalysts by an impregnation method. XRD, Raman spectra, TEM, BET, XPS, H2-TPR, NH3-TPD, DRIFTS and catalytic activity test were used to characterize and study the effect of precursors on the catalytic activity of Cu/graphene catalysts for NH3-SCO reaction. The large specific surface area of Cu/graphene catalysts and high dispersion of the metal particles on the graphene caused the well catalytic activity of NH3-SCO reaction. Compared to Cu/GE(AC), Cu/GE(N) showed better catalytic performance, and the complete NH3 removal efficiency was obtained at 250 °C with N2 selectivity of 85%. The copper-precursors had influence on the distribution of surface Cu species and further affected the catalytic activity of Cu/GE catalysts. The more amount of surface Cu species and highly dispersed CuO particles on the graphene surface formed by using copper nitrate as precursor could significantly improve the reducibility of catalysts and enhance NH3 adsorption, thereby improving the catalytic activity of Cu/graphene catalyst.
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Panneton, Vincent; Nath, Apurba; Sader, Fadi; Delaunay, Nathalie; Pelletier, Ariane; Maier, Dominic; Oh, Karen; Hipfner, David R
2015-08-21
Protein kinases carry out important functions in cells both by phosphorylating substrates and by means of regulated non-catalytic activities. Such non-catalytic functions have been ascribed to many kinases, including some members of the Ste20 family. The Drosophila Ste20 kinase Slik phosphorylates and activates Moesin in developing epithelial tissues to promote epithelial tissue integrity. It also functions non-catalytically to promote epithelial cell proliferation and tissue growth. We carried out a structure-function analysis to determine how these two distinct activities of Slik are controlled. We find that the conserved C-terminal coiled-coil domain of Slik, which is necessary and sufficient for apical localization of the kinase in epithelial cells, is not required for Moesin phosphorylation but is critical for the growth-promoting function of Slik. Slik is auto- and trans-phosphorylated in vivo. Phosphorylation of at least two of three conserved sites in the activation segment is required for both efficient catalytic activity and non-catalytic signaling. Slik function is thus dependent upon proper localization of the kinase via the C-terminal coiled-coil domain and activation via activation segment phosphorylation, which enhances both phosphorylation of substrates like Moesin and engagement of effectors of its non-catalytic growth-promoting activity. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.
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Pressman, Abe; Moretti, Janina E; Campbell, Gregory W; Müller, Ulrich F; Chen, Irene A
2017-08-21
The emergence of catalytic RNA is believed to have been a key event during the origin of life. Understanding how catalytic activity is distributed across random sequences is fundamental to estimating the probability that catalytic sequences would emerge. Here, we analyze the in vitro evolution of triphosphorylating ribozymes and translate their fitnesses into absolute estimates of catalytic activity for hundreds of ribozyme families. The analysis efficiently identified highly active ribozymes and estimated catalytic activity with good accuracy. The evolutionary dynamics follow Fisher's Fundamental Theorem of Natural Selection and a corollary, permitting retrospective inference of the distribution of fitness and activity in the random sequence pool for the first time. The frequency distribution of rate constants appears to be log-normal, with a surprisingly steep dropoff at higher activity, consistent with a mechanism for the emergence of activity as the product of many independent contributions. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.
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Xiao, Junwu; Kuang, Qin; Yang, Shihe; Xiao, Fei; Wang, Shuai; Guo, Lin
2013-01-01
Catalytic activity is primarily a surface phenomenon, however, little is known about Co3O4 nanocrystals in terms of the relationship between the oxygen reduction reaction (ORR) catalytic activity and surface structure, especially when dispersed on a highly conducting support to improve the electrical conductivity and so to enhance the catalytic activity. Herein, we report a controllable synthesis of Co3O4 nanorods (NR), nanocubes (NC) and nano-octahedrons (OC) with the different exposed nanocrystalline surfaces ({110}, {100}, and {111}), uniformly anchored on graphene sheets, which has allowed us to investigate the effects of the surface structure on the ORR activity. Results show that the catalytically active sites for ORR should be the surface Co2+ ions, whereas the surface Co3+ ions catalyze CO oxidation, and the catalytic ability is closely related to the density of the catalytically active sites. These results underscore the importance of morphological control in the design of highly efficient ORR catalysts. PMID:23892418
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2016-01-01
Through the combination of reaction kinetics (both stoichiometric and catalytic), solution- and solid-state characterization of arylpalladium(II) arylsilanolates, and computational analysis, the intermediacy of covalent adducts containing Si–O–Pd linkages in the cross-coupling reactions of arylsilanolates has been unambiguously established. Two mechanistically distinct pathways have been demonstrated: (1) transmetalation via a neutral 8-Si-4 intermediate that dominates in the absence of free silanolate (i.e., stoichiometric reactions of arylpalladium(II) arylsilanolate complexes), and (2) transmetalation via an anionic 10-Si-5 intermediate that dominates in the cross-coupling under catalytic conditions (i.e., in the presence of free silanolate). Arylpalladium(II) arylsilanolate complexes bearing various phosphine ligands have been isolated, fully characterized, and evaluated for their kinetic competence under thermal (stoichiometric) and anionic (catalytic) conditions. Comparison of the rates for thermal and anionic activation suggested, but did not prove, that intermediates containing the Si–O–Pd linkage were involved in the cross-coupling process. The isolation of a coordinatively unsaturated, T-shaped arylpalladium(II) arylsilanolate complex ligated with t-Bu3P allowed the unambiguous demonstration of the operation of both pathways involving 8-Si-4 and 10-Si-5 intermediates. Three kinetic regimes were identified: (1) with 0.5–1.0 equiv of added silanolate (with respect to arylpalladium bromide), thermal transmetalation via a neutral 8-Si-4 intermediate; (2) with 1.0–5.0 equiv of added silanolate, activated transmetalation via an anionic 10-Si-5 intermediate; and (3) with >5.0 equiv of added silanolate, concentration-independent (saturation) activated transmetalation via an anionic 10-Si-5 intermediate. Transition states for the intramolecular transmetalation of neutral (8-Si-4) and anionic (10-Si-5) intermediates have been located computationally, and the anionic pathway is favored by 1.8 kcal/mol. The energies of all intermediates and transition states are highly dependent on the configuration around the palladium atom. PMID:25945516
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Function and maturation of the Fe-S center in dihydroxyacid dehydratase from Arabidopsis.
Gao, Huanyao; Azam, Tamanna; Randeniya, Sajini; Couturier, Jérémy; Rouhier, Nicolas; Johnson, Michael K
2018-03-23
Dihydroxyacid dehydratase (DHAD) is the third enzyme required for branched-chain amino acid biosynthesis in bacteria, fungi, and plants. DHAD enzymes contain two distinct types of active-site Fe-S clusters. The best characterized examples are Escherichia coli DHAD, which contains an oxygen-labile [Fe 4 S 4 ] cluster, and spinach DHAD, which contains an oxygen-resistant [Fe 2 S 2 ] cluster. Although the Fe-S cluster is crucial for DHAD function, little is known about the cluster-coordination environment or the mechanism of catalysis and cluster biogenesis. Here, using the combination of UV-visible absorption and circular dichroism and resonance Raman and electron paramagnetic resonance, we spectroscopically characterized the Fe-S center in DHAD from Arabidopsis thaliana ( At ). Our results indicated that At DHAD can accommodate [Fe 2 S 2 ] and [Fe 4 S 4 ] clusters. However, only the [Fe 2 S 2 ] cluster-bound form is catalytically active. We found that the [Fe 2 S 2 ] cluster is coordinated by at least one non-cysteinyl ligand, which can be replaced by the thiol group(s) of dithiothreitol. In vitro cluster transfer and reconstitution reactions revealed that [Fe 2 S 2 ] cluster-containing NFU2 protein is likely the physiological cluster donor for in vivo maturation of At DHAD. In summary, At DHAD binds either one [Fe 4 S 4 ] or one [Fe 2 S 2 ] cluster, with only the latter being catalytically competent and capable of substrate and product binding, and NFU2 appears to be the physiological [Fe 2 S 2 ] cluster donor for DHAD maturation. This work represents the first in vitro characterization of recombinant At DHAD, providing new insights into the properties, biogenesis, and catalytic role of the active-site Fe-S center in a plant DHAD. © 2018 by The American Society for Biochemistry and Molecular Biology, Inc.
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Amine binding and oxidation at the catalytic site for photosynthetic water oxidation
Ouellette, Anthony J. A.; Anderson, Lorraine B.; Barry, Bridgette A.
1998-01-01
Photosynthetic water oxidation occurs at the Mn-containing catalytic site of photosystem II (PSII). By the use of 14C-labeled amines and SDS-denaturing PAGE, covalent adducts derived from primary amines and the PSII subunits, CP47, D2/D1, and the Mn-stabilizing protein, can be observed. When PSII contains the 18- and 24-kDa extrinsic proteins, which restrict access to the active site, no 14C labeling is obtained. NaCl, but not Na2SO4, competes with 14C labeling in Mn-containing PSII preparations, and the concentration dependence of this competition parallels the activation of oxygen evolution. Formation of 14C-labeled adducts is observed in the presence or in the absence of a functional manganese cluster. However, no significant Cl− effect on 14C labeling is observed in the absence of the Mn cluster. Isolation and quantitation of the 14C-labeled aldehyde product, produced from [14C]benzylamine, gives yields of 1.8 ± 0.3 mol/mol PSII and 2.9 ± 0.2 mol/mol in Mn-containing and Mn-depleted PSII, respectively. The corresponding specific activities are 0.40 ± 0.07 μmol(μmol PSII-hr)−1 and 0.64 ± 0.04 μmol(μmol PSII-hr)−1. Cl− suppresses the production of [14C]benzaldehyde in Mn-containing PSII, but does not suppress the production in Mn-depleted preparations. Control experiments show that these oxidation reactions do not involve the redox-active tyrosines, D and Z. Our results suggest the presence of one or more activated carbonyl groups in protein subunits that form the active site of PSII. PMID:9482863
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Inhibition of AmpC beta-lactamase through a destabilizing interaction in the active site
DOE Office of Scientific and Technical Information (OSTI.GOV)
Trehan, I.; Beadle, B.M.; Shoichet, B.K.
2010-03-08
{beta}-Lactamases hydrolyze {beta}-lactam antibiotics, including penicillins and cephalosporins; these enzymes are the most widespread resistance mechanism to these drugs and pose a growing threat to public health. {beta}-Lactams that contain a bulky 6(7){alpha} substituent, such as imipenem and moxalactam, actually inhibit serine {beta}-lactamases and are widely used for this reason. Although mutant serine {beta}-lactamases have arisen that hydrolyze {beta}-lactamase resistant {beta}-lactams (e.g., ceftazidime) or avoid mechanism-based inhibitors (e.g., clavulanate), mutant serine {beta}-lactamases have not yet arisen in the clinic with imipenemase or moxalactamase activity. Structural and thermodynamic studies suggest that the 6(7){alpha} substituents of these inhibitors form destabilizing contacts withinmore » the covalent adduct with the conserved Asn152 in class C {beta}-lactamases (Asn132 in class A {beta}-lactamases). This unfavorable interaction may be crucial to inhibition. To test this destabilization hypothesis, we replaced Asn152 with Ala in the class C {beta}-lactamase AmpC from Escherichia coli and examined the mutant enzyme's thermodynamic stability in complex with imipenem and moxalactam. Consistent with the hypothesis, the Asn152 {yields} Ala substitution relieved 0.44 and 1.10 kcal/mol of strain introduced by imipenem and moxalactam, respectively, relative to the wild-type complexes. However, the kinetic efficiency of AmpC N152A was reduced by 6300-fold relative to that of the wild-type enzyme. To further investigate the inhibitor's interaction with the mutant enzyme, the X-ray crystal structure of moxalactam in complex with N152A was determined to a resolution of 1.83 {angstrom}. Moxalactam in the mutant complex is significantly displaced from its orientation in the wild-type complex; however, moxalactam does not adopt an orientation that would restore competence for hydrolysis. Although Asn152 forces {beta}-lactams with 6(7){alpha} substituents out of a catalytically competent configuration, making them inhibitors, the residue is essential for orienting {beta}-lactam substrates and cannot simply be replaced with a much smaller residue to restore catalytic activity. Designing {beta}-lactam inhibitors that interact unfavorably with this conserved residue when in the covalent adduct merits further investigation.« less
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Vilella, Laia; Conde, Ana
2017-01-01
A dual mechanism for direct benzene catalytic hydroxylation is described. Experimental studies and DFT calculations have provided a mechanistic explanation for the acid-free, TpxCu-catalyzed hydroxylation of benzene with hydrogen peroxide (Tpx = hydrotrispyrazolylborate ligand). In contrast with other catalytic systems that promote this transformation through Fenton-like pathways, this system operates through a copper-oxyl intermediate that may interact with the arene ring following two different, competitive routes: (a) electrophilic aromatic substitution, with the copper-oxyl species acting as the formal electrophile, and (b) the so-called rebound mechanism, in which the hydrogen is abstracted by the Cu–O moiety prior to the C–O bond formation. Both pathways contribute to the global transformation albeit to different extents, the electrophilic substitution route seeming to be largely favoured. PMID:29619184
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Spin-Center Shift-Enabled Direct Enantioselective α-Benzylation of Aldehydes with Alcohols.
Nacsa, Eric D; MacMillan, David W C
2018-03-07
Nature routinely engages alcohols as leaving groups, as DNA biosynthesis relies on the removal of water from ribonucleoside diphosphates by a radical-mediated "spin-center shift" (SCS) mechanism. Alcohols, however, remain underused as alkylating agents in synthetic chemistry due to their low reactivity in two-electron pathways. We report herein an enantioselective α-benzylation of aldehydes using alcohols as alkylating agents based on the mechanistic principle of spin-center shift. This strategy harnesses the dual activation modes of photoredox and organocatalysis, engaging the alcohol by SCS and capturing the resulting benzylic radical with a catalytically generated enamine. Mechanistic studies provide evidence for SCS as a key elementary step, identify the origins of competing reactions, and enable improvements in chemoselectivity by rational photocatalyst design.
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Liu, Peng; Song, Ke; Zhang, Dongju; Liu, Chengbu
2012-05-01
The detailed mechanisms of catalytic CO oxidation over Au(2)(-) and AuAg(-) dimers, which represent the simplest models for monometal Au and bimetallic Au-Ag nanoparticles, have been studied by performing density functional theory calculations. It is found that both Au(2)(-) and AuAg(-) dimers catalyze the reaction according to the similar mono-center Eley-Rideal mechanism. The catalytic reaction is of the multi-channel and multi-step characteristic, which can proceed along four possible pathways via two or three elementary steps. In AuAg(-), the Au site is more active than the Ag site, and the calculated energy barrier values for the rate-determining step of the Au-site catalytic reaction are remarkably smaller than those for both the Ag-site catalytic reaction and the Au(2)(-) catalytic reaction. The better catalytic activity of bimetallic AuAg(-) dimer is attributed to the synergistic effect between Au and Ag atom. The present results provide valuable information for understanding the higher catalytic activity of Au-Ag nanoparticles and nanoalloys for low-temperature CO oxidation than either pure metallic catalyst.
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Predicting Catalytic Activity of Nanoparticles by a DFT-Aided Machine-Learning Algorithm.
Jinnouchi, Ryosuke; Asahi, Ryoji
2017-09-07
Catalytic activities are often dominated by a few specific surface sites, and designing active sites is the key to realize high-performance heterogeneous catalysts. The great triumphs of modern surface science lead to reproduce catalytic reaction rates by modeling the arrangement of surface atoms with well-defined single-crystal surfaces. However, this method has limitations in the case for highly inhomogeneous atomic configurations such as on alloy nanoparticles with atomic-scale defects, where the arrangement cannot be decomposed into single crystals. Here, we propose a universal machine-learning scheme using a local similarity kernel, which allows interrogation of catalytic activities based on local atomic configurations. We then apply it to direct NO decomposition on RhAu alloy nanoparticles. The proposed method can efficiently predict energetics of catalytic reactions on nanoparticles using DFT data on single crystals, and its combination with kinetic analysis can provide detailed information on structures of active sites and size- and composition-dependent catalytic activities.
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Heterogeneous kinetic modeling of the catalytic conversion of cycloparaffins
NASA Astrophysics Data System (ADS)
Al-Sabawi, Mustafa N.
The limited availability of high value light hydrocarbon feedstocks along with the rise in crude prices has resulted in the international recognition of the vast potential of Canada's oil sands. With the recent expansion of Canadian bitumen production come, however, many technical challenges, one of which is the significant presence of aromatics and cycloparaffins in bitumen-derived feedstocks. In addition to their negative environmental impact, aromatics limit fluid catalytic cracking (FCC) feedstock conversion, decrease the yield and quality of valuable products such as gasoline and middle distillates, increase levels of polyaromatic hydrocarbons prone to form coke on the catalyst, and ultimately compromise the FCC unit performance. Although cycloparaffins do not have such negative impacts, they are precursors of aromatics as they frequently undergo hydrogen transfer reactions. However, cycloparaffin cracking chemistry involves other competing reactions that are complex and need much investigation. This dissertation provides insights and understanding of the fundamentals of the catalytic cracking of cycloparaffins using carefully selected model compounds such as methylcyclohexane (MCH) and decalin. Thermal and catalytic cracking of these cycloparaffins on FCC-type catalysts are carried out using the CREC Riser Simulator under operating conditions similar to those of the industrial FCC units in terms of temperature, reaction time, reactant partial pressure and catalyst-to-hydrocarbon ratio. The crystallite size of the supported zeolites is varied between 0.4 and 0.9 microns, with both activity and selectivity being monitored. Catalytic conversions ranged between 4 to 16 wt% for MCH and between 8 to 27 wt% for decalin. Reaction pathways of cycloparaffins are determined, and these include ring-opening, protolytic cracking, isomerization, hydrogen transfer and transalkylation. The yields and selectivities of over 60 and 140 products, formed during MCH and decalin catalytic conversions respectively, are reported. Using these data, heterogeneous kinetic models accounting for intracrystallite molecular transport, adsorption and thermal and catalytic cracking of both cycloparaffin reactants are established. Results show that undesirable hydrogen transfer reactions are more pronounced and selectively favoured against other reactions at lower reaction temperatures, while the desirable ring-opening and cracking reactions predominate at the higher reaction temperatures. Moreover, results of the present work show that while crystallite size may have an effect on the overall conversion in some situations, there is a definite effect on the selectivity of products obtained during the cracking of MCH and decalin and the cracking of MCH in a mixture with co-reactants such as 1,3,5-triisopropylbenzene. Keywords. cycloparaffins, naphthenes, fluid catalytic cracking, kinetic modeling, Y-zeolites, diffusion, adsorption, ring-opening, hydrogen transfer, catalyst selectivity.
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The mechanism of linkage-specific ubiquitin chain elongation by a single-subunit E2
Wickliffe, Katherine E.; Lorenz, Sonja; Wemmer, David E.; Kuriyan, John; Rape, Michael
2011-01-01
Ubiquitin chains of different topologies trigger distinct functional consequences, including protein degradation and reorganization of complexes. The assembly of most ubiquitin chains is promoted by E2s, yet how these enzymes achieve linkage specificity is poorly understood. We have discovered that the K11-specific Ube2S orients the donor ubiquitin through an essential non-covalent interaction that occurs in addition to the thioester bond at the E2 active site. The E2-donor ubiquitin complex transiently recognizes the acceptor ubiquitin, primarily through electrostatic interactions. The recognition of the acceptor ubiquitin surface around Lys11, but not around other lysines, generates a catalytically competent active site, which is composed of residues of both Ube2S and ubiquitin. Our studies suggest that monomeric E2s promote linkage-specific ubiquitin chain formation through substrate-assisted catalysis. PMID:21376237
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Sakata, Souhei; Jinno, Yuka; Kawanabe, Akira; Okamura, Yasushi
2016-01-01
The cytoplasmic region of voltage-sensing phosphatase (VSP) derives the voltage dependence of its catalytic activity from coupling to a voltage sensor homologous to that of voltage-gated ion channels. To assess the conformational changes in the cytoplasmic region upon activation of the voltage sensor, we genetically incorporated a fluorescent unnatural amino acid, 3-(6-acetylnaphthalen-2-ylamino)-2-aminopropanoic acid (Anap), into the catalytic region of Ciona intestinalis VSP (Ci-VSP). Measurements of Anap fluorescence under voltage clamp in Xenopus oocytes revealed that the catalytic region assumes distinct conformations dependent on the degree of voltage-sensor activation. FRET analysis showed that the catalytic region remains situated beneath the plasma membrane, irrespective of the voltage level. Moreover, Anap fluorescence from a membrane-facing loop in the C2 domain showed a pattern reflecting substrate turnover. These results indicate that the voltage sensor regulates Ci-VSP catalytic activity by causing conformational changes in the entire catalytic region, without changing their distance from the plasma membrane. PMID:27330112
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Sakata, Souhei; Jinno, Yuka; Kawanabe, Akira; Okamura, Yasushi
2016-07-05
The cytoplasmic region of voltage-sensing phosphatase (VSP) derives the voltage dependence of its catalytic activity from coupling to a voltage sensor homologous to that of voltage-gated ion channels. To assess the conformational changes in the cytoplasmic region upon activation of the voltage sensor, we genetically incorporated a fluorescent unnatural amino acid, 3-(6-acetylnaphthalen-2-ylamino)-2-aminopropanoic acid (Anap), into the catalytic region of Ciona intestinalis VSP (Ci-VSP). Measurements of Anap fluorescence under voltage clamp in Xenopus oocytes revealed that the catalytic region assumes distinct conformations dependent on the degree of voltage-sensor activation. FRET analysis showed that the catalytic region remains situated beneath the plasma membrane, irrespective of the voltage level. Moreover, Anap fluorescence from a membrane-facing loop in the C2 domain showed a pattern reflecting substrate turnover. These results indicate that the voltage sensor regulates Ci-VSP catalytic activity by causing conformational changes in the entire catalytic region, without changing their distance from the plasma membrane.
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Formation of alcohol conversion catalysts
Wachs, Israel E.; Cai, Yeping
2001-01-01
The method of the present invention involves a composition containing an intimate mixture of (a) metal oxide support particles and (b) a catalytically active metal oxide from Groups VA, VIA, or VIIA, its method of manufacture, and its method of use for converting alcohols to aldehydes. During the conversion process, catalytically active metal oxide from the discrete catalytic metal oxide particles migrates to the oxide support particles and forms a monolayer of catalytically active metal oxide on the oxide support particle to form a catalyst composition having a higher specific activity than the admixed particle composition.
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Hamasy, A; Wang, Q; Blomberg, K E M; Mohammad, D K; Yu, L; Vihinen, M; Berglöf, A; Smith, C I E
2017-01-01
Irreversible Bruton tyrosine kinase (BTK) inhibitors, ibrutinib and acalabrutinib have demonstrated remarkable clinical responses in multiple B-cell malignancies. Acquired resistance has been identified in a sub-population of patients in which mutations affecting BTK predominantly substitute cysteine 481 in the kinase domain for catalytically active serine, thereby ablating covalent binding of inhibitors. Activating substitutions in the BTK substrate phospholipase Cγ2 (PLCγ2) instead confers resistance independent of BTK. Herein, we generated all six possible amino acid substitutions due to single nucleotide alterations for the cysteine 481 codon, in addition to threonine, requiring two nucleotide substitutions, and performed functional analysis. Replacement by arginine, phenylalanine, tryptophan or tyrosine completely inactivated the catalytic activity, whereas substitution with glycine caused severe impairment. BTK with threonine replacement was catalytically active, similar to substitution with serine. We identify three potential ibrutinib resistance scenarios for cysteine 481 replacement: (1) Serine, being catalytically active and therefore predominating among patients. (2) Threonine, also being catalytically active, but predicted to be scarce, because two nucleotide changes are needed. (3) As BTK variants replaced with other residues are catalytically inactive, they presumably need compensatory mutations, therefore being very scarce. Glycine and tryptophan variants were not yet reported but likely also provide resistance. PMID:27282255
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Schumann, Gerhard; Klauke, Rainer; Canalias, Francesca; Bossert-Reuther, Steffen; Franck, Paul F H; Gella, F-Javier; Jørgensen, Poul J; Kang, Dongchon; Lessinger, Jean-Marc; Panteghini, Mauro; Ceriotti, Ferruccio
2011-09-01
Abstract This paper is the ninth in a series dealing with reference procedures for the measurement of catalytic activity concentrations of enzymes at 37 °C and the certification of reference preparations. Other parts deal with: Part 1. The concept of reference procedures for the measurement of catalytic activity concentrations of enzymes; 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 concentration of γ-glutamyltransferase; Part 7. Certification of four reference materials for the determination of enzymatic activity of γ-glutamyltransferase, lactate dehydrogenase, alanine aminotransferase and creatine kinase at 37 °C; Part 8. Reference procedure for the measurement of catalytic concentration of α-amylase. The procedure described here is derived from the previously described 30 °C IFCC reference method. Differences are tabulated and commented on in Appendix 1.
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Wiley, J C; Wailes, L A; Idzerda, R L; McKnight, G S
1999-03-05
Regulation of protein kinase A by subcellular localization may be critical to target catalytic subunits to specific substrates. We employed epitope-tagged catalytic subunit to correlate subcellular localization and gene-inducing activity in the presence of regulatory subunit or protein kinase inhibitor (PKI). Transiently expressed catalytic subunit distributed throughout the cell and induced gene expression. Co-expression of regulatory subunit or PKI blocked gene induction and prevented nuclear accumulation. A mutant PKI lacking the nuclear export signal blocked gene induction but not nuclear accumulation, demonstrating that nuclear export is not essential to inhibit gene induction. When the catalytic subunit was targeted to the nucleus with a nuclear localization signal, it was not sequestered in the cytoplasm by regulatory subunit, although its activity was completely inhibited. PKI redistributed the nuclear catalytic subunit to the cytoplasm and blocked gene induction, demonstrating that the nuclear export signal of PKI can override a strong nuclear localization signal. With increasing PKI, the export process appeared to saturate, resulting in the return of catalytic subunit to the nucleus. These results demonstrate that both the regulatory subunit and PKI are able to completely inhibit the gene-inducing activity of the catalytic subunit even when the catalytic subunit is forced to concentrate in the nuclear compartment.
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An anthrax toxin variant with an improved activity in tumor targeting
Wein, Alexander N.; Peters, Diane E.; Valivullah, Zaheer; Hoover, Benjamin J.; Tatineni, Aparna; Ma, Qian; Fattah, Rasem; Bugge, Thomas H.; Leppla, Stephen H.; Liu, Shihui
2015-01-01
Anthrax lethal toxin (LT) is an A-B type toxin secreted by Bacillus anthracis, consisting of the cellular binding moiety, protective antigen (PA), and the catalytic moiety, lethal factor (LF). To target cells, PA binds to cell-surface receptors and is then proteolytically processed forming a LF-binding competent PA oligomer where each LF binding site is comprised of three subsites on two adjacent PA monomers. We previously generated PA-U2-R200A, a urokinase-activated PA variant with LF-binding subsite II residue Arg200 mutated to Ala, and PA-L1-I210A, a matrix metalloproteinase-activated PA variant with subsite III residue Ile210 mutated to Ala. PA-U2-R200A and PA-L1-I210A displayed reduced cytotoxicity when used singly. However, when combined, they formed LF-binding competent heterogeneous oligomers by intermolecular complementation, and achieved high specificity in tumor targeting. Nevertheless, each of these proteins, in particular PA-L1-I210A, retained residual LF-binding ability. In this work, we screened a library containing all possible amino acid substitutions for LF-binding site to find variants with activity strictly dependent upon intermolecular complementation. PA-I207R was identified as an excellent replacement for the original clockwise-side variant, PA-I210A. Consequently, the new combination of PA-L1-I207R and PA-U2-R200A showed potent anti-tumor activity and low toxicity, exceeding the performance of the original combination, and warranting further investigation. PMID:26584669
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Struthers, R S; Vale, W W; Arias, C; Sawchenko, P E; Montminy, M R
1991-04-18
Most of the transcriptional effects of cyclic AMP are mediated by the cAMP response element binding protein (CREB). After activation of cAMP-dependent protein kinase A, the catalytic subunits of this enzyme apparently mediate the phosphorylation and activation of CREB. As cAMP serves as a mitogenic signal for anterior pituitary somatotrophic cells, we investigated whether CREB similarly regulates proliferation of these cells. We prepared transgenic mice expressing a transcriptionally inactive mutant of CREB (CREBM1), which cannot be phosphorylated, in cells of the anterior pituitary. If CREB activity is required for proliferation, the overexpressed mutant protein would effectively compete with wild-type CREB activity and thereby block the response to cAMP. As predicted, the CREBM1 transgenic mice exhibited a dwarf phenotype with atrophied pituitary glands markedly deficient in somatotroph but not other cell types. We conclude that transcriptional activation of CREB is necessary for the normal development of a highly restricted cell type, and that environmental cues, possibly provided by the hypothalamic growth hormone-releasing factor, are necessary for population of the pituitary by somatotrophic cells.
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ERIC Educational Resources Information Center
Rains, Larry
This engine performance (emission control systems) module is one of a series of competency-based modules in the Missouri Auto Mechanics Curriculum Guide. Topics of this module's five units are: positive crankcase ventilation (PCV) and evaporative emission control systems; exhaust gas recirculation (EGR); air injection and catalytic converters;…
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All the catalytic active sites of MoS 2 for hydrogen evolution
Li, Guoqing; Zhang, Du; Qiao, Qiao; ...
2016-11-29
MoS 2 presents a promising low-cost catalyst for the hydrogen evolution reaction (HER), but the understanding about its active sites has remained limited. Here we present an unambiguous study of the catalytic activities of all possible reaction sites of MoS 2, including edge sites, sulfur vacancies, and grain boundaries. We demonstrate that, in addition to the well-known catalytically active edge sites, sulfur vacancies provide another major active site for the HER, while the catalytic activity of grain boundaries is much weaker. Here, the intrinsic turnover frequencies (Tafel slopes) of the edge sites, sulfur vacancies, and grain boundaries are estimated tomore » be 7.5 s –1 (65–75 mV/dec), 3.2 s –1 (65–85 mV/dec), and 0.1 s –1 (120–160 mV/dec), respectively. We also demonstrate that the catalytic activity of sulfur vacancies strongly depends on the density of the vacancies and the local crystalline structure in proximity to the vacancies. Unlike edge sites, whose catalytic activity linearly depends on the length, sulfur vacancies show optimal catalytic activities when the vacancy density is in the range of 7–10%, and the number of sulfur vacancies in high crystalline quality MoS 2 is higher than that in low crystalline quality MoS 2, which may be related with the proximity of different local crystalline structures to the vacancies.« less
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Enhanced catalyst activity by decorating of Au on Ag@Cu2O nanoshell
NASA Astrophysics Data System (ADS)
Chen, Lei; Liu, Maomao; Zhao, Yue; Kou, Qiangwei; Wang, Yaxin; Liu, Yang; Zhang, Yongjun; Yang, Jinghai; Jung, Young Mee
2018-03-01
We successfully synthesized Au-decorated Ag@Cu2O heterostructures via a simple galvanic replacement method. As the Au precursor concentration increased, the density of the Au nanoparticles (NPs) on the Ag@Cu2O surface increased, which changed the catalytic activity of the Ag@Cu2O-Au structure. The combination of Au, Ag, and Cu2O exhibited excellent catalytic properties, which can further effect on the catalyst activity of the Ag@Cu2O-Au structure. In addition, the proposed Ag@Cu2O-Au nanocomposite was used to transform the organic, toxic pollutant, 4-nitrophenol (4-NP), into its nontoxic and medicinally important amino derivative via a catalytic reduction to optimize the material performance. The proposed Au-decorated Ag@Cu2O exhibited excellent catalytic activity, and the catalytic reduction time greatly decreased (5 min). Thus, three novel properties of Ag@Cu2O-Au, i.e., charge redistribution and transfer, adsorption, and catalytic reduction of organic pollutants, were ascertained for water remediation. The proposed catalytic properties have potential applications for photocatalysis and localized surface plasmon resonance (LSPR)- and peroxidase-like catalysis.
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Partitioning the Fitness Components of RNA Populations Evolving In Vitro
Díaz Arenas, Carolina; Lehman, Niles
2013-01-01
All individuals in an evolving population compete for resources, and their performance is measured by a fitness metric. The performance of the individuals is relative to their abilities and to the biotic surroundings – the conditions under which they are competing – and involves many components. Molecules evolving in a test tube can also face complex environments and dynamics, and their fitness measurements should reflect the complexity of various contributing factors as well. Here, the fitnesses of a set of ligase ribozymes evolved by the continuous in vitro evolution system were measured. During these evolution cycles there are three different catalytic steps, ligation, reverse transcription, and forward transcription, each with a potential differential influence on the total fitness of each ligase. For six distinct ligase ribozyme genotypes that resulted from continuous evolution experiments, the rates of reaction were measured for each catalytic step by tracking the kinetics of enzymes reacting with their substrates. The reaction products were analyzed for the amount of product formed per time. Each catalytic step of the evolution cycle was found to have a differential incidence in the total fitness of the ligases, and therefore the total fitness of any ligase cannot be inferred from only one catalytic step of the evolution cycle. Generally, the ribozyme-directed ligation step tends to impart the largest effect on overall fitness. Yet it was found that the ligase genotypes have different absolute fitness values, and that they exploit different stages of the overall cycle to gain a net advantage. This is a new example of molecular niche partitioning that may allow for coexistence of more than one species in a population. The dissection of molecular events into multiple components of fitness provides new insights into molecular evolutionary studies in the laboratory, and has the potential to explain heretofore counterintuitive findings. PMID:24391957
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Leandro, João; Stokka, Anne J; Teigen, Knut; Andersen, Ole A; Flatmark, Torgeir
2017-07-01
Mammalian phenylalanine hydroxylase (PAH) is a key enzyme in l-phenylalanine (l-Phe) metabolism and is active as a homotetramer. Biochemical and biophysical work has demonstrated that it cycles between two states with a variably low and a high activity, and that the substrate l-Phe is the key player in this transition. X-ray structures of the catalytic domain have shown mobility of a partially intrinsically disordered Tyr 138 -loop to the active site in the presence of l-Phe. The mechanism by which the loop dynamics are coupled to substrate binding at the active site in tetrameric PAH is not fully understood. We have here conducted functional studies of four Tyr 138 point mutants. A high linear correlation ( r 2 = 0.99) was observed between their effects on the catalytic efficiency of the catalytic domain dimers and the corresponding effect on the catalytic efficiency of substrate-activated full-length tetramers. In the tetramers, a correlation ( r 2 = 0.96) was also observed between the increase in catalytic efficiency (activation) and the global conformational change (surface plasmon resonance signal response) at the same l-Phe concentration. The new data support a similar functional importance of the Tyr 138 -loop in the catalytic domain and the full-length enzyme homotetramer.
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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.
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2016-01-01
The direct catalytic conversion of methane to liquid oxygenated compounds, such as methanol or dimethyl ether, at low temperature using molecular oxygen is a grand challenge in C–H activation that has never been met with synthetic, heterogeneous catalysts. We report the first demonstration of direct, catalytic oxidation of methane into methanol with molecular oxygen over copper-exchanged zeolites at low reaction temperatures (483–498 K). Reaction kinetics studies show sustained catalytic activity and high selectivity for a variety of commercially available zeolite topologies under mild conditions (e.g., 483 K and atmospheric pressure). Transient and steady state measurements with isotopically labeled molecules confirm catalytic turnover. The catalytic rates and apparent activation energies are affected by the zeolite topology, with caged-based zeolites (e.g., Cu-SSZ-13) showing the highest rates. Although the reaction rates are low, the discovery of catalytic sites in copper-exchanged zeolites will accelerate the development of strategies to directly oxidize methane into methanol under mild conditions. PMID:27413787
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Chen, Yaozong; Li, Tin Lok; Lin, Xingbang; Li, Xin; Li, Xiang David; Guo, Zhihong
2017-07-21
o -Succinylbenzoyl-CoA (OSB-CoA) synthetase (MenE) is an essential enzyme in bacterial vitamin K biosynthesis and an important target in the development of new antibiotics. It is a member of the adenylating enzymes (ANL) family, which reconfigure their active site in two different active conformations, one for the adenylation half-reaction and the other for a thioesterification half-reaction, in a domain-alternation catalytic mechanism. Although several aspects of the adenylating mechanism in MenE have recently been uncovered, its thioesterification conformation remains elusive. Here, using a catalytically competent Bacillus subtilis mutant protein complexed with an OSB-CoA analogue, we determined MenE high-resolution structures to 1.76 and 1.90 Å resolution in a thioester-forming conformation. By comparison with the adenylation conformation, we found that MenE's C-domain rotates around the Ser-384 hinge by 139.5° during domain-alternation catalysis. The structures also revealed a thioesterification active site specifically conserved among MenE orthologues and a substrate-binding mode distinct from those of many other acyl/aryl-CoA synthetases. Of note, using site-directed mutagenesis, we identified several residues that specifically contribute to the thioesterification half-reaction without affecting the adenylation half-reaction. Moreover, we observed a substantial movement of the activated succinyl group in the thioesterification half-reaction. These findings provide new insights into the domain-alternation catalysis of a bacterial enzyme essential for vitamin K biosynthesis and of its adenylating homologues in the ANL enzyme family. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.
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Post, C B; Ray, W J; Gorenstein, D G
1989-01-24
Time-dependent 31P saturation-transfer studies were conducted with the Cd2+-activated form of muscle phosphoglucomutase to probe the origin of the 100-fold difference between its catalytic efficiency (in terms of kcat) and that of the more efficient Mg2+-activated enzyme. The present paper describes the equilibrium mixture of phosphoglucomutase and its substrate/product pair when the concentration of the Cd2+ enzyme approaches that of the substrate and how the nine-spin 31P NMR system provided by this mixture was treated. It shows that the presence of abortive complexes is not a significant factor in the reduced activity of the Cd2+ enzyme since the complex of the dephosphoenzyme and glucose 1,6-bisphosphate, which accounts for a large majority of the enzyme present at equilibrium, is catalytically competent. It also shows that rate constants for saturation transfer obtained at three different ratios of enzyme to free substrate are mutually compatible. These constants, which were measured at chemical equilibrium, can be used to provide a quantitative kinetic rationale for the reduced steady-state activity elicited by Cd2+ relative to Mg2+ [cf. Ray, W.J., Post, C.B., & Puvathingal, J.M. (1989) Biochemistry (following paper in this issue)]. They also provide minimal estimates of 350 and 150 s-1 for the rate constants describing (PO3-) transfer from the Cd2+ phosphoenzyme to the 6-position of bound glucose 1-phosphate and to the 1-position of bound glucose 6-phosphate, respectively. These minimal estimates are compared with analogous estimates for the Mg2+ and Li+ forms of the enzyme in the accompanying paper.
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Tararina, Margarita A; Xue, Song; Smith, Lauren C; Muellers, Samantha N; Miranda, Pedro O; Janda, Kim D; Allen, Karen N
2018-05-29
Nicotine oxidoreductase (NicA2) is a bacterial flavoenzyme, which catalyzes the first step of nicotine catabolism by oxidizing S-nicotine into N-methyl-myosmine. Its use has been proposed as a biotherapeutic for nicotine addiction due to its nanomolar substrate binding affinity. The first crystal structure of NicA2 has been reported, establishing NicA2 as a member of the monoamine oxidase (MAO) family. However, substrate specificity and structural determinants of substrate binding/catalysis have not been explored. Herein, analysis of pH-rate profile, single-turnover kinetics and binding data establish that pH does not significantly affect catalytic rate and product release is not rate limiting. The X-ray crystal structure of NicA2 with S-nicotine refined to 2.65 Å resolution reveals a hydrophobic binding site with a solvent exclusive cavity. Hydrophobic interactions predominantly orient the substrate, promoting the binding of a deprotonated species and supporting a hydride-transfer mechanism. Notably, NicA2 showed no activity against neurotransmitters oxidized by the two isoforms of human MAO. To further probe the substrate range of NicA2, enzyme activity was evaluated using a series of substrate analogs, indicating that S-nicotine is the optimal substrate and substitutions within the pyridyl ring abolish NicA2 activity. Moreover, mutagenesis and kinetic analysis of active-site residues reveal that removal of a hydrogen bond between the pyridyl ring of S-nicotine and the hydroxyl group of T381 has a 10-fold effect on KM, supporting the role of this bond in positioning the catalytically competent form of the substrate. Together, crystallography combined with kinetic analysis provide a deeper understanding of this enzyme's remarkable specificity.
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Pedroso, Humberto A; Silveira, Célia M; Almeida, Rui M; Almeida, Ana; Besson, Stéphane; Moura, Isabel; Moura, José J G; Almeida, M Gabriela
2016-09-01
Cytochrome cd1 nitrite reductases (cd1NiRs) catalyze the reduction of nitrite to nitric oxide in denitrifying bacteria, such as Marinobacter hydrocarbonoclasticus. Previous work demonstrated that the enzymatic activity depends on a structural pre-activation triggered by the entry of electrons through the electron transfer (ET) domain, which houses a heme c center. The catalytic activity of M. hydrocarbonoclasticus cd1NiR (Mhcd1NiR) was tested by mediated electrochemistry, using small ET proteins and chemical redox mediators. The rate of enzymatic reaction depends on the nature of the redox partner, with cytochrome (cyt) c552 providing the highest value. In situations where cyt c552 is replaced by either a biological (cyt c from horse heart) or a chemical mediator the catalytic response was only observed at very low scan rates, suggesting that the intermolecular ET rate is much slower. Molecular docking simulations with the 3D model structure of Mhcd1NiR and cyt c552 or cyt c showed that hydrophobic interactions favor the formation of complexes where the heme c domain of the enzyme is the principal docking site. However, only in the case of cyt c552 the preferential areas of contact and Fe-Fe distances between heme c groups of the redox partners allow establishing competent ET pathways. The coupling of the enzyme with chemical redox mediators was also found not to be energetically favorable. These results indicate that although low activity functional complexes can be formed between Mhcd1NiR and different types of redox mediators, efficient ET is only observed with the putative physiological electron donor cyt c552. Copyright © 2016 Elsevier B.V. All rights reserved.
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Blain-Hartung, Matthew D.; Rockwell, Nathan Clarke; Lagarias, J. Clark
2017-10-26
Here, phytochromes and cyanobacteriochromes (CBCRs) use double bond photoisomerization of their linear tetrapyrrole (bilin) chromophores within cGMP-specific phosphodiesterases/Adenylyl cyclases/FhlA (GAF) domain-containing photosensory modules to regulate activity of C-terminal output domains. CBCRs exhibit much more diverse photocycles than phytochromes, and are often found in large modular proteins such as Tlr0924 (SesA), one of three blue light regulators of cell aggregation in the cyanobacterium Thermosynechococcus elongatus. Tlr0924 contains a single bilin-binding GAF domain adjacent to a C-terminal diguanylate cyclase (GGDEF) domain whose catalytic activity requires formation of a dimeric transition state presumably supported by a multi-domain extension at its N-terminus. To probemore » the structural basis of light-mediated signal propagation from the photosensory input domain to a signaling output domain for a representative CBCR, these studies explore the properties of a bidomain GAF-GGDEF construct of Tlr0924 (Tlr0924Δ) that retains light-regulated diguanylate cyclase activity. Surprisingly, CD spectroscopy and size exclusion chromatography data do not support formation of stable dimers in the either the blue-absorbing 15ZP b dark state or the green-absorbing 15EP g photoproduct state of Tlr0924Δ. Analysis of variants containing site-specific mutations reveals that proper signal transmission requires both chromophorylation of the GAF domain and individual residues within the amphipathic linker region between GAF and GGDEF domains. Based on these data, we propose a model in which bilin binding and light signals are propagated from the GAF domain via the linker region to alter the equilibrium and interconversion dynamics between active and inactive conformations of the GGDEF domain to favor or disfavor formation of catalytic competent dimers.« less
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Carmo-Silva, A Elizabete; Salvucci, Michael E
2013-04-01
Rubisco's catalytic chaperone, Rubisco activase (Rca), uses the energy from ATP hydrolysis to restore catalytic competence to Rubisco. In Arabidopsis (Arabidopsis thaliana), inhibition of Rca activity by ADP is fine tuned by redox regulation of the α-isoform. To elucidate the mechanism for Rca regulation in species containing only the redox-insensitive β-isoform, the response of activity to ADP was characterized for different Rca forms. When assayed in leaf extracts, Rubisco activation was significantly inhibited by physiological ratios of ADP to ATP in species containing both α-Rca and β-Rca (Arabidopsis and camelina [Camelina sativa]) or just the β-Rca (tobacco [Nicotiana tabacum]). However, Rca activity was insensitive to ADP inhibition in an Arabidopsis transformant, rwt43, which expresses only Arabidopsis β-Rca, although not in a transformant of Arabidopsis that expresses a tobacco-like β-Rca. ATP hydrolysis by recombinant Arabidopsis β-Rca was much less sensitive to inhibition by ADP than recombinant tobacco β-Rca. Mutation of 17 amino acids in the tobacco β-Rca to the corresponding Arabidopsis residues reduced ADP sensitivity. In planta, Rubisco deactivated at low irradiance except in the Arabidopsis rwt43 transformant containing an ADP-insensitive Rca. Induction of CO2 assimilation after transition from low to high irradiance was much more rapid in the rwt43 transformant compared with plants containing ADP-sensitive Rca forms. The faster rate of photosynthetic induction and a greater enhancement of growth under a fluctuating light regime by the rwt43 transformant compared with wild-type Arabidopsis suggests that manipulation of Rca regulation might provide a strategy for enhancing photosynthetic performance in certain variable light environments.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Blain-Hartung, Matthew D.; Rockwell, Nathan Clarke; Lagarias, J. Clark
Here, phytochromes and cyanobacteriochromes (CBCRs) use double bond photoisomerization of their linear tetrapyrrole (bilin) chromophores within cGMP-specific phosphodiesterases/Adenylyl cyclases/FhlA (GAF) domain-containing photosensory modules to regulate activity of C-terminal output domains. CBCRs exhibit much more diverse photocycles than phytochromes, and are often found in large modular proteins such as Tlr0924 (SesA), one of three blue light regulators of cell aggregation in the cyanobacterium Thermosynechococcus elongatus. Tlr0924 contains a single bilin-binding GAF domain adjacent to a C-terminal diguanylate cyclase (GGDEF) domain whose catalytic activity requires formation of a dimeric transition state presumably supported by a multi-domain extension at its N-terminus. To probemore » the structural basis of light-mediated signal propagation from the photosensory input domain to a signaling output domain for a representative CBCR, these studies explore the properties of a bidomain GAF-GGDEF construct of Tlr0924 (Tlr0924Δ) that retains light-regulated diguanylate cyclase activity. Surprisingly, CD spectroscopy and size exclusion chromatography data do not support formation of stable dimers in the either the blue-absorbing 15ZP b dark state or the green-absorbing 15EP g photoproduct state of Tlr0924Δ. Analysis of variants containing site-specific mutations reveals that proper signal transmission requires both chromophorylation of the GAF domain and individual residues within the amphipathic linker region between GAF and GGDEF domains. Based on these data, we propose a model in which bilin binding and light signals are propagated from the GAF domain via the linker region to alter the equilibrium and interconversion dynamics between active and inactive conformations of the GGDEF domain to favor or disfavor formation of catalytic competent dimers.« less
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Lee, Si Woo; Hong, Jong Wook; Lee, Hyunhwa; Wi, Dae Han; Kim, Sun Mi; Han, Sang Woo; Park, Jeong Young
2018-06-14
The intrinsic correlation between an enhancement of catalytic activity and the flow of hot electrons generated at metal-oxide interfaces suggests an intriguing way to control catalytic reactions and is a significant subject in heterogeneous catalysis. Here, we show surface plasmon-induced catalytic enhancement by the peculiar nanocatalyst design of hexoctahedral (HOH) Au nanocrystals (NCs) with Cu2O clusters. We found that this inverse catalyst comprising a reactive oxide for the catalytic portion and a metal as the source of electrons by localized surface plasmon resonance (localized SPR) exhibits a change in catalytic activity by direct hot electron transfer or plasmon-induced resonance energy transfer (PIRET) when exposed to light. We prepared two types of inverse catalysts, Cu2O at the vertex sites of HOH Au NCs (Cu2O/Au vertex site) and a HOH Au NC-Cu2O core-shell structure (HOH Au@Cu2O), to test the structural effect on surface plasmons. Under broadband light illumination, the Cu2O/Au vertex site catalyst showed 30-90% higher catalytic activity and the HOH Au@Cu2O catalyst showed 10-30% higher catalytic activity than when in the dark. Embedding thin SiO2 layers between the HOH Au NCs and the Cu2O verified that the dominant mechanism for the catalytic enhancement is direct hot electron transfer from the HOH Au to the Cu2O. Finite-difference time domain calculations show that a much stronger electric field was formed on the vertex sites after growing the Cu2O on the HOH Au NCs. These results imply that the catalytic activity is enhanced when hot electrons, created from photon absorption on the HOH Au metal and amplified by the presence of surface plasmons, are transferred to the reactive Cu2O.
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Endrizzi, James A; Beernink, Peter T
2017-11-01
A classical model for allosteric regulation of enzyme activity posits an equilibrium between inactive and active conformations. An alternative view is that allosteric activation is achieved by increasing the potential for conformational changes that are essential for catalysis. In the present study, substitution of a basic residue in the active site of the catalytic (C) trimer of aspartate transcarbamoylase with a non-polar residue results in large interdomain hinge changes in the three chains of the trimer. One conformation is more open than the chains in both the wild-type C trimer and the catalytic chains in the holoenzyme, the second is closed similar to the bisubstrate-analog bound conformation and the third hinge angle is intermediate to the other two. The active-site 240s loop conformation is very different between the most open and closed chains, and is disordered in the third chain, as in the holoenzyme. We hypothesize that binding of anionic substrates may promote similar structural changes. Further, the ability of the three catalytic chains in the trimer to access the open and closed active-site conformations simultaneously suggests a cyclic catalytic mechanism, in which at least one of the chains is in an open conformation suitable for substrate binding whereas another chain is closed for catalytic turnover. Based on the many conformations observed for the chains in the isolated catalytic trimer to date, we propose that allosteric activation of the holoenzyme occurs by release of quaternary constraint into an ensemble of active-site conformations. © 2017 The Protein Society.
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Preparation of Cu@Cu₂O Nanocatalysts by Reduction of HKUST-1 for Oxidation Reaction of Catechol.
Jang, Seongwan; Yoon, Chohye; Lee, Jae Myung; Park, Sungkyun; Park, Kang Hyun
2016-11-02
HKUST-1, a copper-based metal organic framework (MOF), has been investigated as a catalyst in various reactions. However, the HKUST-1 shows low catalytic activity in the oxidation of catechol. Therefore, we synthesized Fe₃O₄@HKUST-1 by layer-by layer assembly strategy and Cu@Cu₂O by reduction of HKUST-1 for enhancement of catalytic activity. Cu@Cu₂O nanoparticles exhibited highly effective catalytic activity in oxidation of 3,5-di- tert -butylcatechol. Through this method, MOF can maintain the original core-shell structure and be used in various other reactions with enhanced catalytic activity.
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Kim, Sun Mi; Park, Dahee; Yuk, Youngji; Kim, Sang Hoon; Park, Jeong Young
2013-01-01
We report the hot carrier-driven catalytic activity of two-dimensional arrays of Pt nanoparticles on GaN substrate under light irradiation. In order to elucidate the effect of a hot carrier in a catalytic chemical reaction, the CO oxidation reaction was carried out on Pt nanoparticles on p- and n-type GaN under light irradiation. Metal catalysts composed of Pt nanoparticles were prepared using two different preparation methods: the one-pot polyol reduction and are plasma deposition methods. Under light irradiation, the catalytic activity of the Pt nanoparticles supported on GaN exhibited a distinct change depending on the doping type. The catalytic activity of the Pt nanoparticles on the n-doped GaN wafer decreased by 8-28% under light irradiation, compared to no irradiation (i.e., in the dark), while the Pt nanoparticles on the p-doped GaN wafer increased by 11-33% under light irradiation, compared to no irradiation. The catalytic activity increased on the smaller Pt nanoparticles, compared to the larger nanoparticles, presumably due to the mean free path of hot carriers. Based on these results, we conclude that the flow of hot carriers generated at the Pt-GaN interface during light irradiation is responsible for the change in catalytic activity on the Pt nanoparticles.
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Kim, J J; Kilani, A F; Zhan, X; Altman, S; Liu, F
1997-01-01
To study the effect proteins have on the catalysis and evolution of RNA enzymes, we simulated evolution of RNase P catalytic M1 RNA in vitro, in the presence and absence of its C5 protein cofactor. In the presence of C5, functional M1 sequence variants (not catalytically active in the absence of C5) were selected in addition to those identical to M1. C5 maintains the catalytically active structure of the variants and allows for an enhanced spectrum of M1 molecules to function in the context of a ribonucleoprotein (RNP) complex. The generation of an RNP enzyme, requiring both RNA and protein components, from a catalytically active RNA molecule has implications for how modern RNP complexes evolved from ancestral RNAs. PMID:9174096
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NASA Astrophysics Data System (ADS)
Song, Shaoqing; Wu, Xi; Lu, Changhai; Wen, Meicheng; Le, Zhanggao; Jiang, Shujuan
2018-06-01
Solid strong base nano-catalytic system of K-modification NaY zeolite supported 0.08% Pt (K-Pt/NaY) were constructed for eliminating HCHO at room temperature. In the catalytic process, activation energy over K-Pt/NaY nano-catalytic system was greatly decreased along with the enhanced reaction rate. Characterization and catalytic tests revealed the surface electron structure of K-Pt/NaY was improved, as reflected by the enhanced HCHO adsorption capability, high sbnd OH concentration, and low-temperature reducibility. Therefore, the optimal K-Pt/NaY showed high catalytic efficiency and strong H2O tolerance for HCHO elimination by directly promoting the reaction between active sbnd OH and formate species. These results may suggest a new way for probing the advanced solid strong base nano-catalytic system for the catalytic elimination of indoor HCHO.
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Mussel-Inspired Polydopamine Functionalized Plasmonic Nanocomposites for Single-Particle Catalysis.
Wang, Jun-Gang; Hua, Xin; Li, Meng; Long, Yi-Tao
2017-01-25
Polydopamine functionalized plasmonic nanocomposites with well-distributed catalytically active small gold nanoislands around large gold core were fabricated without using any chemical reductant or surfactant. The optical properties, surface molecular structures, and ensemble catalytic activity of the gold nanocomposites were investigated by time-of-flight secondary ion mass spectrometry and UV-vis spectroscopy, respectively. Moreover, the considerable catalytic activity of the nanocomposites toward 4-nitrophenol reduction was real time monitored by dark-field spectroscopy techniques at the single-nanoparticle level avoiding averaging effects in bulk systems. According to the obtained plasmonic signals from individual nanocomposites, the electron charging and discharging rates for these nanocomposites during the catalytic process were calculated. Our results offer new insights into the design and synthesis of plasmonic nanocomposites for future catalytic applications as well as a further mechanistic understanding of the electron transfer during the catalytic process at the single-nanoparticle level.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Xiao, Xiao; Yang, Hanjing; Arutiunian, Vagan
The catalytic activity of human cytidine deaminase APOBEC3B (A3B) has been correlated with kataegic mutational patterns within multiple cancer types. The molecular basis of how the N-terminal non-catalytic CD1 regulates the catalytic activity and consequently, biological function of A3B remains relatively unknown. Here, we report the crystal structure of a soluble human A3B-CD1 variant and delineate several structural elements of CD1 involved in molecular assembly, nucleic acid interactions and catalytic regulation of A3B. We show that (i) A3B expressed in human cells exists in hypoactive high-molecular-weight (HMW) complexes, which can be activated without apparent dissociation into low-molecular-weight (LMW) species aftermore » RNase A treatment. (ii) Multiple surface hydrophobic residues of CD1 mediate the HMW complex assembly and affect the catalytic activity, including one tryptophan residue W127 that likely acts through regulating nucleic acid binding. (iii) One of the highly positively charged surfaces on CD1 is involved in RNA-dependent attenuation of A3B catalysis. (iv) Surface hydrophobic residues of CD1 are involved in heterogeneous nuclear ribonucleoproteins (hnRNPs) binding to A3B. The structural and biochemical insights described here suggest that unique structural features on CD1 regulate the molecular assembly and catalytic activity of A3B through distinct mechanisms.« less
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Zheng, Xingqun; Peng, Lishan; Yang, Na; Yang, Yanjun; Li, Jing; Wang, Jianchuan
2018-01-01
The transition-metal compounds (MX) have gained wide attention as hydrogen evolution reaction (HER) electrocatalysts; however, the interaction between the non-metallic atom (X) and the metal atom (M) in MX, and the role of X in the enhanced catalytic activity of MX, are still ambiguous. In this work, we constructed a simple model [X/Ni(100)] to decipher the contribution of X towards enhancing the catalytic activity of NiX, which allows us to accurately predict the trend in HER catalytic activity of NiX based on the easily accessible physico-chemical characteristics of X. Theoretical calculations showed that the electronegativity (χX) and the principle quantum number (nX) of X are two important descriptors for evaluating and predicting the HER catalytic activity of NiX catalysts effectively. X atoms in the VIA group can enhance the HER activity of X/Ni(100) more significantly than those in the second period due to the large χX or nX. At a relatively low X coverage, the S/Ni(100) possesses the best HER activity among all of the discussed X/Ni(100) models, and the optimum surface S : Ni atomic ratio is about 22–33%. Further experiments demonstrated that the Ni–Ni3S2 catalyst with a surface S : Ni atomic ratio of 28.9% exhibits the best catalytic activity and lowest charge transfer resistance. The trend in catalytic activity of NiX with differing X offers a new possible strategy to exploit MX materials and design new active catalysts rationally. PMID:29675227
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Ebselen: Mechanisms of Glutamate Dehydrogenase and Glutaminase Enzyme Inhibition.
Yu, Yan; Jin, Yanhong; Zhou, Jie; Ruan, Haoqiang; Zhao, Han; Lu, Shiying; Zhang, Yue; Li, Di; Ji, Xiaoyun; Ruan, Benfang Helen
2017-12-15
Ebselen modulates target proteins through redox reactions with selenocysteine/cysteine residues, or through binding to the zinc finger domains. However, a recent contradiction in ebselen inhibition of kidney type glutaminase (KGA) stimulated our interest in investigating its inhibition mechanism with glutamate dehydrogenase (GDH), KGA, thioredoxin reductase (TrxR), and glutathione S-transferase. Fluorescein- or biotin-labeled ebselen derivatives were synthesized for mechanistic analyses. Biomolecular interaction analyses showed that only GDH, KGA, and TrxR proteins can bind to the ebselen derivative, and the binding to GDH and KGA could be competed off by glutamine or glutamate. From the gel shift assays, the fluorescein-labeled ebselen derivative could co-migrate with hexameric GDH and monomeric/dimeric TrxR in a dose-dependent manner; it also co-migrated with KGA but disrupted the tetrameric form of the KGA enzyme at a high compound concentration. Further proteomic analysis demonstrated that the ebselen derivative could cross-link with proteins through a specific cysteine at the active site of GDH and TrxR proteins, but for KGA protein, the binding site is at the N-terminal appendix domain outside of the catalytic domain, which might explain why ebselen is not a potent KGA enzyme inhibitor in functional assays. In conclusion, ebselen could inhibit enzyme activity by binding to the catalytic domain or disruption of the protein complex. In addition, ebselen is a relatively potent selective GDH inhibitor that might provide potential therapeutic opportunities for hyperinsulinism-hyperammonemia syndrome patients who have the mutational loss of GTP inhibition.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Wang, Tianyu; University of Chinese Academy of Sciences, Beijing 100049; Ding, Jinjing
The structure of the Tse3–Tsi3 complex associated with the bacterial type VI secretion system of P. aeruginosa has been solved and refined at 1.9 Å resolution. The structural basis of the recognition of the muramidase effector and its inactivation by its cognate immunity protein is revealed. The type VI secretion system (T6SS) is a bacterial protein-export machine that is capable of delivering virulence effectors between Gram-negative bacteria. The T6SS of Pseudomonas aeruginosa transports two lytic enzymes, Tse1 and Tse3, to degrade cell-wall peptidoglycan in the periplasm of rival bacteria that are competing for niches via amidase and muramidase activities, respectively.more » Two cognate immunity proteins, Tsi1 and Tsi3, are produced by the bacterium to inactivate the two antibacterial effectors, thereby protecting its siblings from self-intoxication. Recently, Tse1–Tsi1 has been structurally characterized. Here, the structure of the Tse3–Tsi3 complex is reported at 1.9 Å resolution. The results reveal that Tse3 contains a C-terminal catalytic domain that adopts a soluble lytic transglycosylase (SLT) fold in which three calcium-binding sites were surprisingly observed close to the catalytic Glu residue. The electrostatic properties of the substrate-binding groove are also distinctive from those of known structures with a similar fold. All of these features imply that a unique catalytic mechanism is utilized by Tse3 in cleaving glycosidic bonds. Tsi3 comprises a single domain showing a β-sandwich architecture that is reminiscent of the immunoglobulin fold. Three loops of Tsi3 insert deeply into the groove of Tse3 and completely occlude its active site, which forms the structural basis of Tse3 inactivation. This work is the first crystallographic report describing the three-dimensional structure of the Tse3–Tsi3 effector–immunity pair.« less
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The Structural Basis of Oncogenic Mutations G12, G13 and Q61 in Small GTPase K-Ras4B
NASA Astrophysics Data System (ADS)
Lu, Shaoyong; Jang, Hyunbum; Nussinov, Ruth; Zhang, Jian
2016-02-01
Ras mediates cell proliferation, survival and differentiation. Mutations in K-Ras4B are predominant at residues G12, G13 and Q61. Even though all impair GAP-assisted GTP → GDP hydrolysis, the mutation frequencies of K-Ras4B in human cancers vary. Here we aim to figure out their mechanisms and differential oncogenicity. In total, we performed 6.4 μs molecular dynamics simulations on the wild-type K-Ras4B (K-Ras4BWT-GTP/GDP) catalytic domain, the K-Ras4BWT-GTP-GAP complex, and the mutants (K-Ras4BG12C/G12D/G12V-GTP/GDP, K-Ras4BG13D-GTP/GDP, K-Ras4BQ61H-GTP/GDP) and their complexes with GAP. In addition, we simulated ‘exchanged’ nucleotide states. These comprehensive simulations reveal that in solution K-Ras4BWT-GTP exists in two, active and inactive, conformations. Oncogenic mutations differentially elicit an inactive-to-active conformational transition in K-Ras4B-GTP; in K-Ras4BG12C/G12D-GDP they expose the bound nucleotide which facilitates the GDP-to-GTP exchange. These mechanisms may help elucidate the differential mutational statistics in K-Ras4B-driven cancers. Exchanged nucleotide simulations reveal that the conformational transition is more accessible in the GTP-to-GDP than in the GDP-to-GTP exchange. Importantly, GAP not only donates its R789 arginine finger, but stabilizes the catalytically-competent conformation and pre-organizes catalytic residue Q61; mutations disturb the R789/Q61 organization, impairing GAP-mediated GTP hydrolysis. Together, our simulations help provide a mechanistic explanation of key mutational events in one of the most oncogenic proteins in cancer.
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Liu, Hu; Yu, Yongsheng; Yang, Weiwei; Lei, Wenjuan; Gao, Manyi; Guo, Shaojun
2017-07-13
Controlling the surface defects of nanocrystals is a new way of tuning/boosting their catalytic properties. Herein, we report networked PdAg nanowires (NWs) with high-density defects as catalytic hot spots for efficient catalytic dehydrogenation of formic acid (FA) and catalytic reduction of nitrates. The networked PdAg NWs exhibit composition-dependent catalytic activity for the dehydrogenation reaction of FA without any additive, with Pd 5 Ag 5 NWs exhibiting the highest activity. They also show good durability, reflected by the retention of their initial activity during the dehydrogenation reaction of FA even after five cycles. Their initial TOF is 419 h -1 at 60 °C in water solution, much higher than those of the most Pd-based catalysts with a support. Moreover, they can efficiently reduce nitrates to alleviate nitrate pollution in water (conversion yield >99%). This strategy opens up a new green synthetic technique to design support-free heterogeneous catalysts with high-density defects as catalytic hot spots for efficient dehydrogenation catalysis of FA to meet the requirement of fuel cell applications and catalytic reduction of nitrates in water polluted with nitrates.
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NASA Astrophysics Data System (ADS)
Nugrahaningtyas, K. D.; Suharbiansah, R. S. R.; Rahmawati, F.
2018-03-01
This research aims to prepare, characterize, and study the catalytic activity of Molybdenum (Mo) and Cobalt (Co) metal with supporting material Ultra Stable Y-Zeolite (USY), to produce catalysts with activity in hydrotreatment reaction and in order to eliminate impurities compounds that containing unwanted groups heteroatoms. The bimetallic catalysts MoCo/USY were prepared by wet impregnation method with weight variation of Co metal 0%, 2%, 4%, 6%, 8%, and Mo metal 8% (w/w), respectively. Activation method of the catalyst included calcination, oxidation, reduction and the crystallinity was characterized using X-ray diffraction (XRD), the acidity of the catalyst was analyzed using Fourier Transform Infrared Spectroscopy (FT-IR) and gravimetry method, minerals present in the catalyst was analyzed using X-Ray Fluorescence (XRF), and surface of the catalyst was analyzed using Surface Area Analyzer (SAA). Catalytic activity test (benzene yield product) of MoCo/USY on hydrodeoxigenation reaction of anisole aimed to determine the effect of Mo-Co/USY for catalytic activity in the reaction hydrodeoxigenation (HDO) anisole. Based on characterization and test of catalytic activity, it is known that catalytic of MoCo/USY 2% (catalyst B) shows best activities with acidity of 10.209 mmol/g, specific area of catalyst of 426.295 m2/g, pore average of 14.135 Å, total pore volume 0.318 cc/g, and total yield of HDO products 6.06%.
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Gas phase heterogeneous catalytic oxidation of alkanes to aliphatic ketones and/or other oxygenates
DOE Office of Scientific and Technical Information (OSTI.GOV)
Lin, Manhua; Wang, Xiang; Yeom, Younghoon
A catalyst, its method of preparation and its use for producing aliphatic ketones by subjecting alkanes C.sub.3 to C.sub.9 to a gas phase catalytic oxidation in the presence of air or oxygen, and, optionally, steam and/or one or more diluting gases. The catalyst comprises a catalytically active mixed metal oxide phase and a suitable support material onto and/or into which the active catalytic phase id dispersed.
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Gas phase heterogeneous catalytic oxidation of alkanes to aliphatic ketones and/or other oxygenates
DOE Office of Scientific and Technical Information (OSTI.GOV)
Lin, Manhua; Wang, Xiang; Yeom, Younghoon
A catalyst, its method of preparation and its use for producing aliphatic ketones by subjecting alkanes C.sub.3 to C.sub.9 to a gas phase catalytic oxidation in the presence of air or oxygen, and, optionally, steam and/or one or more diluting gases. The catalyst comprises a catalytically active mixed metal oxide phase and a suitable support material onto and/or into which the active catalytic phase is dispersed.
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Wójcik, T; Kieć-Kononowicz, K
2008-01-01
Catalytic activity of certain antibodies was proposed by Linus Pauling for the very first time more than six decades ago. Since then few examples of catalytic antibodies (abzymes) were found in human organism. From late 80's many synthetic abzymes were obtained after immunization by Transition State Analogs (TSA). Another approach is based on functional mimicry of antibody to an active site of an enzyme. Detection of an abzymatic activity requires special immunoassays. This unique strategy can be employed for new methods of drug synthesis, as well as for in vivo therapies. Catalytic antibodies seem to be a promising tool for therapeutic purposes, because of their specifity and stereoselectivity.
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Bajaj, Sonal; Nayak, Arpan Kumar; Pradhan, Debabrata; Tekade, Pradip
2017-01-01
We report enhanced catalytic activity of CuO nanopetals synthesized by microwave-assisted wet chemical synthesis. The catalytic reaction of CuO nanopetals and H2O2 was studied with the application of external light source and also under dark conditions for the degradation of the hazardous dye methylene blue. The CuO nanopetals showed significant catalytic activity for the fast degradation of methylene blue and rhodamine B (RhB) under dark conditions, without the application of an external light source. This increased catalytic activity was attributed to the co-operative role of H2O2 and the large specific surface area (≈40 m2·g−1) of the nanopetals. We propose a detail mechanism for this fast degradation. A separate study of the effect of different H2O2 concentrations for the degradation of methylene blue under dark conditions is also illustrated. PMID:28685117
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Preparation of PdCu Alloy Nanocatalysts for Nitrate Hydrogenation and Carbon Monoxide Oxidation
Cai, Fan; Yang, Lefu; Shan, Shiyao; ...
2016-06-30
Alloying Pd with Cu is important for catalytic reactions such as denitrification reaction and CO oxidation reaction, but understanding of the catalyst preparation and its correlation with the catalyst’s activity and selectivity remains elusive. Herein, we report the results of investigations of the preparation of PdCu alloy nanocatalysts using different methods and the catalytic properties of the catalysts in catalytic denitrification reaction and CO oxidation reaction. PdCu alloy nanocatalysts were prepared by conventional dry impregnation method and ligand-capping based wet chemical synthesis method, and subsequent thermochemical activation as well. The alloying characteristics depend on the bimetallic composition. PdCu/Al 2O 3more » with a Pd/Cu ratio of 50:50 was shown to exhibit an optimized hydrogenation activity for the catalytic denitrification reaction. The catalytic activity of the PdCu catalysts was shown to be highly dependent on the support, as evidenced by the observation of an enhanced catalytic activity for CO oxidation reaction using TiO 2 and CeO 2 supports with high oxygen storage capacity. Lastly, we discussed the implications of the results to the refinement of the preparation of the alloy nanocatalysts.« less
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Aligned carbon nanotube with electro-catalytic activity for oxygen reduction reaction
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.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Meemken, Fabian; Müller, Philipp; Hungerbühler, Konrad
Design and performance of a reactor set-up for attenuated total reflection infrared (ATR-IR) spectroscopy suitable for simultaneous reaction monitoring of bulk liquid and catalytic solid-liquid-gas interfaces under working conditions are presented. As advancement of in situ spectroscopy an operando methodology for gas-liquid-solid reaction monitoring was developed that simultaneously combines catalytic activity and molecular level detection at the catalytically active site of the same sample. Semi-batch reactor conditions are achieved with the analytical set-up by implementing the ATR-IR flow-through cell in a recycle reactor system and integrating a specifically designed gas feeding system coupled with a bubble trap. By the usemore » of only one spectrometer the design of the new ATR-IR reactor cell allows for simultaneous detection of the bulk liquid and the catalytic interface during the working reaction. Holding two internal reflection elements (IRE) the sample compartments of the horizontally movable cell are consecutively flushed with reaction solution and pneumatically actuated, rapid switching of the cell (<1 s) enables to quasi simultaneously follow the heterogeneously catalysed reaction at the catalytic interface on a catalyst-coated IRE and in the bulk liquid on a blank IRE. For a complex heterogeneous reaction, the asymmetric hydrogenation of 2,2,2-trifluoroacetophenone on chirally modified Pt catalyst the elucidation of catalytic activity/enantioselectivity coupled with simultaneous monitoring of the catalytic solid-liquid-gas interface is shown. Both catalytic activity and enantioselectivity are strongly dependent on the experimental conditions. The opportunity to gain improved understanding by coupling measurements of catalytic performance and spectroscopic detection is presented. In addition, the applicability of modulation excitation spectroscopy and phase-sensitive detection are demonstrated.« less
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Structure and folding of the Tetrahymena telomerase RNA pseudoknot
Cash, Darian D.; Feigon, Juli
2016-11-28
Telomerase maintains telomere length at the ends of linear chromosomes using an integral telomerase RNA (TER) and telomerase reverse transcriptase (TERT). An essential part of TER is the template/pseudoknot domain (t/PK) which includes the template, for adding telomeric repeats, template boundary element (TBE), and pseudoknot, enclosed in a circle by stem 1. The Tetrahymena telomerase holoenzyme catalytic core (p65-TER-TERT) was recently modeled in our 9 Å resolution cryo-electron microscopy map by fitting protein and TER domains, including a solution NMR structure of the Tetrahymena pseudoknot. Here, we describe in detail the structure and folding of the isolated pseudoknot, which formsmore » a compact structure with major groove U•A-U and novel C•G-A + base triples. Base substitutions that disrupt the base triples reduce telomerase activity in vitro. NMR studies also reveal that the pseudoknot does not form in the context of full-length TER in the absence of TERT, due to formation of a competing structure that sequesters pseudoknot residues. The residues around the TBE remain unpaired, potentially providing access by TERT to this high affinity binding site during an early step in TERT-TER assembly. A model for the assembly pathway of the catalytic core is proposed.« less
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Structure and folding of the Tetrahymena telomerase RNA pseudoknot
DOE Office of Scientific and Technical Information (OSTI.GOV)
Cash, Darian D.; Feigon, Juli
Telomerase maintains telomere length at the ends of linear chromosomes using an integral telomerase RNA (TER) and telomerase reverse transcriptase (TERT). An essential part of TER is the template/pseudoknot domain (t/PK) which includes the template, for adding telomeric repeats, template boundary element (TBE), and pseudoknot, enclosed in a circle by stem 1. The Tetrahymena telomerase holoenzyme catalytic core (p65-TER-TERT) was recently modeled in our 9 Å resolution cryo-electron microscopy map by fitting protein and TER domains, including a solution NMR structure of the Tetrahymena pseudoknot. Here, we describe in detail the structure and folding of the isolated pseudoknot, which formsmore » a compact structure with major groove U•A-U and novel C•G-A + base triples. Base substitutions that disrupt the base triples reduce telomerase activity in vitro. NMR studies also reveal that the pseudoknot does not form in the context of full-length TER in the absence of TERT, due to formation of a competing structure that sequesters pseudoknot residues. The residues around the TBE remain unpaired, potentially providing access by TERT to this high affinity binding site during an early step in TERT-TER assembly. A model for the assembly pathway of the catalytic core is proposed.« less
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Wu, Chang-Hsun; Lin, Jyun-Ting; Lin, Kun-Yi Andrew
2018-05-01
Direct carbonization of cobalt complexes represents as a convenient approach to prepare magnetic carbon/cobalt nanocomposites (MCCNs) as heterogeneous environmental catalysts. However, most of MCCNs derived from consist of sheet-like carbon matrices with very sparse cobaltic nanoparticles (NPs), making them exhibit relatively low catalytic activities, porosity and magnetism. In this study, dipicolinic acid (DPA) is selected to prepare a 3-dimensional cobalt coordination polymer (CoDPA). MCCN derived from CoDPA can consist of a porous carbon matrix embedded with highly-dense Co 0 and Co 3 O 4 NPs. This magnetic Co 0 /Co 3 O 4 NP-anchored carbon composite (MCNC) appears as a promising heterogeneous catalyst for oxidative and reductive environmental catalytic reactions. As peroxymonosulfate (PMS) activation is selected as a model catalytic oxidative reaction, MCNC exhibits a much higher catalytic activity than Co 3 O 4 , a benchmark catalyst for PMS activation. The reductive catalytic activity of MCNC is demonstrated through 4-nitrophenol (4-NP) reduction in the presence of NaBH 4 . MCNC could rapidly react with NaBH 4 to generate H 2 for hydrogenation of 4-NP to 4-aminophenol (4-AP). In comparison with other precious metallic catalysts, MCNC also shows a relatively high catalytic activity. These results indicate that MCNC is a conveniently prepared and highly effective and stable carbon-supported cobaltic heterogeneous catalyst for versatile environmental catalytic applications. Copyright © 2018 Elsevier Inc. All rights reserved.
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NASA Astrophysics Data System (ADS)
Yu, Jie; He, Dedong; Chen, Dingkai; Liu, Jiangping; Lu, Jichang; Liu, Feng; Liu, Pan; Zhao, Yutong; Xu, Zhizhi; Luo, Yongming
2017-10-01
Na-modified HZSM-5 catalysts with different Na loading amounts were prepared by incipient-wetness impregnation method and their catalytic activities for methyl mercaptan catalytic elimination were analyzed. XRD, N2 adsorption-desorption, NH3-TPD, CO2-TPD and FT-IR measurements were carried out to investigate the effects of modification of alkali metal Na on the physicochemical properties of the HZSM-5 zeolite catalyst. Research results illustrated that the introduction of alkali metal Na can improve catalytic activity for CH3SH catalytic elimination. CH3SH can be almost completely converted over 3%-Na/HZSM-5 at 450 °C compared to pure HZSM-5 at 600 °C based on our experimental results and the results from previous research. The improved catalytic activity could be attributed to the regulated acid-base properties of the HZSM-5 catalysts by doping with alkali metal Na. High alkali concentration treatment, however, may destroy the framework structure of the catalyst sample, thus causing the poor stability performance of the obtained catalyst.
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Dong, Minghui; Liu, Haiyan
2008-08-21
The Escherichia coli peptide deformylase (PDF) and Bacillus thermoproteolyticus thermolysin (TLN) are two representative metal-requiring peptidases having remarkably similar active centers but distinctively different metal preferences. Zinc is a competent catalytic cofactor for TLN but not for PDF. Reaction pathways and the associated energetics for both enzymes were determined using combined semiempirical and ab initio quantum mechanical/molecular mechanical modeling, without presuming reaction coordinates. The results confirmed that both enzymes catalyze via the same chemical steps, and reproduced their different preferences for zinc or iron as competent cofactors. Further analyses indicated that different feasibility of the nucleophilic attack step leads to different metal preferences of the two enzymes. In TLN, the substrate is strongly activated and can serve as the fifth coordination ligand of zinc prior to the chemical steps. In PDF, the substrate carbonyl is activated by the chemical step itself, and becomes the fifth coordination partner of zinc only in a later stage of the nucleophilic attack. These leads to a much more difficult nucleophilic attack in PDF than in TLN. Different from some earlier suggestions, zinc has no difficulty in accepting an activated substrate as the fifth ligand to switch from tetra- to penta-coordination in either PDF or TLN. When iron replaces zinc, its stronger interaction with the hydroxide ligand may lead to higher activation barrier in TLN. In PDF, the stronger interactions of iron with ligands allow iron-substrate coordination to take place either before or at a very early stage of the chemical step, leading to effective catalysis. Our calculations also show combined semiempirical and ab initio quantum mechanical modeling can be efficient approaches to explore complicated reaction pathways in enzyme systems.
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Brown, Eric L; Nishiyama, Yasuhiro; Dunkle, Jesse W; Aggarwal, Shreya; Planque, Stephanie; Watanabe, Kenji; Csencsits-Smith, Keri; Bowden, M Gabriela; Kaplan, Sheldon L; Paul, Sudhir
2012-03-23
Antibodies that recognize microbial B lymphocyte superantigenic epitopes are produced constitutively with no requirement for adaptive immune maturation. We report cleavage of the Staphylococcus aureus virulence factor extracellular fibrinogen-binding protein (Efb) by catalytic antibodies produced with no exposure to the bacterium and reduction of the catalytic antibody activity following infection. IgG catalytic antibodies that specifically hydrolyzed Efb via a nucleophilic catalytic mechanism were found in the blood of healthy humans and aseptic mice free of S. aureus infection. IgG hydrolyzed peptide bonds on the C-terminal side of basic amino acids, including a bond located within the C3b-binding domain of Efb. Efb digested with the IgG lost its ability to bind C3b and inhibit complement-dependent antibody-mediated red blood cell lysis. In addition to catalysis, the IgG expressed saturable Efb binding activity. IgG from S. aureus-infected mice displayed reduced Efb cleaving activity and increased Efb binding activity compared with uninfected controls, suggesting differing effects of the infection on the antibody subsets responsible for the two activities. IgG from children hospitalized for S. aureus infection also displayed reduced Efb cleavage compared with healthy children. These data suggest a potential defense function for constitutively produced catalytic antibodies to a putative superantigenic site of Efb, but an adaptive catalytic response appears to be proscribed.
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Tang, Shoufeng; Yuan, Deling; Zhang, Qi; Liu, Yameng; Zhang, Qi; Liu, Zhengquan; Huang, Haiming
2016-09-01
A Fe-Mn bi-metallic oxide supported on granular activated carbon (Fe-Mn GAC) has been fabricated by an impregnation-desiccation method and tested in the catalytic ozonation of methyl orange (MO) degradation and mineralization. X-ray diffraction, scanning electron microscopy, and Fourier transform infrared spectroscopy characterizations revealed that Fe-Mn oxides were successfully loaded and uniformly distributed on the GAC, and nitrogen adsorption isotherms showed that the supported GAC retained a large surface area and a high pore volume compared with the pristine GAC. The catalytic activity was systematically assessed by monitoring the MO removal efficiencies at different operational parameters, such as catalyst dosage, initial solution pH, and ozone flow rate. The Fe-Mn GAC exhibited better catalytic activity relative to ozone alone and GAC alone, improving the TOC removal by 24.5 and 11.5 % and COD removal by 13.6 and 7.3 %, respectively. The reusability of the hybrid was examined over five consecutive cyclic treatments. The Fe-Mn GAC catalytic activity was only a slight loss in the cycles, showing good stability. The addition of Na2CO3 as hydroxyl radicals (•OH) scavengers proved that the catalytic ozonation mechanism was the enhanced generation of •OH by the Fe-Mn GAC. The above results render the Fe-Mn GAC an industrially promising candidate for catalytic ozonation of dye contaminant removal.
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Thomas, Joice; Dong, Zeyuan; Dehaen, Wim; Smet, Mario
2012-12-21
A series of novel hyperbranched polyselenides and polytellurides with multiple catalytic sites at the branching units has been synthesized via the polycondensation of A2 + B3 monomers. The GPx-like activities of these polymer mimics were assessed and it was found that the polytellurides showed higher GPx-like activities than the corresponding polyselenides. Interestingly, the polymers with higher molecular weights and degree of branching (DB) showed higher GPx-like activities than the analogous lower molecular weight polymer. The enhancement in the catalytical activity of the hyperbranched polymers with increasing molecular weight affirmed the importance of the incorporation of multiple catalytic groups in the macromolecule which increases the local concentration of catalytic sites. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
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Perovskite-type catalytic materials for environmental applications.
Labhasetwar, Nitin; Saravanan, Govindachetty; Kumar Megarajan, Suresh; Manwar, Nilesh; Khobragade, Rohini; Doggali, Pradeep; Grasset, Fabien
2015-06-01
Perovskites are mixed-metal oxides that are attracting much scientific and application interest owing to their low price, adaptability, and thermal stability, which often depend on bulk and surface characteristics. These materials have been extensively explored for their catalytic, electrical, magnetic, and optical properties. They are promising candidates for the photocatalytic splitting of water and have also been extensively studied for environmental catalysis applications. Oxygen and cation non-stoichiometry can be tailored in a large number of perovskite compositions to achieve the desired catalytic activity, including multifunctional catalytic properties. Despite the extensive uses, the commercial success for this class of perovskite-based catalytic materials has not been achieved for vehicle exhaust emission control or for many other environmental applications. With recent advances in synthesis techniques, including the preparation of supported perovskites, and increasing understanding of promoted substitute perovskite-type materials, there is a growing interest in applied studies of perovskite-type catalytic materials. We have studied a number of perovskites based on Co, Mn, Ru, and Fe and their substituted compositions for their catalytic activity in terms of diesel soot oxidation, three-way catalysis, N 2 O decomposition, low-temperature CO oxidation, oxidation of volatile organic compounds, etc. The enhanced catalytic activity of these materials is attributed mainly to their altered redox properties, the promotional effect of co-ions, and the increased exposure of catalytically active transition metals in certain preparations. The recent lowering of sulfur content in fuel and concerns over the cost and availability of precious metals are responsible for renewed interest in perovskite-type catalysts for environmental applications.
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Perovskite-type catalytic materials for environmental applications
Labhasetwar, Nitin; Saravanan, Govindachetty; Kumar Megarajan, Suresh; Manwar, Nilesh; Khobragade, Rohini; Doggali, Pradeep; Grasset, Fabien
2015-01-01
Perovskites are mixed-metal oxides that are attracting much scientific and application interest owing to their low price, adaptability, and thermal stability, which often depend on bulk and surface characteristics. These materials have been extensively explored for their catalytic, electrical, magnetic, and optical properties. They are promising candidates for the photocatalytic splitting of water and have also been extensively studied for environmental catalysis applications. Oxygen and cation non-stoichiometry can be tailored in a large number of perovskite compositions to achieve the desired catalytic activity, including multifunctional catalytic properties. Despite the extensive uses, the commercial success for this class of perovskite-based catalytic materials has not been achieved for vehicle exhaust emission control or for many other environmental applications. With recent advances in synthesis techniques, including the preparation of supported perovskites, and increasing understanding of promoted substitute perovskite-type materials, there is a growing interest in applied studies of perovskite-type catalytic materials. We have studied a number of perovskites based on Co, Mn, Ru, and Fe and their substituted compositions for their catalytic activity in terms of diesel soot oxidation, three-way catalysis, N2O decomposition, low-temperature CO oxidation, oxidation of volatile organic compounds, etc. The enhanced catalytic activity of these materials is attributed mainly to their altered redox properties, the promotional effect of co-ions, and the increased exposure of catalytically active transition metals in certain preparations. The recent lowering of sulfur content in fuel and concerns over the cost and availability of precious metals are responsible for renewed interest in perovskite-type catalysts for environmental applications. PMID:27877813
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Charge Transfer and Catalysis at the Metal Support Interface
DOE Office of Scientific and Technical Information (OSTI.GOV)
Baker, Lawrence Robert
Kinetic, electronic, and spectroscopic characterization of model Pt–support systems are used to demonstrate the relationship between charge transfer and catalytic activity and selectivity. The results show that charge flow controls the activity and selectivity of supported metal catalysts. This dissertation builds on extensive existing knowledge of metal–support interactions in heterogeneous catalysis. The results show the prominent role of charge transfer at catalytic interfaces to determine catalytic activity and selectivity. Further, this research demonstrates the possibility of selectively driving catalytic chemistry by controlling charge flow and presents solid-state devices and doped supports as novel methods for obtaining electronic control over catalyticmore » reaction kinetics.« less
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Polypeptides having xylanase activity and polynucleotides encoding same
DOE Office of Scientific and Technical Information (OSTI.GOV)
Spodsberg, Nikolaj; Shaghasi, Tarana
The present invention relates to polypeptides having xylanase activity, catalytic domains, and carbohydrate binding domains, and polynucleotides encoding the polypeptides, catalytic domains, and carbohydrate binding domains. The present invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides, catalytic domains, and carbohydrate binding domains.
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Polypeptides having endoglucanase activity and polynucleotides encoding same
DOE Office of Scientific and Technical Information (OSTI.GOV)
Spodsberg, Nikolaj; Shagasi, Tarana
The present invention relates to isolated polypeptides having endoglucanase activity, catalytic domains, cellulose binding domains and polynucleotides encoding the polypeptides, catalytic domains or cellulose binding domains. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides, catalytic domains or cellulose binding domains.
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Polypeptides having endoglucanase activity and polynucleotides encoding same
Spodsberg, Nikolaj; Shagasi, Tarana
2015-06-30
The present invention relates to isolated polypeptides having endoglucanase activity, catalytic domains, cellulose binding domains and polynucleotides encoding the polypeptides, catalytic domains or cellulose binding domains. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides, catalytic domains or cellulose binding domains.
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Polypeptides having cellobiohydrolase activity and polynucleotides encoding same
DOE Office of Scientific and Technical Information (OSTI.GOV)
Stringer, Mary Ann; McBrayer, Brett
2016-11-29
The present invention relates to isolated polypeptides having cellobiohydrolase activity, catalytic domains, and cellulose binding domains and polynucleotides encoding the polypeptides, catalytic domains, and cellulose binding domains. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides, catalytic domains, or cellulose binding domains.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Kamiguchi, Satoshi, E-mail: kamigu@riken.jp; Organometallic Chemistry Laboratory, RIKEN, 2-1 Hirosawa, Wako City, Saitama 351-0198; Okumura, Kazu
Graphical abstract: - Highlights: • Solid-state molybdenum sulfide clusters catalyzed the dehydrogenation of alcohol. • The dehydrogenation proceeded without the addition of any oxidants. • The catalytic activity developed when the cluster was activated at 300–500 °C in H{sub 2}. • The Lewis-acidic molybdenum atom and basic sulfur ligand were catalytically active. • The clusters function as bifunctional acid–base catalysts. - Abstract: Solid-state molybdenum sulfide clusters with an octahedral metal framework, the superconducting Chevrel phases, are applied to catalysis. A copper salt of a nonstoichiometric sulfur-deficient cluster, Cu{sub x}Mo{sub 6}S{sub 8–δ} (x = 2.94 and δ ≈ 0.3), is storedmore » in air for more than 90 days. When the oxygenated cluster is thermally activated in a hydrogen stream above 300 °C, catalytic activity for the dehydrogenation of primary alcohols to aldehydes and secondary alcohols to ketones develops. The addition of pyridine or benzoic acid decreases the dehydrogenation activity, indicating that both a Lewis-acidic coordinatively unsaturated molybdenum atom and a basic sulfur ligand synergistically act as the catalytic active sites.« less
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Inhibition of Canonical NF-κB Signaling by a Small Molecule Targeting NEMO-Ubiquitin Interaction
Vincendeau, Michelle; Hadian, Kamyar; Messias, Ana C.; Brenke, Jara K.; Halander, Jenny; Griesbach, Richard; Greczmiel, Ute; Bertossi, Arianna; Stehle, Ralf; Nagel, Daniel; Demski, Katrin; Velvarska, Hana; Niessing, Dierk; Geerlof, Arie; Sattler, Michael; Krappmann, Daniel
2016-01-01
The IκB kinase (IKK) complex acts as the gatekeeper of canonical NF-κB signaling, thereby regulating immunity, inflammation and cancer. It consists of the catalytic subunits IKKα and IKKβ and the regulatory subunit NEMO/IKKγ. Here, we show that the ubiquitin binding domain (UBAN) in NEMO is essential for IKK/NF-κB activation in response to TNFα, but not IL-1β stimulation. By screening a natural compound library we identified an anthraquinone derivative that acts as an inhibitor of NEMO-ubiquitin binding (iNUB). Using biochemical and NMR experiments we demonstrate that iNUB binds to NEMOUBAN and competes for interaction with methionine-1-linked linear ubiquitin chains. iNUB inhibited NF-κB activation upon UBAN-dependent TNFα and TCR/CD28, but not UBAN-independent IL-1β stimulation. Moreover, iNUB was selectively killing lymphoma cells that are addicted to chronic B-cell receptor triggered IKK/NF-κB activation. Thus, iNUB disrupts the NEMO-ubiquitin protein-protein interaction interface and thereby inhibits physiological and pathological NF-κB signaling. PMID:26740240
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Lenormand, Hélène; Deschrevel, Brigitte; Vincent, Jean-Claude
2010-05-01
Hyaluronan (HA) hydrolysis catalysed by hyaluronidase (HAase) is strongly inhibited when performed at a low ratio of HAase to HA concentrations and at low ionic strength. This is because long HA chains can form non-active complexes with HAase. Bovine serum albumin (BSA) is able to compete with HAase to form electrostatic complexes with HA so freeing HAase which then recovers its catalytic activity. This BSA-dependence is characterised by two main domains separated by the optimal BSA concentration: below this concentration the HAase activity increases when the BSA concentration is increased, above this concentration the HAase activity decreases. This occurs provided that HA is negatively charged and BSA is positively charged, i.e. in a pH range from 3 to 5.25. The higher the pH value the higher the optimal BSA concentration. Other proteins can also modulate HAase activity. Lysozyme, which has a pI higher than that of BSA, is also able to compete with HAase to form electrostatic complexes with HA and liberate HAase. This occurs over a wider pH range that extends from 3 to 9. These results mean that HAase can form complexes with HA and recover its enzymatic activity at pH as high as 9, consistent with HAase having either a high pI value or positively charged patches on its surface at high pH. Finally, the pH-dependence of HAase activity, which results from the influence of pH on both the intrinsic HAase activity and the formation of complexes between HAase and HA, shows a maximum at pH 4 and a significant activity up to pH 9. Copyright 2009 International Society of Matrix Biology. Published by Elsevier B.V. All rights reserved.
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Hwa, Kuo Yuan; Subramani, Boopathi; Shen, San-Tai; Lee, Yu-May
2015-09-01
β-Glycosidase from Thermococcus kodakarensis KOD1 is a hyperthermophilic enzyme with β-glucosidase, β-mannosidase, β-fucosidase and β-galactosidase activities. Sequence alignment with other β-glycosidases from hyperthermophilic archaea showed two unique active site residues, Gln77 and Asp206. These residues were represented by Arg and Asp in all other hyperthermophilic β-glycosidases. The two active site residues were mutated to Q77R, D206N and D206Q, to study the role of these unique active site residues in catalytic activity and to alter the substrate specificity to enhance its β-glucosidase activity. The secondary structure analysis of all the mutants showed no change in their structure and exhibited in similar conformation like wild-type as they all existed in dimer form in an SDS-PAGE under non-reducing conditions. Q77R and D206Q affected the catalytic activity of the enzyme whereas the D206N altered the catalytic turn-over rate for glucosidase and mannosidase activities with fucosidase activity remain unchanged. Gln77 is reported to interact with catalytic nucleophile and Asp206 with axial C2-hydroxyl group of substrates. Q77R might have made some changes in three dimensional structure due to its electrostatic effect and lost its catalytic activity. The extended side chains of D206Q is predicted to affect the substrate binding during catalysis. The high-catalytic turn-over rate by D206N for β-glucosidase activity makes it a useful enzyme in cellulose degradation at high temperatures. Copyright © 2015 Elsevier Inc. All rights reserved.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Thoi, VanSara; Kornienko, Nick; Margarit, C
2013-06-07
The solar-driven reduction of carbon dioxide to value-added chemical fuels is a longstanding challenge in the fields of catalysis, energy science, and green chemistry. In order to develop effective CO2 fixation, several key considerations must be balanced, including (1) catalyst selectivity for promoting CO2 reduction over competing hydrogen generation from proton reduction, (2) visible-light harvesting that matches the solar spectrum, and (3) the use of cheap and earth-abundant catalytic components. In this report, we present the synthesis and characterization of a new family of earth-abundant nickel complexes supported by N-heterocyclic carbene amine ligands that exhibit high selectivity and activity formore » the electrocatalytic and photocatalytic conversion of CO2 to CO. Systematic changes in the carbene and amine donors of the ligand have been surveyed, and [Ni(Prbimiq1)]2+ (1c, where Prbimiq1 = bis(3-(imidazolyl)isoquinolinyl)propane) emerges as a catalyst for electrochemical reduction of CO2 with the lowest cathodic onset potential (Ecat = 1.2 V vs SCE). Using this earth-abundant catalyst with Ir(ppy)3 (where ppy = 2-phenylpyridine) and an electron donor, we have developed a visible-light photoredox system for the catalytic conversion of CO2 to CO that proceeds with high selectivity and activity and achieves turnover numbers and turnover frequencies reaching 98,000 and 3.9 s1, respectively. Further studies reveal that the overall efficiency of this solar-to-fuel cycle may be limited by the formation of the active Ni catalyst and/or the chemical reduction of CO2 to CO at the reduced nickel center and provide a starting point for improved photoredox systems for sustainable carbon-neutral energy conversion.« less
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Pedroso, Marcelo M; Ely, Fernanda; Carpenter, Margaret C; Mitić, Nataša; Gahan, Lawrence R; Ollis, David L; Wilcox, Dean E; Schenk, Gerhard
2017-07-05
Glycerophosphodiesterase (GpdQ) from Enterobacter aerogenes is a binuclear metallohydrolase with a high affinity for metal ions at its α site but a lower affinity at its β site in the absence of a substrate. Isothermal titration calorimetry (ITC) has been used to quantify the Co(II) and Mn(II) binding affinities and thermodynamics of the two sites in wild-type GpdQ and two mutants, both in the absence and in the presence of phosphate. Metal ions bind to the six-coordinate α site in an entropically driven process with loss of a proton, while binding at the β site is not detected by ITC. Phosphate enhances the metal affinity of the α site by increasing the binding entropy and the metal affinity of the β site by enthalpic (Co) or entropic (Mn) contributions, but no additional loss of protons. Mutations of first- and second-coordination sphere residues at the β site increase the metal affinity of both sites by enhancing the binding enthalpy. In particular, loss of the hydrogen bond from second-sphere Ser127 to the metal-coordinating Asn80 has a significant effect on the metal binding thermodynamics that result in a resting binuclear active site with high catalytic activity. While structural and spectroscopic data with excess metal ions have indicated a bridging hydroxide in the binuclear GpdQ site, analysis of ITC data here reveals the loss of a single proton in the assembly of this site, indicating that the metal-bound hydroxide nucleophile is formed in the resting inactive mononuclear form, which becomes catalytically competent upon binding the second metal ion.
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Mechanism of substrate specificity in 5′-methylthioadenosine/S-adenosylhomocysteine nucleosidases
Siu, Karen K.W.; Asmus, Kyle; Zhang, Allison N.; Horvatin, Cathy; Li, Sheng; Liu, Tong; Moffatt, Barbara; Woods, Virgil L.; Howell, P. Lynne
2010-01-01
5′-Methylthioadenosine/S-adenosylhomocysteine (MTA/SAH) nucleosidase (MTAN) plays a key role in the methionine-recycling pathway of bacteria and plants. Despite extensive structural and biochemical studies, the molecular mechanism of substrate specificity for MTAN remains an outstanding question. Bacterial MTANs show comparable efficiency in hydrolyzing MTA and SAH, while the plant enzymes select preferentially for MTA, with either no or significantly reduced activity towards SAH. Bacterial and plant MTANs show significant conservation in the overall structure, and the adenine- and ribose-binding sites. The observation of a more constricted 5′-alkylthio binding site in Arabidopsis thaliana AtM-TAN1 and AtMTAN2, two plant MTAN homologues, led to the hypothesis that steric hindrance may play a role in substrate selection in plant MTANs. We show using isothermal titration calorimetry that SAH binds to both Escherichia coli MTAN (EcMTAN) and AtMTAN1 with comparable micromolar affinity. To understand why AtMTAN1 can bind but not hydrolyze SAH, we determined the structure of the protein–SAH complex at 2.2 Å resolution. The lack of catalytic activity appears to be related to the enzyme’s inability to bind the substrate in a catalytically competent manner. The role of dynamics in substrate selection was also examined by probing the amide proton exchange rates of EcMTAN and AtMTAN1 via deuterium–hydrogen exchange coupled mass spectrometry. These results correlate with the B factors of available structures and the thermodynamic parameters associated with substrate binding, and suggest a higher level of conformational flexibility in the active site of EcMTAN. Our results implicate dynamics as an important factor in substrate selection in MTAN. PMID:20554051
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Improvement of activity and stability of chloroperoxidase by chemical modification
Liu, Jian-Zhong; Wang, Min
2007-01-01
Background Enzymes show relative instability in solvents or at elevated temperature and lower activity in organic solvent than in water. These limit the industrial applications of enzymes. Results In order to improve the activity and stability of chloroperoxidase, chloroperoxidase was modified by citraconic anhydride, maleic anhydride or phthalic anhydride. The catalytic activities, thermostabilities and organic solvent tolerances of native and modified enzymes were compared. In aqueous buffer, modified chloroperoxidases showed similar Km values and greater catalytic efficiencies kcat/Km for both sulfoxidation and oxidation of phenol compared to native chloroperoxidase. Of these modified chloroperoxidases, citraconic anhydride-modified chloroperoxidase showed the greatest catalytic efficiency in aqueous buffer. These modifications of chloroperoxidase increased their catalytic efficiencies for sulfoxidation by 12%~26% and catalytic efficiencies for phenol oxidation by 7%~53% in aqueous buffer. However, in organic solvent (DMF), modified chloroperoxidases had lower Km values and higher catalytic efficiencies kcat/Km than native chloroperoxidase. These modifications also improved their thermostabilities by 1~2-fold and solvent tolerances of DMF. CD studies show that these modifications did not change the secondary structure of chloroperoxidase. Fluorescence spectra proved that these modifications changed the environment of tryptophan. Conclusion Chemical modification of epsilon-amino groups of lysine residues of chloroperoxidase using citraconic anhydride, maleic anhydride or phthalic anhydride is a simple and powerful method to enhance catalytic properties of enzyme. The improvements of the activity and stability of chloroperoxidase are related to side chain reorientations of aromatics upon both modifications. PMID:17511866
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Jin, Ying-Hua; Fan, Jun; Sun, Fei
2014-01-01
3-hydroxyacyl-CoA dehydrogenase (HAD, EC 1.1.1.35) is a homodimeric enzyme localized in the mitochondrial matrix, which catalyzes the third step in fatty acid β-oxidation. The crystal structures of human HAD and subsequent complexes with cofactor/substrate enabled better understanding of HAD catalytic mechanism. However, numerous human diseases were found related to mutations at HAD dimerization interface that is away from the catalytic pocket. The role of HAD dimerization in its catalytic activity needs to be elucidated. Here, we solved the crystal structure of Caenorhabditis elegans HAD (cHAD) that is highly conserved to human HAD. Even though the cHAD mutants (R204A, Y209A and R204A/Y209A) with attenuated interactions on the dimerization interface still maintain a dimerization form, their enzymatic activities significantly decrease compared to that of the wild type. Such reduced activities are in consistency with the reduced ratios of the catalytic intermediate formation. Further molecular dynamics simulations results reveal that the alteration of the dimerization interface will increase the fluctuation of a distal region (a.a. 60–80) that plays an important role in the substrate binding. The increased fluctuation decreases the stability of the catalytic intermediate formation, and therefore the enzymatic activity is attenuated. Our study reveals the molecular mechanism about the essential role of the HAD dimerization interface in its catalytic activity via allosteric effects. PMID:24763278
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NASA Astrophysics Data System (ADS)
Yang, Sena; Lee, Hangil
2017-11-01
The modified TiO2 nanoparticles (NPs) to enhance their catalytic activities by doping them with the five transition metals (Cr, Mn, Fe, Co, and Ni) have been investigated using various surface analysis techniques such as scanning electron microscopy (SEM), Raman spectroscopy, scanning transmission X-ray microscopy (STXM), and high-resolution photoemission spectroscopy (HRPES). To compare catalytic activities of these transition metal-doped TiO2 nanoparticles (TM-TiO2) with those of TiO2 NPs, we monitored their performances in the catalytic oxidation of 2-aminothiophenol (2-ATP) by using HRPES and on the oxidation of 2-ATP in aqueous solution by taking electrochemistry (EC) measurements. As a result, we clearly investigate that the increased defect structures induced by the doped transition metal are closely correlated with the enhancement of catalytic activities of TiO2 NPs and confirm that Fe- and Co-doped TiO2 NPs can act as efficient catalysts.
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Zhuang, Haifeng; Han, Hongjun; Hou, Baolin; Jia, Shengyong; Zhao, Qian
2014-08-01
Sewage sludge of biological wastewater treatment plant was converted into sewage sludge based activated carbon (SBAC) with ZnCl₂ as activation agent, which supported manganese and ferric oxides as catalysts (including SBAC) to improve the performance of ozonation of real biologically pretreated Lurgi coal gasification wastewater. The results indicated catalytic ozonation with the prepared catalysts significantly enhanced performance of pollutants removal and the treated wastewater was more biodegradable and less toxic than that in ozonation alone. On the basis of positive effect of higher pH and significant inhibition of radical scavengers in catalytic ozonation, it was deduced that the enhancement of catalytic activity was responsible for generating hydroxyl radicals and the possible reaction pathway was proposed. Moreover, the prepared catalysts showed superior stability and most of toxic and refractory compounds were eliminated at successive catalytic ozonation runs. Thus, the process with economical, efficient and sustainable advantages was beneficial to engineering application. Copyright © 2014 Elsevier Ltd. All rights reserved.
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Mutational analysis of polynucleotide phosphorylase from Escherichia coli.
Jarrige, Anne; Bréchemier-Baey, Dominique; Mathy, Nathalie; Duché, Ophélie; Portier, Claude
2002-08-16
Polynucleotide phosphorylase (PNPase), a homotrimeric exoribonuclease present in bacteria, is involved in mRNA degradation. In Escherichia coli, expression of this enzyme is autocontrolled at the translational level. We introduced about 30 mutations in the pnp gene by site-directed mutagenesis, most of them in phylogenetically conserved residues, and determined their effects on the three catalytic activities of PNPase, phosphorolysis, polymerisation and phosphate exchange, as well as on the efficiency of translational repression. The data are presented and discussed in the light of the crystallographic structure of PNPase from Streptomyces antibioticus. The results show that both PNPase activity and the presence of the KH and S1 RNA-binding domains are required for autocontrol. Deletions of these RNA-binding domains do not abolish any of the three catalytic activities, indicating that they are contained in a domain independent of the catalytic centre. Moreover, the catalytic centre was located around the tungsten-binding site identified by crystallography. Some mutations affect the three catalytic activities differently, an observation consistent with the presence of different subsites.
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Iwanowicz, Edwin J; Kimball, S David; Lin, James; Lau, Wan; Han, W-C; Wang, Tammy C; Roberts, Daniel G M; Schumacher, W A; Ogletree, Martin L; Seiler, Steven M
2002-11-04
A series of retro-binding inhibitors of human alpha-thrombin was prepared to elucidate structure-activity relationships (SAR) and optimize in vivo performance. Compounds 9 and 11, orally active inhibitors of thrombin catalytic activity, were identified to be efficacious in a thrombin-induced lethality model in mice.
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Tabler, M; Homann, M; Tzortzakaki, S; Sczakiel, G
1994-01-01
Trans-cleaving hammerhead ribozymes with long target-specific antisense sequences flanking the catalytic domain share some features with conventional antisense RNA and are therefore termed 'catalytic antisense RNAs'. Sequences 5' to the catalytic domain form helix I and sequences 3' to it form helix III when complexed with the target RNA. A catalytic antisense RNA of more than 400 nucleotides, and specific for the human immunodeficiency virus type 1 (HIV-1), was systematically truncated within the arm that constituted originally a helix I of 128 base pairs. The resulting ribozymes formed helices I of 13, 8, 5, 3, 2, 1 and 0 nucleotides, respectively, and a helix III of about 280 nucleotides. When their in vitro cleavage activity was compared with the original catalytic antisense RNA, it was found that a helix I of as little as three nucleotides was sufficient for full endonucleolytic activity. The catalytically active constructs inhibited HIV-1 replication about four-fold more effectively than the inactive ones when tested in human cells. A conventional hammerhead ribozyme having helices of just 8 nucleotides on either side failed to cleave the target RNA in vitro when tested under the conditions for catalytic antisense RNA. Cleavage activity could only be detected after heat-treatment of the ribozyme substrate mixture which indicates that hammerhead ribozymes with short arms do not associate as efficiently to the target RNA as catalytic antisense RNA. The requirement of just a three-nucleotide helix I allows simple PCR-based generation strategies for asymmetric hammerhead ribozymes. Advantages of an asymmetric design will be discussed. Images PMID:7937118
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Lu, Chang; Liu, Xin; Zhang, Chen-Song; Gong, Haipeng; Wu, Jia-Wei; Wang, Zhi-Xin
2017-11-21
The mitogen-activated protein kinases (MAPKs) are key components of cellular signal transduction pathways, which are down-regulated by the MAPK phosphatases (MKPs). Catalytic activity of the MKPs is controlled both by their ability to recognize selective MAPKs and by allosteric activation upon binding to MAPK substrates. Here, we use a combination of experimental and computational techniques to elucidate the molecular mechanism for the ERK2-induced MKP3 activation. Mutational and kinetic study shows that the 334 FNFM 337 motif in the MKP3 catalytic domain is essential for MKP3-mediated ERK2 inactivation and is responsible for ERK2-mediated MKP3 activation. The long-term molecular dynamics (MD) simulations further reveal a complete dynamic process in which the catalytic domain of MKP3 gradually changes to a conformation that resembles an active MKP catalytic domain over the time scale of the simulation, providing a direct time-dependent observation of allosteric signal transmission in ERK2-induced MKP3 activation.
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Nomikos, Michail; Mulgrew-Nesbitt, Anna; Pallavi, Payal; Mihalyne, Gyongyi; Zaitseva, Irina; Swann, Karl; Lai, F Anthony; Murray, Diana; McLaughlin, Stuart
2007-06-01
Phospholipase C-zeta (PLC-zeta) is a sperm-specific enzyme that initiates the Ca2+ oscillations in mammalian eggs that activate embryo development. It shares considerable sequence homology with PLC-delta1, but lacks the PH domain that anchors PLC-delta1 to phosphatidylinositol 4,5-bisphosphate, PIP2. Thus it is unclear how PLC-zeta interacts with membranes. The linker region between the X and Y catalytic domains of PLC-zeta, however, contains a cluster of basic residues not present in PLC-delta1. Application of electrostatic theory to a homology model of PLC-zeta suggests this basic cluster could interact with acidic lipids. We measured the binding of catalytically competent mouse PLC-zeta to phospholipid vesicles: for 2:1 phosphatidylcholine/phosphatidylserine (PC/PS) vesicles, the molar partition coefficient, K, is too weak to be of physiological significance. Incorporating 1% PIP2 into the 2:1 PC/PS vesicles increases K about 10-fold, to 5x10(3) M-1, a biologically relevant value. Expressed fragments corresponding to the PLC-zeta X-Y linker region also bind with higher affinity to polyvalent than monovalent phosphoinositides on nitrocellulose filters. A peptide corresponding to the basic cluster (charge=+7) within the linker region, PLC-zeta-(374-385), binds to PC/PS vesicles with higher affinity than PLC-zeta, but its binding is less sensitive to incorporating PIP2. The acidic residues flanking this basic cluster in PLC-zeta may account for both these phenomena. FRET experiments suggest the basic cluster could not only anchor the protein to the membrane, but also enhance the local concentration of PIP2 adjacent to the catalytic domain.
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Understanding Anionic "Ligandless" Palladium Species in the Mizoroki-Heck Reaction.
Schroeter, Felix; Strassner, Thomas
2018-05-07
The anionic complex [NBu 4 ][Pd(DMSO)Cl 3 ], as a "ligandless" system, was shown to be an active catalyst in the Mizoroki-Heck coupling of aryl chlorides in the absence of strongly σ-donating ligands. To investigate the experimentally observed influence of halides and the amount of water on the catalytic activity, we employed a combination of experiments and theoretical calculations. The presence of water was shown to be critical for the formation of the active palladium(0) species by oxidation of in situ generated tributylamine. Oxidative addition to an anionic palladium(0) species was found to be the rate-determining step of the catalytic cycle. For the ensuing steps, both neutral and anionic pathways were considered. It was shown that, in the absence of strongly σ-donating neutral ligands, chloride ions stabilize the catalytic intermediates. Therefore, an anionic pathway is preferred, which explains the need for tetrabutylammonium chloride as an additive. The study of the influence of bromide ions on the catalytic activity revealed that the strongly exergonic displacement of the neutral substrates by bromide ions lowers the catalytic activity.
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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
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NASA Astrophysics Data System (ADS)
Li, Shuo; Zhang, Guangshan; Zheng, Heshan; Zheng, Yongjie; Wang, Peng
2018-05-01
In this study, BiFeO3 (BFO) powders decorated on nickel foam (NF) with a high catalytic activity are prepared via a one-step microwave-assisted hydrothermal method. The factors that influence the degradation of bisphenol A (BPA) with BFO/NFs as catalysts are optimized to improve the catalytic activity in a microwave-enhanced Fenton-like process. BFO/NF exhibit a superior catalytic activity with a high BPA removal ratio (98.4%) and TOC removal ratio (69.5%) within 5 min. Results indicate that NF significantly affect the improvement of the catalytic activity of BFO because it served as a source of hydroxyl radicals (•OH) during degradation. The amount of •OH generated by BFO/NF is approximately 1.65-fold higher than that by pure BFO. After six reaction cycles, the stability and reusability of •OH remain high. These findings provide new insights into the synthesis of composites on heterogeneous catalysts with high efficiency and easy recyclability for water treatment applications.
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Bergmann, Arno; Martinez-Moreno, Elias; Teschner, Detre; Chernev, Petko; Gliech, Manuel; de Araújo, Jorge Ferreira; Reier, Tobias; Dau, Holger; Strasser, Peter
2015-10-12
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.
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Mishanina, Tatiana V.; Yadav, Pramod K.; Ballou, David P.; Banerjee, Ruma
2015-01-01
The first step in the mitochondrial sulfide oxidation pathway is catalyzed by sulfide quinone oxidoreductase (SQR), which belongs to the family of flavoprotein disulfide oxidoreductases. During the catalytic cycle, the flavin cofactor is intermittently reduced by sulfide and oxidized by ubiquinone, linking H2S oxidation to the electron transfer chain and to energy metabolism. Human SQR can use multiple thiophilic acceptors, including sulfide, sulfite, and glutathione, to form as products, hydrodisulfide, thiosulfate, and glutathione persulfide, respectively. In this study, we have used transient kinetics to examine the mechanism of the flavin reductive half-reaction and have determined the redox potential of the bound flavin to be −123 ± 7 mV. We observe formation of an unusually intense charge-transfer (CT) complex when the enzyme is exposed to sulfide and unexpectedly, when it is exposed to sulfite. In the canonical reaction, sulfide serves as the sulfur donor and sulfite serves as the acceptor, forming thiosulfate. We show that thiosulfate is also formed when sulfide is added to the sulfite-induced CT intermediate, representing a new mechanism for thiosulfate formation. The CT complex is formed at a kinetically competent rate by reaction with sulfide but not with sulfite. Our study indicates that sulfide addition to the active site disulfide is preferred under normal turnover conditions. However, under pathological conditions when sulfite concentrations are high, sulfite could compete with sulfide for addition to the active site disulfide, leading to attenuation of SQR activity and to an alternate route for thiosulfate formation. PMID:26318450
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Mishanina, Tatiana V; Yadav, Pramod K; Ballou, David P; Banerjee, Ruma
2015-10-09
The first step in the mitochondrial sulfide oxidation pathway is catalyzed by sulfide quinone oxidoreductase (SQR), which belongs to the family of flavoprotein disulfide oxidoreductases. During the catalytic cycle, the flavin cofactor is intermittently reduced by sulfide and oxidized by ubiquinone, linking H2S oxidation to the electron transfer chain and to energy metabolism. Human SQR can use multiple thiophilic acceptors, including sulfide, sulfite, and glutathione, to form as products, hydrodisulfide, thiosulfate, and glutathione persulfide, respectively. In this study, we have used transient kinetics to examine the mechanism of the flavin reductive half-reaction and have determined the redox potential of the bound flavin to be -123 ± 7 mV. We observe formation of an unusually intense charge-transfer (CT) complex when the enzyme is exposed to sulfide and unexpectedly, when it is exposed to sulfite. In the canonical reaction, sulfide serves as the sulfur donor and sulfite serves as the acceptor, forming thiosulfate. We show that thiosulfate is also formed when sulfide is added to the sulfite-induced CT intermediate, representing a new mechanism for thiosulfate formation. The CT complex is formed at a kinetically competent rate by reaction with sulfide but not with sulfite. Our study indicates that sulfide addition to the active site disulfide is preferred under normal turnover conditions. However, under pathological conditions when sulfite concentrations are high, sulfite could compete with sulfide for addition to the active site disulfide, leading to attenuation of SQR activity and to an alternate route for thiosulfate formation. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.
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Dong, Xiao-li; Zhang, Zhen-cheng; An, Qing-da; Zhang, Shao-yin; Wang, Shao-jun
2007-12-01
A new kind of iron-porphyrin/vanadium-substituted polyoxometalate coordination compound was synthesized by the ion exchange reaction of FeTTMAPPI and H5PMo10V2o40 in solution. The new catalyst was characterized by IR spectrometry and UV-Vis spectrometry. As an excellent catalyst, its effects on benzene hydroxylation and catalytic capabilities were studied with H2O2 solution as the oxidant. The results indicated that the products contained the conjugated structure of porphyrin and the cage structure of polyoxometalate, the V atom in polyoxometalate is the main centre of catalytic activity, meanwhile the presence of iron-porphyrin could increase its catalytic activity greatly.
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Liu, Haoliang; Feng, Juan; Chen, Liuping
2015-01-01
A novel dynamic covalent gel strategy is reported to immobilize an asymmetric catalyst within the channels of a microfluidic flow reactor. A layer of a catalytically active Mn–salen dynamic covalent imine gel matrix was coated onto a functionalized capillary. Mn–salen active moiety was incorporated into dynamic covalent imine gel matrix via the reaction of a chiral Mn–salen dialdehyde unit with a tetraamine linker. The catalytic activity of the capillary reactor has been demonstrated in enantioselective kinetic resolution of secondary alcohols. PMID:28706652
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Qin, Hangdao; Xiao, Rong; Chen, Jing
2018-06-01
The parent activated carbon (ACP) was modified with urea and thiourea to obtain N-doped activated carbon (ACN) and N, S co-doped activated carbon (ACNS), respectively. Iron supported on activated carbon (Fe/ACP, Fe/ACN and Fe/ACNS) were prepared and worked as catalyst for catalytic wet peroxide oxidation of benzoic acid (BA). The catalysts were characterized by N 2 adsorption-desorption, X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS) and transmission electron microscope (TEM), and their performance was evaluated in terms of benzoic acid and TOC removal. The results indicated the doped N and S improved the adsorption capacity as well as catalytic activity of activated carbon. Besides, the catalytic activity toward benzoic acid degradation was found to be enhanced by Fe/ACNS compared to that of Fe/ACP and Fe/ACN. The enhanced catalytic performance was attributed to the presence of the nitrogen and sulfur atoms may serve to improve the relative amount of Fe 2+ on iron oxide surface and also help prevent leaching of Fe. It was also observed that the stability or reutilization of Fe/ACNS catalyst was fairly good. Copyright © 2018 Elsevier B.V. All rights reserved.
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Tsai, Li-Chun Lisa; Xie, Lei; Dore, Kim; Xie, Li; Del Rio, Jason C; King, Charles C; Martinez-Ariza, Guillermo; Hulme, Christopher; Malinow, Roberto; Bourne, Philip E; Newton, Alexandra C
2015-09-04
Atypical protein kinase C (aPKC) enzymes signal on protein scaffolds, yet how they are maintained in an active conformation on scaffolds is unclear. A myristoylated peptide based on the autoinhibitory pseudosubstrate fragment of the atypical PKCζ, zeta inhibitory peptide (ZIP), has been extensively used to inhibit aPKC activity; however, we have previously shown that ZIP does not inhibit the catalytic activity of aPKC isozymes in cells (Wu-Zhang, A. X., Schramm, C. L., Nabavi, S., Malinow, R., and Newton, A. C. (2012) J. Biol. Chem. 287, 12879-12885). Here we sought to identify a bona fide target of ZIP and, in so doing, unveiled a novel mechanism by which aPKCs are maintained in an active conformation on a protein scaffold. Specifically, we used protein-protein interaction network analysis, structural modeling, and protein-protein docking to predict that ZIP binds an acidic surface on the Phox and Bem1 (PB1) domain of p62, an interaction validated by peptide array analysis. Using a genetically encoded reporter for PKC activity fused to the p62 scaffold, we show that ZIP inhibits the activity of wild-type aPKC, but not a construct lacking the pseudosubstrate. These data support a model in which the pseudosubstrate of aPKCs is tethered to the acidic surface on p62, locking aPKC in an open, signaling-competent conformation. ZIP competes for binding to the acidic surface, resulting in displacement of the pseudosubstrate of aPKC and re-engagement in the substrate-binding cavity. This study not only identifies a cellular target for ZIP, but also unveils a novel mechanism by which scaffolded aPKC is maintained in an active conformation. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.
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Chughtai, Adeel H; Ahmad, Nazir; Younus, Hussein A; Laypkov, A; Verpoort, Francis
2015-10-07
Novel catalytic materials are highly demanded to perform a variety of catalytic organic reactions. MOFs combine the benefits of heterogeneous catalysis like easy post reaction separation, catalyst reusability, high stability and homogeneous catalysis such as high efficiency, selectivity, controllability and mild reaction conditions. The possible organization of active centers like metallic nodes, organic linkers, and their chemical synthetic functionalization on the nanoscale shows potential to build up MOFs particularly modified for catalytic challenges. In this review, we have summarized the recent research progress in heterogeneous catalysis by MOFs and their catalytic behavior in various organic reactions, highlighting the key features of MOFs as catalysts based on the active sites in the framework. Examples of their post functionalization, inclusion of active guest species and metal nanoparticles have been discussed. Finally, the use of MOFs as catalysts for asymmetric heterogeneous catalysis and stability of MOFs has been presented as separate sections.
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Zhang, Xin; Zhao, Haitao; Wang, Jianhui
2010-08-01
Au nanoparticles stabilized by polystyrene-co-polymethacrylic acid microspheres (PS-co-PMAA) were prepared and characterized via X-ray diffraction (XRD), and transmission electron microscope (TEM). The Au nanoparticles supported on the microspheres showed highly selective catalytic activity for homo-coupling reactions of arylboronic acids in a system of aryl-halides and arylboronic acids. X-ray photoelectron spectroscopy (XPS) spectra of the catalyst shows large amounts of Au(I) complexes band to the surface of the Au nanoparticles, which contributes to the selective homocoupling of the arylboronic acids. More importantly, this supported Au complex is a highly recyclable catalyst. The supported Au catalyst can be recycled and reused at least 6 times for a phenylboronic acid reactant, whereas the parent complex shows very low catalytic activity for this compound. The high catalytic activity of this material is attributed to: (1) the high surface to volume ratio which leads to more active sites being exposed to reactants; (2) the strong surface binding of the Au nanoparticle to the Au(I) complexes, which enhances both the stability and the catalytic activity of these complexes.
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Rangarajan, Srinivas; Maravelias, Christos T.; Mavrikakis, Manos
2017-11-09
Here, we present a general optimization-based framework for (i) ab initio and experimental data driven mechanistic modeling and (ii) optimal catalyst design of heterogeneous catalytic systems. Both cases are formulated as a nonlinear optimization problem that is subject to a mean-field microkinetic model and thermodynamic consistency requirements as constraints, for which we seek sparse solutions through a ridge (L 2 regularization) penalty. The solution procedure involves an iterative sequence of forward simulation of the differential algebraic equations pertaining to the microkinetic model using a numerical tool capable of handling stiff systems, sensitivity calculations using linear algebra, and gradient-based nonlinear optimization.more » A multistart approach is used to explore the solution space, and a hierarchical clustering procedure is implemented for statistically classifying potentially competing solutions. An example of methanol synthesis through hydrogenation of CO and CO 2 on a Cu-based catalyst is used to illustrate the framework. The framework is fast, is robust, and can be used to comprehensively explore the model solution and design space of any heterogeneous catalytic system.« less
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Rangarajan, Srinivas; Maravelias, Christos T.; Mavrikakis, Manos
Here, we present a general optimization-based framework for (i) ab initio and experimental data driven mechanistic modeling and (ii) optimal catalyst design of heterogeneous catalytic systems. Both cases are formulated as a nonlinear optimization problem that is subject to a mean-field microkinetic model and thermodynamic consistency requirements as constraints, for which we seek sparse solutions through a ridge (L 2 regularization) penalty. The solution procedure involves an iterative sequence of forward simulation of the differential algebraic equations pertaining to the microkinetic model using a numerical tool capable of handling stiff systems, sensitivity calculations using linear algebra, and gradient-based nonlinear optimization.more » A multistart approach is used to explore the solution space, and a hierarchical clustering procedure is implemented for statistically classifying potentially competing solutions. An example of methanol synthesis through hydrogenation of CO and CO 2 on a Cu-based catalyst is used to illustrate the framework. The framework is fast, is robust, and can be used to comprehensively explore the model solution and design space of any heterogeneous catalytic system.« less
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Fukuzumi, Shunichi; Kobayashi, Takeshi; Suenobu, Tomoyoshi
2008-01-01
Formic acid (HCOOH) decomposes efficiently to afford H2 and CO2 selectively in the presence of a catalytic amount of a water-soluble rhodium aqua complex, [Rh(III)(Cp*)(bpy)(H2O)]2+ (Cp*=pentamethylcyclopentadienyl, bpy=2,2'-bipyridine) in aqueous solution at 298 K. No CO was produced in this catalytic decomposition of HCOOH. The decomposition rate reached a maximum value at pH 3.8. No deterioration of the catalyst was observed during the catalytic decomposition of HCOOH, and the catalytic activity remained the same for the repeated addition of HCOOH. The rhodium-hydride complex was detected as the catalytic active species that undergoes efficient H/D exchange with water. When the catalytic decomposition of HCOOH was performed in D2O, D2 was produced selectively. Such an efficient H/D exchange and the observation of a deuterium kinetic isotope effect in the catalytic decomposition of DCOOH in H2O provide valuable mechanistic insight into this efficient and selective decomposition process.
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Johnson, Glynis; Moore, Samuel W
2009-01-01
We have previously described anti-acetylcholinesterase antibodies that display acetylcholinesterase-like catalytic activity. No evidence of contaminating enzymes was found, and the antibodies are kinetically and apparently structurally distinct from both acetylcholinesterase (AChE) and butyrylcholinesterase. We have also mimicked the antibody catalytic sites in anti-anti-idiotypic (Ab3) antibodies. Independently from us, similar acetylcholinesterase-like antibodies have been raised as anti-idiotypic (Ab2) antibodies against a non-catalytic anti-acetylcholinesterase antibody, AE-2. In this paper, we describe an epitope analysis, using synthetic peptides in ELISA and competition ELISA, and a peptide array, of five catalytic anti-acetylcholinesterase antibodies (Ab1s), three catalytic Ab3s, as well as antibody AE-2 and a non-catalytic Ab2. The catalytic Ab1s and Ab3s recognized three Pro- and Gly-containing sequences ((40)PPMGPRRFL, (78)PGFEGTE, and (258)PPGGTGGNDTELVAC) on the AChE surface. As these sequences do not adjoin in the AChE structure, recognition would appear to be due to cross-reaction. This was confirmed by the observation that the sequences superimpose structurally. The non-catalytic antibodies, AE-2 and the Ab2, recognized AChE's peripheral anionic site (PAS), in particular, the sequence (70)YQYVD, which contains two of the site's residues. The crystal structure of the AChE tetramer (Bourne et al., 1999) shows direct interaction and high complementarity between the (257)CPPGGTGGNDTELVAC sequence and the PAS. Antibodies recognizing the sequence and the PAS may, in turn, be complementary; this may account for the apparent paradox of catalytic development in both Ab1s and Ab2s. The PAS binds, but does not hydrolyze, substrate. The catalytic Ab1s, therefore, recognize a site that may function as a substrate analog, and this, together with the presence of an Arg-Glu salt bridge in the epitope, suggests mechanisms whereby catalytic activity may have developed. In conclusion, the development of AChE-like catalytic activity in anti-AChE Ab1s and Ab2s appears to be the result of a combination of structural complementarity to a substrate-binding site, charge complementarity to a salt bridge, and specific structural peculiarities of the AChE molecule. Copyright 2008 John Wiley & Sons, Ltd.
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Totten, Ryan K; Kim, Ye-Seong; Weston, Mitchell H; Farha, Omar K; Hupp, Joseph T; Nguyen, SonBinh T
2013-08-14
An Al(porphyrin) functionalized with a large axial ligand was incorporated into a porous organic polymer (POP) using a cobalt-catalyzed acetylene trimerization strategy. Removal of the axial ligand afforded a microporous POP that is catalytically active in the methanolysis of a nerve agent simulant. Supercritical CO2 processing of the POP dramatically increased the pore size and volume, allowing for significantly higher catalytic activities.
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2011-12-01
8 C. Catalytic activity of evolved variants with GA ................................................................. 11 D...several variants of rePON1 with enhanced activity towards a racemic mixture of CMP-Coumarin by screening ‘neutral drift’ libraries of rePON1 (e.g. 1G3, 2G9...22. The most active variant was 3B3, which had ~250-fold higher catalytic efficiency (kcat/Km 20x106 M-1min-1) compared to the wild-type-like
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Wachs, Israel E.; Cai, Yeping
2002-01-01
Preparing an aldehyde from an alcohol by contacting the alcohol in the presence of oxygen with a catalyst prepared by contacting an intimate mixture containing metal oxide support particles and particles of a catalytically active metal oxide from Groups VA, VIA, or VIIA, with a gaseous stream containing an alcohol to cause metal oxide from the discrete catalytically active metal oxide particles to migrate to the metal oxide support particles and to form a monolayer of catalytically active metal oxide on said metal oxide support particles.
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Grover, Prerna; Shi, Haibin; Baumgartner, Matthew; Camacho, Carlos J.; Smithgall, Thomas E.
2015-01-01
The ABL protein-tyrosine kinase regulates intracellular signaling pathways controlling diverse cellular processes and contributes to several forms of cancer. The kinase activity of ABL is repressed by intramolecular interactions involving its regulatory Ncap, SH3 and SH2 domains. Small molecules that allosterically regulate ABL kinase activity through its non-catalytic domains may represent selective probes of ABL function. Here we report a screening assay for chemical modulators of ABL kinase activity that target the regulatory interaction of the SH3 domain with the SH2-kinase linker. This fluorescence polarization (FP) assay is based on a purified recombinant ABL protein consisting of the N-cap, SH3 and SH2 domains plus the SH2-kinase linker (N32L protein) and a short fluorescein-labeled probe peptide that binds to the SH3 domain. In assay development experiments, we found that the probe peptide binds to the recombinant ABL N32L protein in vitro, producing a robust FP signal that can be competed with an excess of unlabeled peptide. The FP signal is not observed with control N32L proteins bearing either an inactivating mutation in the SH3 domain or enhanced SH3:linker interaction. A pilot screen of 1200 FDA-approved drugs identified four compounds that specifically reduced the FP signal by at least three standard deviations from the untreated controls. Secondary assays showed that one of these hit compounds, the antithrombotic drug dipyridamole, enhances ABL kinase activity in vitro to a greater extent than the previously described ABL agonist, DPH. Docking studies predicted that this compound binds to a pocket formed at the interface of the SH3 domain and the linker, suggesting that it activates ABL by disrupting this regulatory interaction. These results show that screening assays based on the non-catalytic domains of ABL can identify allosteric small molecule regulators of kinase function, providing a new approach to selective drug discovery for this important kinase system. PMID:26222440
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Grover, Prerna; Shi, Haibin; Baumgartner, Matthew; Camacho, Carlos J; Smithgall, Thomas E
2015-01-01
The ABL protein-tyrosine kinase regulates intracellular signaling pathways controlling diverse cellular processes and contributes to several forms of cancer. The kinase activity of ABL is repressed by intramolecular interactions involving its regulatory Ncap, SH3 and SH2 domains. Small molecules that allosterically regulate ABL kinase activity through its non-catalytic domains may represent selective probes of ABL function. Here we report a screening assay for chemical modulators of ABL kinase activity that target the regulatory interaction of the SH3 domain with the SH2-kinase linker. This fluorescence polarization (FP) assay is based on a purified recombinant ABL protein consisting of the N-cap, SH3 and SH2 domains plus the SH2-kinase linker (N32L protein) and a short fluorescein-labeled probe peptide that binds to the SH3 domain. In assay development experiments, we found that the probe peptide binds to the recombinant ABL N32L protein in vitro, producing a robust FP signal that can be competed with an excess of unlabeled peptide. The FP signal is not observed with control N32L proteins bearing either an inactivating mutation in the SH3 domain or enhanced SH3:linker interaction. A pilot screen of 1200 FDA-approved drugs identified four compounds that specifically reduced the FP signal by at least three standard deviations from the untreated controls. Secondary assays showed that one of these hit compounds, the antithrombotic drug dipyridamole, enhances ABL kinase activity in vitro to a greater extent than the previously described ABL agonist, DPH. Docking studies predicted that this compound binds to a pocket formed at the interface of the SH3 domain and the linker, suggesting that it activates ABL by disrupting this regulatory interaction. These results show that screening assays based on the non-catalytic domains of ABL can identify allosteric small molecule regulators of kinase function, providing a new approach to selective drug discovery for this important kinase system.
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Becker, Holger M.; Klier, Michael; Schüler, Christina; McKenna, Robert; Deitmer, Joachim W.
2011-01-01
Carbonic anhydrases (CAs) catalyze the reversible hydration of CO2 to HCO3− and H+. The rate-limiting step in this reaction is the shuttle of protons between the catalytic center of the enzyme and the bulk solution. In carbonic anhydrase II (CAII), the fastest and most wide-spread isoform, this H+ shuttle is facilitated by the side chain of His64, whereas CA isoforms such as carbonic anhydrase III (CAIII), which lack such a shuttle, have only low catalytic activity in vitro. By using heterologous protein expression in Xenopus oocytes, we tested the role of this intramolecular H+ shuttle on CA activity in an intact cell. The data revealed that CAIII, shown in vitro to have ∼1,000-fold reduced activity as compared with CAII, displays significant catalytic activity in the intact cell. Furthermore, we tested the hypothesis that the H+ shuttle in CAII itself can facilitate transport activity of the monocarboxylate transporters 1 and 4 (MCT1/4) independent of catalytic activity. Our results show that His64 is essential for the enhancement of lactate transport via MCT1/4, because a mutation of this residue to alanine (CAII-H64A) abolishes the CAII-induced increase in MCT1/4 activity. However, injection of 4-methylimidazole, which acts as an exogenous H+ donor/acceptor, can restore the ability of CAII-H64A to enhance transport activity of MCT1/4. These findings support the hypothesis that the H+ shuttle in CAII not only facilitates CAII catalytic activity but also can enhance activity of acid-/base-transporting proteins such as MCT1/4 in a direct, noncatalytic manner, possibly by acting as an “H+-collecting antenna.” PMID:21282642
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NASA Astrophysics Data System (ADS)
Cherkezova-Zheleva, Z.; Mitov, I.
2010-03-01
The aim of the study is to obtain the exact state of iron oxide catalyst active phase in reaction conditions, as well as the correlation between the active phase and catalytic properties of iron-containing catalysts. In situ Mössbauer spectroscopy is the major investigation technique. It is established that the change of reaction conditions (temperature and gas reaction mixture) lead to redistribution of the relative weight of spectra components and influence mainly tetrahedrally and octahedrally coordinated cations in Fe3O4 phase. It was concluded, that the active sites of the catalyst in studied reaction are probably pairs of Fe3++Fe2+-(Fe2.5+) ions, i.e. the mixed valance iron ions. The obtained catalytic activity can be explained with combination of the natural thermo-activated and catalytically induced electron exchange and better synchronizing of oxidation and reduction steps of the catalytic reaction.
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Methods of increasing secretion of polypeptides having biological activity
Merino, Sandra
2014-05-27
The present invention relates to methods for producing a secreted polypeptide having biological activity, comprising: (a) transforming a fungal host cell with a fusion protein construct encoding a fusion protein, which comprises: (i) a first polynucleotide encoding a signal peptide; (ii) a second polynucleotide encoding at least a catalytic domain of an endoglucanase or a portion thereof; and (iii) a third polynucleotide encoding at least a catalytic domain of a polypeptide having biological activity; wherein the signal peptide and at least the catalytic domain of the endoglucanase increases secretion of the polypeptide having biological activity compared to the absence of at least the catalytic domain of the endoglucanase; (b) cultivating the transformed fungal host cell under conditions suitable for production of the fusion protein; and (c) recovering the fusion protein, a component thereof, or a combination thereof, having biological activity, from the cultivation medium.
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Methods of increasing secretion of polypeptides having biological activity
Merino, Sandra
2014-10-28
The present invention relates to methods for producing a secreted polypeptide having biological activity, comprising: (a) transforming a fungal host cell with a fusion protein construct encoding a fusion protein, which comprises: (i) a first polynucleotide encoding a signal peptide; (ii) a second polynucleotide encoding at least a catalytic domain of an endoglucanase or a portion thereof; and (iii) a third polynucleotide encoding at least a catalytic domain of a polypeptide having biological activity; wherein the signal peptide and at least the catalytic domain of the endoglucanase increases secretion of the polypeptide having biological activity compared to the absence of at least the catalytic domain of the endoglucanase; (b) cultivating the transformed fungal host cell under conditions suitable for production of the fusion protein; and (c) recovering the fusion protein, a component thereof, or a combination thereof, having biological activity, from the cultivation medium.
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Methods of increasing secretion of polypeptides having biological activity
Merino, Sandra
2015-04-14
The present invention relates to methods for producing a secreted polypeptide having biological activity, comprising: (a) transforming a fungal host cell with a fusion protein construct encoding a fusion protein, which comprises: (i) a first polynucleotide encoding a signal peptide; (ii) a second polynucleotide encoding at least a catalytic domain of an endoglucanase or a portion thereof; and (iii) a third polynucleotide encoding at least a catalytic domain of a polypeptide having biological activity; wherein the signal peptide and at least the catalytic domain of the endoglucanase increases secretion of the polypeptide having biological activity compared to the absence of at least the catalytic domain of the endoglucanase; (b) cultivating the transformed fungal host cell under conditions suitable for production of the fusion protein; and (c) recovering the fusion protein, a component thereof, or a combination thereof, having biological activity, from the cultivation medium.
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Methods of increasing secretion of polypeptides having biological activity
Merino, Sandra
2013-10-01
The present invention relates to methods for producing a secreted polypeptide having biological activity, comprising: (a) transforming a fungal host cell with a fusion protein construct encoding a fusion protein, which comprises: (i) a first polynucleotide encoding a signal peptide; (ii) a second polynucleotide encoding at least a catalytic domain of an endoglucanase or a portion thereof; and (iii) a third polynucleotide encoding at least a catalytic domain of a polypeptide having biological activity; wherein the signal peptide and at least the catalytic domain of the endoglucanase increases secretion of the polypeptide having biological activity compared to the absence of at least the catalytic domain of the endoglucanase; (b) cultivating the transformed fungal host cell under conditions suitable for production of the fusion protein; and (c) recovering the fusion protein, a component thereof, or a combination thereof, having biological activity, from the cultivation medium.
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NASA Astrophysics Data System (ADS)
Jabłońska, Magdalena; Nocuń, Marek; Gołąbek, Kinga; Palkovits, Regina
2017-11-01
The selective oxidation of ammonia into nitrogen and water vapour (NH3-SCO) was studied over Cu-Mg(Zn)-Al-(Zr) mixed metal oxides, obtained by coprecipitation and their subsequent calcination. The effect of acid-base properties of Cu-Mg-Al-Ox on catalytic activity was investigated by changing the Mg/Al molar ratio. Other Cu-containing oxides were prepared by rehydration of calcined Mg-Al hydrotalcite-like compounds or thermal decomposition of metal nitrate precursors. XRD, BET, NH3-TPD, H2-TPR, XPS, FTIR with adsorption of pyridine and CO as well as TEM techniques were used for catalysts characterization. The results of catalytic tests revealed a crucial role of easily reducible highly dispersed copper oxide species to obtain enhanced activity and N2 selectivity in NH3-SCO. The selective catalytic reduction of NO by NH3 (NH3-SCR) and in situ DRIFT of NH3 sorption indicated that NH3-SCO proceeds according to the internal selective catalytic reduction mechanism (i-SCR).
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Wang, Hao; Yin, Feng-Xiang; Chen, Biao-Hua
Developing carbon catalyst materials using natural, abundant and renewable resources as precursors plays an increasingly important role in clean energy generation and environmental protection. In this work, N-doped pomelo-peel-derived carbon (NPC) materials were prepared using a widely available food waste-pomelo peels and melamine. The synthetic NPC exhibits well-defined porosities and a highly doped-N content (e.g. 6.38 at% for NPC-2), therefore affords excellent oxygen reduction reaction (ORR) catalytic activities in alkaline electrolytes. NPC was further integrated with ZIF-67 to form ZIF-67@NPC hybrids through solvothermal reactions. The hybrid catalysts show substantially enhanced ORR catalytic activities comparable to that of commercial 20 wamore » Pt/C. Furthermore, the catalysts also exhibit excellent oxygen evolution reaction (OER) catalytic activities. Among all prepared ZIF-67@NPC hybrids, the optimal composition with ZIF-67 to NPC ratio of 2:1 exhibits the best ORR and OER bifunctional catalytic performance and the smallest Delta E (E-OER@10 mA cm(-2)-E-ORR@-1 mA cm(-2)) value of 0.79 V. The catalyst also demonstrated desirable 4-electron transfer pathways and superior catalytic stabilities. The Co-N-4 in ZIF-67, electrochemical active surface area, and the strong interactions between ZIF-67 and NPC are attributed as the main contributors to the bifunctional catalytic activities. These factors act synergistically, resulting in substantially enhanced bifunctional catalytic activities and stabilities; consequently, this hybrid catalyst is among the best of the reported bifunctional electrocatalysts and is promising for use in metal-air batteries and fuel cells. (C) 2016 Elsevier B.V. All rights reserved.« less
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Tyrosyl Radicals in Dehaloperoxidase
Dumarieh, Rania; D'Antonio, Jennifer; Deliz-Liang, Alexandria; Smirnova, Tatyana; Svistunenko, Dimitri A.; Ghiladi, Reza A.
2013-01-01
Dehaloperoxidase (DHP) from Amphitrite ornata, having been shown to catalyze the hydrogen peroxide-dependent oxidation of trihalophenols to dihaloquinones, is the first oxygen binding globin that possesses a biologically relevant peroxidase activity. The catalytically competent species in DHP appears to be Compound ES, a reactive intermediate that contains both a ferryl heme and a tyrosyl radical. By simulating the EPR spectra of DHP activated by H2O2, Thompson et al. (Thompson, M. K., Franzen, S., Ghiladi, R. A., Reeder, B. J., and Svistunenko, D. A. (2010) J. Am. Chem. Soc. 132, 17501–17510) proposed that two different radicals, depending on the pH, are formed, one located on either Tyr-34 or Tyr-28 and the other on Tyr-38. To provide additional support for these simulation-based assignments and to deduce the role(s) that tyrosyl radicals play in DHP, stopped-flow UV-visible and rapid-freeze-quench EPR spectroscopic methods were employed to study radical formation in DHP when three tyrosine residues, Tyr-28, Tyr-34, and Tyr-38, were replaced either individually or in combination with phenylalanines. The results indicate that radicals form on all three tyrosines in DHP. Evidence for the formation of DHP Compound I in several tyrosine mutants was obtained. Variants that formed Compound I showed an increase in the catalytic rate for substrate oxidation but also an increase in heme bleaching, suggesting that the tyrosines are necessary for protecting the enzyme from oxidizing itself. This protective role of tyrosines is likely an evolutionary adaptation allowing DHP to avoid self-inflicted damage in the oxidative environment. PMID:24100039
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Boyko, Konstantin M., E-mail: kmb@inbi.ras.ru; National Research Center “Kurchatov Institute”, Kurchatov Complex of NBICS-technologies, Akad. Kurchatova sqr., 1, Moscow, 123182; Gorbacheva, Marina A.
2016-09-02
Aminoglycoside phosphotransferases represent a broad class of enzymes that promote bacterial resistance to aminoglycoside antibiotics via the phosphorylation of hydroxyl groups in the latter. Here we report the spatial structure of the 3′-aminoglycoside phosphotransferase of novel VIII class (AphVIII) solved by X-ray diffraction method with a resolution of 2.15 Å. Deep analysis of APHVIII structure and its comparison with known structures of aminoglycoside phosphotransferases of various types reveals that AphVIII has a typical two-domain fold and, however, possesses some unique characteristics that distinguish the enzyme from its known homologues. The most important difference is the presence of the activation loop withmore » unique Ser146 residue. We demonstrate that in the apo-state of the enzyme the activation loop does not interact with other parts of the enzyme and seems to adopt catalytically competent state only after substrate binding. - Highlights: • 3D structure of the novel aminoglycoside phosphotransferase AphVIII was obtained. • AphVIII activation loop is clearly identified in the electron density. • AphVIII has some unique structural features in its substrate C-ring binding pocket.« less
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Enzymatic and antisense effects of a specific anti-Ki-ras ribozyme in vitro and in cell culture.
Giannini, C D; Roth, W K; Piiper, A; Zeuzem, S
1999-01-01
Due to their mode of action, ribozymes show antisense effects in addition to their specific cleavage activity. In the present study we investigated whether a hammerhead ribozyme is capable of cleaving mutated Ki-ras mRNA in a pancreatic carcinoma cell line and whether antisense effects contribute to the activity of the ribozyme. A 2[prime]-O-allyl modified hammerhead ribozyme was designed to cleave specifically the mutated form of the Ki- ras mRNA (GUU motif in codon 12). The activity was monitored by RT-PCR on Ki- ras RNA expression by determination of the relative amount of wild type to mutant Ki-ras mRNA, by 5-bromo-2[prime]-deoxy-uridine incorporation on cell proliferation and by colony formation in soft agar on malignancy in the human pancreatic adenocarcinoma cell line CFPAC-1, which is heterozygous for the Ki-ras mutation. A catalytically inactive ribozyme was used as control to differentiate between antisense and cleavage activity and a ribozyme with random guide sequences as negative control. The catalytically active anti-Ki-ras ribozyme was at least 2-fold more potent in decreasing cellular Ki-ras mRNA levels, inhibiting cell proliferation and colony formation in soft agar than the catalytically inactive ribozyme. The catalytically active anti-Ki-ras ribozyme, but not the catalytically inactive or random ribozyme, increased the ratio of wild type to mutated Ki-ras mRNA in CFPAC-1 cells. In conclusion, both cleavage activity and antisense effects contribute to the activity of the catalytically active anti-Ki-ras hammerhead ribozyme. Specific ribozymes might be useful in the treatment of pancreatic carcinomas containing an oncogenic GTT mutation in codon 12 of the Ki-ras gene. PMID:10373591
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NASA Astrophysics Data System (ADS)
Chen, Sihui; Chi, Maoqiang; Zhu, Yun; Gao, Mu; Wang, Ce; Lu, Xiaofeng
2018-05-01
Superaramagnetic Fe3O4 nanomaterials are good candidates as enzyme mimics due to their excellent catalytic activity, high stability and facile synthesis. However, the morphology of Fe3O4 nanomaterials has much influence on their enzyme-like catalytic activity. In this work, we have developed a simple polymer-assisted thermochemical reduction approach to prepare Fe3O4 nanofibers for peroxidase-like catalytic applications. The as-prepared Fe3O4 nanofibers show a higher catalytic activity than commercial Fe3O4 nanoparticles. The steady-state kinetic assay result shows that the Michaelis-Menten constant value of the as-obtained Fe3O4 nanofibers is similar to that of horseradish peroxidase (HRP), indicating their superior affinity to the 3,3‧,5,5‧-tetramethylbenzidine (TMB) and H2O2 substrate. Based on the outstanding catalytic activity, a sensing platform for the detection of L-cysteine has been performed and the limit of detection is as low as 0.028 μM. In addition, an excellent selectivity toward L-cysteine over other types of amino acids, glucose and metal ions has been achieved as well. This work offers an original means for the fabrication of superparamagnetic Fe3O4 nanofibers and demonstrates their delightful potential applications in the fields of biosensing, environmental monitoring, and medical diagnostics.
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NASA Astrophysics Data System (ADS)
Kimi, Melody; Jaidie, Mohd Muazmil Hadi; Pang, Suh Cem
2018-01-01
A series of bimetallic copper-nickel (CuNix, x = 0.1, 0.2, 0.5 and 1) nanoparticles supported on activated carbon (AC) were prepared by deposition-precipitation method for the oxidation of benzyl alcohol to benzaldehyde using hydrogen peroxide as oxidising agent. Analyses by means of X-ray Diffraction (XRD) and Scanning Electron Microscopy (SEM) confirmed that Cu and Ni was successfully added on the surface of activated carbon. CuNi1/AC showed the best catalytic activity for the oxidation of benzyl alcohols to the corresponding aldehyde within a short reaction period at 80 °C. The catalytic performance is significantly enhanced by the addition of equal amount of Ni as compared to the monometallic counterpart. This result indicates the synergistic effect between Ni and Cu particles in the catalytic oxidation reaction.
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Mechanistic Studies on the Copper-Catalyzed N-Arylation of Amides
Strieter, Eric R.; Bhayana, Brijesh; Buchwald, Stephen L.
2009-01-01
The copper-catalyzed N-arylation of amides, i.e., the Goldberg reaction, is an efficient method for the construction of products relevant to both industry and academic settings. Herein, we present mechanistic details concerning the catalytic and stoichiometric N-arylation of amides. In the context of the catalytic reaction, our findings reveal the importance of chelating diamine ligands in controlling the concentration of the active catalytic species. The consistency between the catalytic and stoichiometric results suggest that the activation of aryl halides occurs through a 1,2-diamine-ligated copper(I) amidate complex. Kinetic studies on the stoichiometric N-arylation of aryl iodides using 1,2-diamine ligated Cu(I) amidates also provide insights into the mechanism of aryl halide activation. PMID:19072233
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Reversible Regulation of Catalytic Activity of Gold Nanoparticles with DNA Nanomachines
NASA Astrophysics Data System (ADS)
Zhou, Peipei; Jia, Sisi; Pan, Dun; Wang, Lihua; Gao, Jimin; Lu, Jianxin; Shi, Jiye; Tang, Zisheng; Liu, Huajie
2015-09-01
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.
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Probing active cocaine vaccination performance through catalytic and noncatalytic hapten design.
Cai, Xiaoqing; Whitfield, Timothy; Hixon, Mark S; Grant, Yanabel; Koob, George F; Janda, Kim D
2013-05-09
Presently, there are no FDA-approved medications to treat cocaine addiction. Active vaccination has emerged as one approach to intervene through the rapid sequestering of the circulating drug, thus terminating both psychoactive effects and drug toxicity. Herein, we report our efforts examining two complementary, but mechanistically distinct active vaccines, i.e., noncatalytic and catalytic, for cocaine treatment. A cocaine-like hapten GNE and a cocaine transition-state analogue GNT were used to generate the active vaccines, respectively. GNE-KLH (keyhole limpet hemocyannin) was found to elicit persistent high-titer, cocaine-specific antibodies and blunt cocaine-induced locomotor behaviors. Catalytic antibodies induced by GNT-KLH were also shown to produce potent titers and suppress locomotor response in mice; however, upon repeated cocaine challenges, the vaccine's protecting effects waned. In depth kinetic analysis suggested that loss of catalytic activity was due to antibody modification by cocaine. The work provides new insights for the development of active vaccines for the treatment of cocaine abuse.
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Probing Active Cocaine Vaccination Performance through Catalytic and Noncatalytic Hapten Design
Cai, Xiaoqing; Whitfield, Timothy; Hixon, Mark S.; Grant, Yanabel; Koob, George F.; Janda, Kim D.
2013-01-01
Presently, there are no FDA-approved medications to treat cocaine addiction. Active vaccination has emerged as one approach to intervene through the rapid sequestering of the circulating drug, thus terminating both psychoactive effects and drug toxicity. Herein, we report our efforts examining two complimentary, but mechanistically distinct active vaccines, i.e., noncatalytic and catalytic, for cocaine treatment. A cocaine-like hapten GNE and a cocaine transition-state analogue GNT were used to generate the active vaccines, respectively. GNE-KLH was found to elicit persistent high-titer, cocaine-specific antibodies, and blunt cocaine induced locomotor behaviors. Catalytic antibodies induced by GNT-KLH were also shown to produce potent titers and suppress locomotor response in mice; however, upon repeated cocaine challenges the vaccine’s protecting effects waned. In depth kinetic analysis suggested that loss of catalytic activity was due to antibody modification by cocaine. The work provides new insights for the development of active vaccines for the treatment of cocaine abuse. PMID:23627877
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CuNi NPs supported on MIL-101 as highly active catalysts for the hydrolysis of ammonia borane
NASA Astrophysics Data System (ADS)
Gao, Doudou; Zhang, Yuhong; Zhou, Liqun; Yang, Kunzhou
2018-01-01
The catalysts containing Cu, Ni bi-metallic nanoparticles were successfully synthesized by in-situ reduction of Cu2+ and Ni2+ salts into the highly porous and hydrothermally stable metal-organic framework MIL-101 via a simple liquid impregnation method. When the total amount of loading metal is 3 × 10-4 mol, Cu2Ni1@MIL-101 catalyst shows higher catalytic activity comparing to CuxNiy@MIL-101 with different molar ratio of Cu and Ni (x, y = 0, 0.5, 1.5, 2, 2.5, 3). Cu2Ni1@MIL-101 catalyst has the highest catalytic activity comparing to mono-metallic Cu and Ni counterparts and pure bi-metallic CuNi nanoparticles in hydrolytic dehydrogeneration of ammonia borane (AB) at room temperature. Additionally, in the hydrolysis reaction, the Cu2Ni1@MIL- 101 catalyst possesses excellent catalytic performances, which exhibit highly catalytic activity with turn over frequency (TOF) value of 20.9 mol H2 min-1 Cu mol-1 and a very low activation energy value of 32.2 kJ mol-1. The excellent catalytic activity has been successfully achieved thanks to the strong bi-metallic synergistic effects, uniform distribution of nanoparticles and the bi-functional effects between CuNi nanoparticles and the host of MIL-101. Moreover, the catalyst also displays satisfied durable stability after five cycles for the hydrolytically releasing H2 from AB. The non-noble metal catalysts have broad prospects for commercial applications in the field of hydrogen-stored materials due to the low prices and excellent catalytic activity.
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Wang, Mengfan; Lv, Yuqi; Liu, Xiaojing; Qi, Wei; Su, Rongxin; He, Zhimin
2016-06-08
In this study, an artificial hydrolase was developed by combining the catalytic Ser/His/Asp triad with N-fluorenylmethoxycarbonyl diphenylalanine (Fmoc-FF), followed by coassembly of the peptides into nanofibers (CoA-HSD). The peptide-based nanofibers provide an ideal supramolecular framework to support the functional groups. Compared with the self-assembled catalytic nanofibers (SA-H), which contain only the catalytic histidine residue, the highest activity of CoA-HSD occurs when histidine, serine, and aspartate residues are at a ratio of 40:1:1. This indicates that the well-ordered nanofiber structure and the synergistic effects of serine and aspartate residues contribute to the enhancement in activity. Additionally, for the first time, molecular imprinting was applied to further enhance the activity of the peptide-based artificial enzyme (CoA-HSD). p-NPA was used as the molecular template to arrange the catalytic Ser/His/Asp triad residues in the proper orientation. As a result, the activity of imprinted coassembled CoA-HSD nanofibers is 7.86 times greater than that of nonimprinted CoA-HSD and 13.48 times that of SA-H.
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High-temperature catalytically assisted combustion. Final report, 1 August 1981-31 July 1983
DOE Office of Scientific and Technical Information (OSTI.GOV)
Bracco, F.V.; Royce, B.S.H.; Santavicca, D.A.
1983-07-31
Results of research on a two-dimensional, transient catalytic combustion model and on a high temperature perovskite catalyst are presented. A recently developed two-dimensional, transient model was used to study the ignition of carbon monoxide/air mixtures in a platinum-coated catalytic honeycomb. Comparisons between calculated and measured steady-state substrate temperature profiles and exhaust-gas compositions show good agreement. A platinum-doped perovskite catalyst proposed will exhibit low-temperature light off and high-temperature stability. Preliminary tests using a perovskite powder with 1 wt.% platinium are encouraging, showing very little change in surface activity when used with propane fuel. Variations in catalytic activity from sample to samplemore » were also found, and after extensive testing the cause of these variations could not be identified. However, preliminary tests using Fourier-transform infrared photoacoustic spectroscopy do indicate differences in the various catalyst samples that may be related to the difference in catalytic activity. The use of bench-top-oven and differential-scanning-calorimetry techniques for screening catalysts in terms of relative activity and aging characteristics were also demonstrated.« less
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Murphy, Jesse R.; Donini, Stefano; Kappock, T. Joseph
2015-01-01
Citrate synthase (CS) plays a central metabolic role in aerobes and many other organisms. The CS reaction comprises two half-reactions: a Claisen aldol condensation of acetyl-CoA (AcCoA) and oxaloacetate (OAA) that forms citryl-CoA (CitCoA), and CitCoA hydrolysis. Protein conformational changes that ‘close’ the active site play an important role in the assembly of a catalytically competent condensation active site. CS from the thermoacidophile Thermoplasma acidophilum (TpCS) possesses an endogenous Trp fluorophore that can be used to monitor the condensation reaction. The 2.2 Å resolution crystal structure of TpCS fused to a C-terminal hexahistidine tag (TpCSH6) reported here is an ‘open’ structure that, when compared with several liganded TpCS structures, helps to define a complete path for active-site closure. One active site in each dimer binds a neighboring His tag, the first nonsubstrate ligand known to occupy both the AcCoA and OAA binding sites. Solution data collectively suggest that this fortuitous interaction is stabilized by the crystalline lattice. As a polar but almost neutral ligand, the active site–tail interaction provides a new starting point for the design of bisubstrate-analog inhibitors of CS. PMID:26457521
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Murphy, Jesse R.; Donini, Stefano; Kappock, T. Joseph
2015-10-01
Citrate synthase (CS) plays a central metabolic role in aerobes and many other organisms. The CS reaction comprises two half-reactions: a Claisen aldol condensation of acetyl-CoA (AcCoA) and oxaloacetate (OAA) that forms citryl-CoA (CitCoA), and CitCoA hydrolysis. Protein conformational changes that `close' the active site play an important role in the assembly of a catalytically competent condensation active site. CS from the thermoacidophile Thermoplasma acidophilum (TpCS) possesses an endogenous Trp fluorophore that can be used to monitor the condensation reaction. The 2.2 Å resolution crystal structure of TpCS fused to a C-terminal hexahistidine tag (TpCSH6) reported here is an `open'more » structure that, when compared with several liganded TpCS structures, helps to define a complete path for active-site closure. One active site in each dimer binds a neighboring His tag, the first nonsubstrate ligand known to occupy both the AcCoA and OAA binding sites. Solution data collectively suggest that this fortuitous interaction is stabilized by the crystalline lattice. In conclusion, as a polar but almost neutral ligand, the active site-tail interaction provides a new starting point for the design of bisubstrate-analog inhibitors of CS.« less
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Murphy, Jesse R; Donini, Stefano; Kappock, T Joseph
2015-10-01
Citrate synthase (CS) plays a central metabolic role in aerobes and many other organisms. The CS reaction comprises two half-reactions: a Claisen aldol condensation of acetyl-CoA (AcCoA) and oxaloacetate (OAA) that forms citryl-CoA (CitCoA), and CitCoA hydrolysis. Protein conformational changes that `close' the active site play an important role in the assembly of a catalytically competent condensation active site. CS from the thermoacidophile Thermoplasma acidophilum (TpCS) possesses an endogenous Trp fluorophore that can be used to monitor the condensation reaction. The 2.2 Å resolution crystal structure of TpCS fused to a C-terminal hexahistidine tag (TpCSH6) reported here is an `open' structure that, when compared with several liganded TpCS structures, helps to define a complete path for active-site closure. One active site in each dimer binds a neighboring His tag, the first nonsubstrate ligand known to occupy both the AcCoA and OAA binding sites. Solution data collectively suggest that this fortuitous interaction is stabilized by the crystalline lattice. As a polar but almost neutral ligand, the active site-tail interaction provides a new starting point for the design of bisubstrate-analog inhibitors of CS.
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Li, Chao; Wang, Dan; Wang, Yan; Li, Guode; Hu, Guijuan; Wu, Shiwei; Cao, Zhongqiu; Zhang, Ke
2018-08-15
In this work, nanostructured Co-W-B films are successfully synthesized on the foam sponge by electroless plating method and employed as the catalysts with enhanced catalytic activity towards hydrogen evolution from the hydrolysis of ammonia borane (NH 3 BH 3 , AB) at room temperature. The particle size of the as-prepared Co-W-B film catalysts is varied by adjusting the depositional pH value to identify the most suitable particle size for hydrogen evolution of AB hydrolysis. The Co-W-B film catalyst with the particle size of about 67.3 nm shows the highest catalytic activity and can reach a hydrogen generation rate of 3327.7 mL min -1 g cat -1 at 298 K. The activation energy of the hydrolysis reaction of AB is determined to be 32.2 kJ mol -1 . Remarkably, the as-obtained Co-W-B film is also a reusable catalyst preserving 78.4% of their initial catalytic activity even after 5 cycles in hydrolysis of AB at room temperature. Thus, the enhanced catalytic activity illustrates that the Co-W-B film is a promising catalyst for AB hydrolytic dehydrogenation in fuel cells and the related fields. Copyright © 2018 Elsevier Inc. All rights reserved.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Xue, Teng; Lin, Zhaoyang; Chiu, Chin-Yi
Metallic nanoparticles are emerging as an exciting class of heterogeneous catalysts with the potential advantages of exceptional activity, stability, recyclability, and easier separation than homogeneous catalysts. The traditional colloid nanoparticle syntheses usually involve strong surface binding ligands that could passivate the surface active sites and result in poor catalytic activity. The subsequent removal of surface ligands could reactivate the surface but often leads to metal ion leaching and/or severe Ostwald ripening with diminished catalytic activity or poor stability. Molecular ligand engineering represents a powerful strategy for the design of homogeneous molecular catalysts but is insufficiently explored for nanoparticle catalysts tomore » date. We report a systematic investigation on molecular ligand modulation of palladium (Pd) nanoparticle catalysts. Our studies show that β-functional groups of butyric acid ligand on Pd nanoparticles can significantly modulate the catalytic reaction process to modify the catalytic activity and stability for important aerobic reactions. With a β-hydroxybutyric acid ligand, the Pd nanoparticle catalysts exhibit exceptional catalytic activity and stability with an unsaturated turnover number (TON) >3000 for dehydrogenative oxidation of cyclohexenone to phenol, greatly exceeding that of homogeneous Pd(II) catalysts (TON, ~30). This study presents a systematic investigation of molecular ligand modulation of nanoparticle catalysts and could open up a new pathway toward the design and construction of highly efficient and robust heterogeneous catalysts through molecular ligand engineering.« less
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Gao, Shuiying; Li, Weijin; Cao, Rong
2015-03-01
Palladium-pyridyl catalytic films, (PdCl2/bpy)n, were created by alternating immersions of a substrate in PdCl2 and bpy (bpy=4, 4'-bipyridyl) solutions. The as-prepared (PdCl2/bpy)10 catalyst demonstrated a remarkable catalytic activity toward hydrogenation of styrene under mild conditions and the turnover frequency (TOF) is as high as 6944h(-1). Pd(II) ions of (PdCl2/bpy)n films are in situ reduced to Pd nanoparticles (NPs) during the hydrogenation of styrene process, which results in the catalytic activity of the films. The results of X-ray photoelectron spectroscopy (XPS) and transmission electron microscopy (TEM) further demonstrate that Pd(II) ions of (PdCl2/bpy)n films were gradually converted to Pd(0) states. The catalytic activity is related to bilayer numbers and the activity increases with the number of bilayers below 10 bilayers. The solid substrates coated with (PdCl2/bpy)n multilayer catalysts were easily removed from the reaction mixture without separation filtration. Moreover, (PdCl2/bpy)n catalysts were reused for 10 consecutive reactions without loss of activity. The present (PdCl2/bpy)n heterogeneous catalysts have the advantages of easy separation and good recyclability. Copyright © 2014 Elsevier Inc. All rights reserved.
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Radical SAM catalysis via an organometallic intermediate with an Fe-[5'-C]-deoxyadenosyl bond.
Horitani, Masaki; Shisler, Krista; Broderick, William E; Hutcheson, Rachel U; Duschene, Kaitlin S; Marts, Amy R; Hoffman, Brian M; Broderick, Joan B
2016-05-13
Radical S-adenosylmethionine (SAM) enzymes use a [4Fe-4S] cluster to cleave SAM to initiate diverse radical reactions. These reactions are thought to involve the 5'-deoxyadenosyl radical intermediate, which has not yet been detected. We used rapid freeze-quenching to trap a catalytically competent intermediate in the reaction catalyzed by the radical SAM enzyme pyruvate formate-lyase activating enzyme. Characterization of the intermediate by electron paramagnetic resonance and (13)C, (57)Fe electron nuclear double-resonance spectroscopies reveals that it contains an organometallic center in which the 5' carbon of a SAM-derived deoxyadenosyl moiety forms a bond with the unique iron site of the [4Fe-4S] cluster. Discovery of this intermediate extends the list of enzymatic bioorganometallic centers to the radical SAM enzymes, the largest enzyme superfamily known, and reveals intriguing parallels to B12 radical enzymes. Copyright © 2016, American Association for the Advancement of Science.
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Origins of stereoselectivity in evolved ketoreductases.
Noey, Elizabeth L; Tibrewal, Nidhi; Jiménez-Osés, Gonzalo; Osuna, Sílvia; Park, Jiyong; Bond, Carly M; Cascio, Duilio; Liang, Jack; Zhang, Xiyun; Huisman, Gjalt W; Tang, Yi; Houk, Kendall N
2015-12-22
Mutants of Lactobacillus kefir short-chain alcohol dehydrogenase, used here as ketoreductases (KREDs), enantioselectively reduce the pharmaceutically relevant substrates 3-thiacyclopentanone and 3-oxacyclopentanone. These substrates differ by only the heteroatom (S or O) in the ring, but the KRED mutants reduce them with different enantioselectivities. Kinetic studies show that these enzymes are more efficient with 3-thiacyclopentanone than with 3-oxacyclopentanone. X-ray crystal structures of apo- and NADP(+)-bound selected mutants show that the substrate-binding loop conformational preferences are modified by these mutations. Quantum mechanical calculations and molecular dynamics (MD) simulations are used to investigate the mechanism of reduction by the enzyme. We have developed an MD-based method for studying the diastereomeric transition state complexes and rationalize different enantiomeric ratios. This method, which probes the stability of the catalytic arrangement within the theozyme, shows a correlation between the relative fractions of catalytically competent poses for the enantiomeric reductions and the experimental enantiomeric ratio. Some mutations, such as A94F and Y190F, induce conformational changes in the active site that enlarge the small binding pocket, facilitating accommodation of the larger S atom in this region and enhancing S-selectivity with 3-thiacyclopentanone. In contrast, in the E145S mutant and the final variant evolved for large-scale production of the intermediate for the antibiotic sulopenem, R-selectivity is promoted by shrinking the small binding pocket, thereby destabilizing the pro-S orientation.
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Origins of stereoselectivity in evolved ketoreductases
Noey, Elizabeth L.; Tibrewal, Nidhi; Jiménez-Osés, Gonzalo; Osuna, Sílvia; Park, Jiyong; Bond, Carly M.; Cascio, Duilio; Liang, Jack; Zhang, Xiyun; Huisman, Gjalt W.; Tang, Yi; Houk, Kendall N.
2015-01-01
Mutants of Lactobacillus kefir short-chain alcohol dehydrogenase, used here as ketoreductases (KREDs), enantioselectively reduce the pharmaceutically relevant substrates 3-thiacyclopentanone and 3-oxacyclopentanone. These substrates differ by only the heteroatom (S or O) in the ring, but the KRED mutants reduce them with different enantioselectivities. Kinetic studies show that these enzymes are more efficient with 3-thiacyclopentanone than with 3-oxacyclopentanone. X-ray crystal structures of apo- and NADP+-bound selected mutants show that the substrate-binding loop conformational preferences are modified by these mutations. Quantum mechanical calculations and molecular dynamics (MD) simulations are used to investigate the mechanism of reduction by the enzyme. We have developed an MD-based method for studying the diastereomeric transition state complexes and rationalize different enantiomeric ratios. This method, which probes the stability of the catalytic arrangement within the theozyme, shows a correlation between the relative fractions of catalytically competent poses for the enantiomeric reductions and the experimental enantiomeric ratio. Some mutations, such as A94F and Y190F, induce conformational changes in the active site that enlarge the small binding pocket, facilitating accommodation of the larger S atom in this region and enhancing S-selectivity with 3-thiacyclopentanone. In contrast, in the E145S mutant and the final variant evolved for large-scale production of the intermediate for the antibiotic sulopenem, R-selectivity is promoted by shrinking the small binding pocket, thereby destabilizing the pro-S orientation. PMID:26644568
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Khodaverdi, Zeinab; Bahram, Abbas; Khalaji, Hassan; Kazemnejad, Anoshirvan
2013-10-01
The main purpose of this study was to determine which correlate, perceived motor competence or motor skill competence, best predicts girls' physical activity behavior. A sample of 352 girls (mean age=8.7, SD=0.3 yr) participated in this study. To assess motor skill competence and perceived motor competence, each child completed the Test of Gross Motor Development-2 and Physical Ability sub-scale of Marsh's Self-Description Questionnaire. Children's physical activity was assessed by the Physical Activity Questionnaire for Older Children. Multiple linear regression model was used to determine whether perceived motor competence or motor skill competence best predicts moderate-to-vigorous self-report physical activity. Multiple regression analysis indicated that motor skill competence and perceived motor competence predicted 21% variance in physical activity (R(2)=0.21, F=48.9, P=0.001), and motor skill competence (R(2)=0.15, ᵝ=0.33, P= 0.001) resulted in more variance than perceived motor competence (R(2)=0.06, ᵝ=0.25, P=0.001) in physical activity. Results revealed motor skill competence had more influence in comparison with perceived motor competence on physical activity level. We suggest interventional programs based on motor skill competence and perceived motor competence should be administered or implemented to promote physical activity in young girls.
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Recent Advances in Metal-Organic Frameworks for Heterogeneous Catalyzed Organic Transformations
DOE Office of Scientific and Technical Information (OSTI.GOV)
Sabale, Sandip R.; Zheng, Jian; Vemuri, Venkata Rama Ses
2016-12-12
In this review, we have summarized the recent advances in MOF based heterogeneous catalytic chemistry. Catalytic performance of various configurations of MOFs such as active sites, post synthetic modification and MOF derived catalyst, has been summarized in the context of various organic transformation reactions. Post synthetic modification of MOFs via functionalization of organic linkers with active catalytic moieties was deliberated. Also, efficacy of carbonaceous catalysts derived from MOFs was discussed.
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Clay catalyzed RNA synthesis under Martian conditions: Application for Mars return samples.
Joshi, Prakash C; Dubey, Krishna; Aldersley, Michael F; Sausville, Meaghen
2015-06-26
Catalysis by montmorillonites clay minerals is regarded as a feasible mechanism for the abiotic production and polymerization of key biomolecules on early Earth. We have investigated a montmorillonite-catalyzed reaction of the 5'-phosphorimidazolide of nucleosides as a model to probe prebiotic synthesis of RNA-type oligomers. Here we show that this model is specific for the generation of RNA oligomers despite deoxy-mononucleotides adsorbing equally well onto the montmorillonite catalytic surfaces. Optimum catalytic activity was observed over a range of pH (6-9) and salinity (1 ± 0.2 M NaCl). When the weathering steps of early Earth that generated catalytic montmorillonite were modified to meet Martian soil conditions, the catalytic activity remained intact without altering the surface layer charge. Additionally, the formation of oligomers up to tetramer was detected using as little as 0.1 mg of Na⁺-montmorillonite, suggesting that the catalytic activity of a Martian clay return sample can be investigated with sub-milligram scale samples. Copyright © 2015 Elsevier Inc. All rights reserved.
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Determination of a kinetic region in catalytic oxidation of carbon monoxide
NASA Technical Reports Server (NTRS)
Sultanov, M. Y.; Sadykhova, K. A.
1981-01-01
The catalytic activity of cupric oxide activated with ceric oxide in a braod interval of volumetric velocities was investigated. It was determined that for practical catalysts used in the diffuse region, dilution of the active substance by an inert diluent increases the effectiveness of the catalysts.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Onoda, M.; Haniu, M.; Yanagibashi, K.
1987-01-27
The affinity alkylating progesterone analogue 17-(bromoacetoxy)progesterone has been used to label the active site of a microsomal cytochrome P-450 enzyme from neonatal pig testis. The enzyme causes removal of the C/sub 20/ and C/sub 21/ side chains from the substrates progesterone and pregnenolone by catalyzing both 17-hydroxylase and C/sub 17,20/-lyase reactions, which produce the corresponding C/sub 1//sup 9/ steroidal precursors of testosterone. The progesterone analogue causes simultaneous inactivation of the two catalytic activities of the enzyme by a first-order kinetic process that obeys saturation kinetics. Progesterone and 17-hydroxyprogesterone each protect the enzyme against inactivation. The progesterone analogue is a competitivemore » inhibitor of the enzyme with K/sub i/ values of 8.4 ..mu..M and 7.8 ..mu..M for progesterone and 17-hydroxyprogesterone, respectively. The enzyme inactivation and kinetic data are consistent with a theory proposing that the analogue and the two substrates compete for the same active site. The radioactive analogue 17-((/sup 14/C)bromoacetoxy)progesterone causes inactivation of the enzyme with incorporation of 1.5-2.2 mol of the analogue per mole of inactivated enzyme. When this experiment is carried out in the presence of a substrate, then 0.9-1.2 mol of radioactive analogue is incorporated per mole of inactivated enzyme. The data suggest that the analogue can bind to two different sites, one of which is related to the catalytic site. Radiolabeled enzyme samples, from reactions of the /sup 14/C-labeled analogue with the enzyme alone or with enzyme in the presence of a substrate, were subjected to amino acid analysis and also in tryptic digestion and peptide mapping.« less
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Jack Preiss
Conversion of the Potato tuber ADP-glucose Pyrophopshorylase Regulatory Subunit into a Catalytic Subunit. ADP-glucose synthesis, a rate-limiting reaction in starch synthesis, is catalyzed by ADP-glucose pyrophosphorylase (ADPGlc PPase). The enzyme in plants is allosterically activated by 3-phosphoglycerate (3PGA) and inhibited by inorganic phosphate (Pi) and is composed of two subunits as a heterotetramer, a2b2. Subunit a is the catalytic subunit and subunit b is designated as the regulatory subunit.The b subunit increases the affinty of the activator for the catalytic subunit. Recent results have shown that the subunits are derived from the same ancestor subunit as the regulatory subunit canmore » be converted to a catalytically subunit via mutation of just two amino acids. Lys44 and Thr54 in the large subunit from potato tuber were converted to the homologous catalytic subunit residues, Arg33 and Lys43. The activity of the large subunit mutants cannot be readily tested with a co-expressed wild-type small (catalytic) subunit because of the intrinsic activity of the latter. We co-expressed the regulatory-subunit mutants with SmallD145N, an inactive S subunit in which the catalytic Asp145 was mutated. The activity of the small (catalytic) subunit was reduced more than three orders of magnitude. Coexpression of the L subunit double mutant LargeK44R/T54K with SmallD145N generated an enzyme with considerable activity, 10% and 18% of the wildtype enzyme, in the ADP-glucose synthetic and pyrophosphorolytic direction, respectively. Replacement of those two residues in the small subunit by the homologous amino acids in the L subunits (mutations R33K and K43T) decreased the activity one and two orders of magnitude. The wild-type enzyme and SmallD145NLargeK44R/T54K had very similar kinetic properties indicating that the substrate site has been conserved. The fact that only two mutations in the L subunit restored enzyme activity is very strong evidence that the large subunit is derived from the catalytic ancestor. Previous results showed that Asp145 in the small subunit of the wild-type is essential for catalysis, whereas the homologous Asp160 in the Large WT subunit is not. However, in this study, mutation D160N or D160E in the LK44R/T54K subunit abolished the activity, which shows the ancestral essential role of this residue and confirms that the catalysis of SmallD145NLarge K44R/T54K occurs in the L(b) subunit. A phylogenetic tree of the ADP-Glc PPases present in photosynthetic eukaryotes also sheds information about the origin of the subunits. The tree showed that plant Small and Large subunits can be divided into two and four distinct groups, respectively. The two main groups of S subunits are from dicot and monocot plants, whereas Large subunit groups correlate better with their documented tissue expression. The first Large-subunit group is generally expressed in photosynthetic tissues and comprises Large subunits from dicots and monocots. Group II displays a broader expression pattern, whereas groups III and IV are expressed in storage organs (roots, stems, tubers, seeds). Subunits from group III are only from dicot plants, whereas group IV are seed-specific subunits from monocots. These last two groups stem from the same branch of the phylogenetic tree and split before monocot and dicot separation. Thus few as two mutations turned the L subunit from Solanum tuberosum catalytic, showing that L and S subunits share a common catalytic ancestor, rather than a non-catalytic one. The L subunit evolved to have a regulatory role, lost catalytic residues more than 130 million years ago before monocots and dicots diverged, and preserved, possibly as a byproduct, the active site domain.« less
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Khodaverdi, Zeinab; Bahram, Abbas; Khalaji, Hassan; Kazemnejad, Anoshirvan
2013-01-01
Abstract Background The main purpose of this study was to determine which correlate, perceived motor competence or motor skill competence, best predicts girls’ physical activity behavior. Methods A sample of 352 girls (mean age=8.7, SD=0.3 yr) participated in this study. To assess motor skill competence and perceived motor competence, each child completed the Test of Gross Motor Development-2 and Physical Ability sub-scale of Marsh’s Self-Description Questionnaire. Children’s physical activity was assessed by the Physical Activity Questionnaire for Older Children. Multiple linear regression model was used to determine whether perceived motor competence or motor skill competence best predicts moderate-to-vigorous self-report physical activity. Results Multiple regression analysis indicated that motor skill competence and perceived motor competence predicted 21% variance in physical activity (R2=0.21, F=48.9, P=0.001), and motor skill competence (R2=0.15, ᵝ=0.33, P= 0.001) resulted in more variance than perceived motor competence (R2=0.06, ᵝ=0.25, P=0.001) in physical activity. Conclusion Results revealed motor skill competence had more influence in comparison with perceived motor competence on physical activity level. We suggest interventional programs based on motor skill competence and perceived motor competence should be administered or implemented to promote physical activity in young girls. PMID:26060623
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Radiofrequency treatment enhances the catalytic function of an immobilized nanobiohybrid catalyst
NASA Astrophysics Data System (ADS)
San, Boi Hoa; Ha, Eun-Ju; Paik, Hyun-Jong; Kim, Kyeong Kyu
2014-05-01
Biocatalysis, the use of enzymes in chemical transformation, has undergone intensive development for a wide range of applications. As such, maximizing the functionality of enzymes for biocatalysis is a major priority to enable industrial use. To date, many innovative technologies have been developed to address the future demand of enzymes for these purposes, but maximizing the catalytic activity of enzymes remains a challenge. In this study, we demonstrated that the functionality of a nanobiocatalyst could be enhanced by combining immobilization and radiofrequency (RF) treatment. Aminopeptidase PepA-encapsulating 2 nm platinum nanoparticles (PepA-PtNPs) with the catalytic activities of hydrolysis and hydrogenation were employed as multifunctional nanobiocatalysts. Immobilizing the nanobiocatalysts in a hydrogel using metal chelation significantly enhanced their functionalities, including catalytic power, thermal-stability, pH tolerance, organic solvent tolerance, and reusability. Most importantly, RF treatment of the hydrogel-immobilized PepA-PtNPs increased their catalytic power by 2.5 fold greater than the immobilized PepA. Our findings indicate that the catalytic activities and functionalities of PepA-PtNPs are greatly enhanced by the combination of hydrogel-immobilization and RF treatment. Based on our findings, we propose that RF treatment of nanobiohybrid catalysts immobilized on the bulk hydrogel represents a new strategy for achieving efficient biocatalysis.Biocatalysis, the use of enzymes in chemical transformation, has undergone intensive development for a wide range of applications. As such, maximizing the functionality of enzymes for biocatalysis is a major priority to enable industrial use. To date, many innovative technologies have been developed to address the future demand of enzymes for these purposes, but maximizing the catalytic activity of enzymes remains a challenge. In this study, we demonstrated that the functionality of a nanobiocatalyst could be enhanced by combining immobilization and radiofrequency (RF) treatment. Aminopeptidase PepA-encapsulating 2 nm platinum nanoparticles (PepA-PtNPs) with the catalytic activities of hydrolysis and hydrogenation were employed as multifunctional nanobiocatalysts. Immobilizing the nanobiocatalysts in a hydrogel using metal chelation significantly enhanced their functionalities, including catalytic power, thermal-stability, pH tolerance, organic solvent tolerance, and reusability. Most importantly, RF treatment of the hydrogel-immobilized PepA-PtNPs increased their catalytic power by 2.5 fold greater than the immobilized PepA. Our findings indicate that the catalytic activities and functionalities of PepA-PtNPs are greatly enhanced by the combination of hydrogel-immobilization and RF treatment. Based on our findings, we propose that RF treatment of nanobiohybrid catalysts immobilized on the bulk hydrogel represents a new strategy for achieving efficient biocatalysis. Electronic supplementary information (ESI) available. See DOI: 10.1039/c4nr00407h
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Buchneva, Olga; Gallo, Alessandro; Rossetti, Ilenia
2012-11-05
LaMnO(3), either pure or doped with 10 mol % Sr, has been prepared by flame pyrolysis in nanostructured form. Such catalysts have been tested for the catalytic flameless combustion of methane, achieving very high catalytic activity. The resistance toward poisoning by some model N-containing impurities has been checked in order to assess the possibility of operating the flameless catalytic combustion with biogas, possibly contaminated by S- or N-based compounds. This would be a significant improvement from the environmental point of view because the application of catalytic combustion to gas turbines would couple improved energy conversion efficiency and negligible noxious emissions, while the use of biogas would open the way to energy production from a renewable source by means of very efficient technologies. A different behavior has been observed for the two catalysts; namely, the undoped sample was more or less heavily poisoned, whereas the Sr-doped sample showed slightly increasing activity upon dosage of N-containing compounds. A possible reaction mechanism has been suggested, based on the initial oxidation of the organic backbone, with the formation of NO. The latter may adsorb more or less strongly depending on the availability of surface oxygen vacancies (i.e., depending on doping). Decomposition of NO may leave additional activated oxygen species on the surface, available for low-temperature methane oxidation and so improving the catalytic performance.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Corrêa, L. C.; Marchi-Salvador, D. P.; Cintra, A. C. O.
2006-08-01
A myotoxic Asp49-PLA{sub 2} with low catalytic activity from B. jararacussu (BthTX-II) was crystallized in the monoclinic crystal system; a complete X-ray diffraction data set was collected and a molecular-replacement solution was obtained. The oligomeric structure of BthTX-II resembles those of the Asp49-PLA{sub 2} PrTX-III and all bothropic Lys49-PLA{sub 2}s. For the first time, a complete X-ray diffraction data set has been collected from a myotoxic Asp49-phospholipase A{sub 2} (Asp49-PLA{sub 2}) with low catalytic activity (BthTX-II from Bothrops jararacussu venom) and a molecular-replacement solution has been obtained with a dimer in the asymmetric unit. The quaternary structure of BthTX-II resemblesmore » the myotoxin Asp49-PLA{sub 2} PrTX-III (piratoxin III from B. pirajai venom) and all non-catalytic and myotoxic dimeric Lys49-PLA{sub 2}s. In contrast, the oligomeric structure of BthTX-II is different from the highly catalytic and non-myotoxic BthA-I (acidic PLA{sub 2} from B. jararacussu). Thus, comparison between these structures should add insight into the catalytic and myotoxic activities of bothropic PLA{sub 2}s.« less
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Pt@Ag and Pd@Ag core/shell nanoparticles for catalytic degradation of Congo red in aqueous solution.
Salem, Mohamed A; Bakr, Eman A; El-Attar, Heba G
2018-01-05
Platinum/silver (Pt@Ag) and palladium/silver (Pd@Ag) core/shell NPs have been synthesized in two steps reaction using the citrate method. The progress of nanoparticle formation was followed by the UV/Vis spectroscopy. Transmission electron microscopy revealed spherical shaped core/shell nanoparticles with average particle diameter 32.17nm for Pt@Ag and 8.8nm for Pd@Ag. The core/shell NPs were further characterized by FT-IR and XRD. Reductive degradation of the Congo red dye was chosen to demonstrate the excellent catalytic activity of these core/shell nanostructures. The nanocatalysts act as electron mediators for the transfer of electrons from the reducing agent (NaBH 4 ) to the dye molecules. Effect of reaction parameters such as nanocatalyst dose, dye and NaBH 4 concentrations on the dye degradation was investigated. A comparison between the catalytic activities of both nanocatalysts was made to realize which of them the best in catalytic performance. Pd@Ag was the higher in catalytic activity over Pt@Ag. Such greater activity is originated from the smaller particle size and larger surface area. Pd@Ag nanocatalyst was catalytically stable through four subsequent reaction runs under the utilized reaction conditions. These findings can thus be considered as possible economical alternative for environmental safety against water pollution by dyes. Copyright © 2017. Published by Elsevier B.V.
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Pt@Ag and Pd@Ag core/shell nanoparticles for catalytic degradation of Congo red in aqueous solution
NASA Astrophysics Data System (ADS)
Salem, Mohamed A.; Bakr, Eman A.; El-Attar, Heba G.
2018-01-01
Platinum/silver (Pt@Ag) and palladium/silver (Pd@Ag) core/shell NPs have been synthesized in two steps reaction using the citrate method. The progress of nanoparticle formation was followed by the UV/Vis spectroscopy. Transmission electron microscopy revealed spherical shaped core/shell nanoparticles with average particle diameter 32.17 nm for Pt@Ag and 8.8 nm for Pd@Ag. The core/shell NPs were further characterized by FT-IR and XRD. Reductive degradation of the Congo red dye was chosen to demonstrate the excellent catalytic activity of these core/shell nanostructures. The nanocatalysts act as electron mediators for the transfer of electrons from the reducing agent (NaBH4) to the dye molecules. Effect of reaction parameters such as nanocatalyst dose, dye and NaBH4 concentrations on the dye degradation was investigated. A comparison between the catalytic activities of both nanocatalysts was made to realize which of them the best in catalytic performance. Pd@Ag was the higher in catalytic activity over Pt@Ag. Such greater activity is originated from the smaller particle size and larger surface area. Pd@Ag nanocatalyst was catalytically stable through four subsequent reaction runs under the utilized reaction conditions. These findings can thus be considered as possible economical alternative for environmental safety against water pollution by dyes.
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NASA Astrophysics Data System (ADS)
Huang, Haibao; Lu, Haoxian; Zhan, Yujie; Liu, Gaoyuan; Feng, Qiuyu; Huang, Huiling; Wu, Muyan; Ye, Xinguo
2017-01-01
Volatile organic compounds (VOCs) cause the major air pollution concern. In this study, a series of ZSM-5 supported transition metals were prepared by impregnation method. They were combined with vacuum UV (VUV) photo-oxidation in a continuous-flow packed-bed reactor and used for the degradation of benzene, a typical toxic VOCs. Compared with VUV photo-oxidation alone, the introduction of catalysts can greatly enhance benzene oxidation under the help of O3, the by-products from VUV irradiation, via ozone-assisted catalytic oxidation (OZCO). The catalytic activity of transition metals towards benzene oxidation followed the order: Mn > Co > Cu > Ni > Fe. Mn achieved the best catalytic activity due to the strongest capability for O3 catalytic decomposition and utilization. Benzene and O3 removal efficiency reached as high as 97% and 100% after 360 min, respectively. O3 was catalytically decomposed, generating highly reactive oxidants such as rad OH and rad O for benzene oxidation.
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Lee, Joungmin; Kim, Minjae; Seo, Youngsil; Lee, Yeonjin; Park, Hyunjoon; Byun, Sung June; Kwon, Myung-Hee
2017-11-01
The antigen-binding properties of single chain Fv antibodies (scFvs) can vary depending on the position and type of fusion tag used, as well as the host cells used for expression. The issue is even more complicated with a catalytic scFv antibody that binds and hydrolyses a specific antigen. Herein, we investigated the antigen-binding and -hydrolysing activities of the catalytic anti-nucleic acid antibody 3D8 scFv expressed in Escherichia coli or HEK293f cells with or without additional amino acid residues at the N- and C-termini. DNA-binding activity was retained in all recombinant forms. However, the DNA-hydrolysing activity varied drastically between forms. The DNA-hydrolysing activity of E. coli-derived 3D8 scFvs was not affected by the presence of a C-terminal human influenza haemagglutinin (HA) or His tag. By contrast, the activity of HEK293f-derived 3D8 scFvs was completely lost when additional residues were included at the N-terminus and/or when a His tag was incorporated at the C-terminus, whereas a HA tag at the C-terminus did not diminish activity. Thus, we demonstrate that the antigen-binding and catalytic activities of a catalytic antibody can be separately affected by the presence of additional residues at the N- and C-termini, and by the host cell type. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.
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Rubisco Activity: Effects of Drought Stress
PARRY, MARTIN A. J.; ANDRALOJC, P. JOHN; KHAN, SHAHNAZ; LEA, PETER J.; KEYS, ALFRED J.
2002-01-01
Ribulose‐1,5‐bisphosphate carboxylase/oxygenase (Rubisco) activity is modulated in vivo either by reaction with CO2 and Mg2+ to carbamylate a lysine residue in the catalytic site, or by the binding of inhibitors within the catalytic site. Binding of inhibitors blocks either activity or the carbamylation of the lysine residue that is essential for activity. At night, in many species, 2‐carboxyarabinitol‐1‐phosphate (CA1P) is formed which binds tightly to Rubisco, inhibiting catalytic activity. Recent work has shown that tight‐binding inhibitors can also decrease Rubisco activity in the light and contribute to the regulation of Rubisco activity. Here we determine the influence that such inhibitors of Rubisco exert on catalytic activity during drought stress. In tobacco plants, ‘total Rubisco activity’, i.e. the activity following pre‐incubation with CO2 and Mg2+, was positively correlated with leaf relative water content. However, ‘total Rubisco activity’ in extracts from leaves with low water potential increased markedly when tightly bound inhibitors were removed, thus increasing the number of catalytic sites available. This suggests that in tobacco the decrease of Rubisco activity under drought stress is not primarily the result of changes in activation by CO2 and Mg2+ but due rather to the presence of tight‐binding inhibitors. The amounts of inhibitor present in leaves of droughted tobacco based on the decrease in Rubisco activity per mg soluble protein were usually much greater than the amounts of the known inhibitors (CA1P and ‘daytime inhibitor’) that can be recovered in acid extracts. Alternative explanations for the difference between maximal and total activities are discussed. PMID:12102509
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Blakeslee, Weston W.; Demos-Davies, Kimberly M.; Lemon, Douglas D.; Lutter, Katharina M.; Cavasin, Maria A.; Payne, Sam; Nunley, Karin; Long, Carlin S.; McKinsey, Timothy A.; Miyamoto, Shelley D.
2017-01-01
Background Histone deacetylase (HDAC) inhibitors are promising therapeutics for various forms of cardiac disease. The purpose of this study was to assess cardiac HDAC catalytic activity and expression in children with single ventricle heart disease of right ventricular morphology (SV), as well as in a rodent model of right ventricular hypertrophy (RVH). Methods Homogenates of RV explants from non-failing controls and SV children were assayed for HDAC catalytic activity and HDAC isoform expression. Postnatal 1-day old rat pups were placed in hypoxic conditions and echocardiographic analysis, gene expression, HDAC catalytic activity and isoform expression studies of the RV were performed. Results Class I, IIa, and IIb HDAC catalytic activity and protein expression were elevated in hearts of SV children. Hypoxic neonatal rats demonstrated RVH, abnormal gene expression and elevated class I and class IIb HDAC catalytic activity and protein expression in the RV compared to control. Conclusions These data suggest that myocardial HDAC adaptations occur in the SV heart and could represent a novel therapeutic target. While further characterization of the hypoxic neonatal rat is needed, this animal model may be suitable for pre-clinical investigations of pediatric RV disease and could serve as a useful model for future mechanistic studies. PMID:28549058
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Dynamic restructuring drives catalytic activity on nanoporous gold–silver alloy catalysts
Zugic, Branko; Wang, Lucun; Heine, Christian; ...
2016-12-19
Bimetallic, nanostructured materials hold promise for improving catalyst activity and selectivity, yet little is known about the dynamic compositional and structural changes that these systems undergo during pretreatment that leads to efficient catalyst function. Here we use ozone-activated silver–gold alloys in the form of nanoporous gold as a case study to demonstrate the dynamic behaviour of bimetallic systems during activation to produce a functioning catalyst. We show that it is these dynamic changes that give rise to the observed catalytic activity. Advanced in situ electron microscopy and X-ray photoelectron spectroscopy are used to demonstrate that major restructuring and compositional changesmore » occur along the path to catalytic function for selective alcohol oxidation. Transient kinetic measurements correlate the restructuring to three types of oxygen on the surface. The direct influence of changes in surface silver concentration and restructuring at the nanoscale on oxidation activity is demonstrated. Finally, our results demonstrate that characterization of these dynamic changes is necessary to unlock the full potential of bimetallic catalytic materials.« less
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Dynamic restructuring drives catalytic activity on nanoporous gold–silver alloy catalysts
DOE Office of Scientific and Technical Information (OSTI.GOV)
Zugic, Branko; Wang, Lucun; Heine, Christian
Bimetallic, nanostructured materials hold promise for improving catalyst activity and selectivity, yet little is known about the dynamic compositional and structural changes that these systems undergo during pretreatment that leads to efficient catalyst function. Here we use ozone-activated silver–gold alloys in the form of nanoporous gold as a case study to demonstrate the dynamic behaviour of bimetallic systems during activation to produce a functioning catalyst. We show that it is these dynamic changes that give rise to the observed catalytic activity. Advanced in situ electron microscopy and X-ray photoelectron spectroscopy are used to demonstrate that major restructuring and compositional changesmore » occur along the path to catalytic function for selective alcohol oxidation. Transient kinetic measurements correlate the restructuring to three types of oxygen on the surface. The direct influence of changes in surface silver concentration and restructuring at the nanoscale on oxidation activity is demonstrated. Finally, our results demonstrate that characterization of these dynamic changes is necessary to unlock the full potential of bimetallic catalytic materials.« less
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Direct 3D Printing of Catalytically Active Structures
Manzano, J. Sebastian; Weinstein, Zachary B.; Sadow, Aaron D.; ...
2017-09-22
3D printing of materials with active functional groups can provide custom-designed structures that promote chemical conversions. Catalytically active architectures were produced by photopolymerizing bifunctional molecules using a commercial stereolithographic 3D printer. Functionalities in the monomers included a polymerizable vinyl group to assemble the 3D structures and a secondary group to provide them with active sites. The 3D-printed architectures containing accessible carboxylic acid, amine, and copper carboxylate functionalities were catalytically active for the Mannich, aldol, and Huisgen cycloaddition reactions, respectively. The functional groups in the 3D-printed structures were also amenable to post-printing chemical modification. And as proof of principle, chemically activemore » cuvette adaptors were 3D printed and used to measure in situ the kinetics of a heterogeneously catalyzed Mannich reaction in a conventional solution spectrophotometer. In addition, 3D-printed millifluidic devices with catalytically active copper carboxylate complexes were used to promote azide-alkyne cycloaddition under flow conditions. The importance of controlling the 3D architecture of the millifluidic devices was evidenced by enhancing reaction conversion upon increasing the complexity of the 3D prints.« less
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Direct 3D Printing of Catalytically Active Structures
DOE Office of Scientific and Technical Information (OSTI.GOV)
Manzano, J. Sebastian; Weinstein, Zachary B.; Sadow, Aaron D.
3D printing of materials with active functional groups can provide custom-designed structures that promote chemical conversions. Catalytically active architectures were produced by photopolymerizing bifunctional molecules using a commercial stereolithographic 3D printer. Functionalities in the monomers included a polymerizable vinyl group to assemble the 3D structures and a secondary group to provide them with active sites. The 3D-printed architectures containing accessible carboxylic acid, amine, and copper carboxylate functionalities were catalytically active for the Mannich, aldol, and Huisgen cycloaddition reactions, respectively. The functional groups in the 3D-printed structures were also amenable to post-printing chemical modification. And as proof of principle, chemically activemore » cuvette adaptors were 3D printed and used to measure in situ the kinetics of a heterogeneously catalyzed Mannich reaction in a conventional solution spectrophotometer. In addition, 3D-printed millifluidic devices with catalytically active copper carboxylate complexes were used to promote azide-alkyne cycloaddition under flow conditions. The importance of controlling the 3D architecture of the millifluidic devices was evidenced by enhancing reaction conversion upon increasing the complexity of the 3D prints.« less
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NASA Astrophysics Data System (ADS)
Chen, Xin; Zhou, Junwei; Chen, Shuangjing; Zhang, Hui
2018-06-01
To reduce the use of precious metals and maintain the catalytic activity for NH3 decomposition reaction, it is an effective way to construct bimetallic nanoparticles with special structures. In this paper, by using density functional theory methods, we investigated NH3 decomposition reaction on three types of core-shell nanoparticles M@Ni (M = Fe, Ru, Ir) with 13 core M atoms and 42 shell Ni atoms. The size of these three particles is about 1 nm. Benefit from alloying with Ru in this nanocluster, Ru@Ni core-shell nanoparticles exhibit catalytic activity comparable to that of single metal Ru, based on the analysis of the adsorption energy and potential energy diagram of NH3 decomposition, as well as N2 desorption processes. However, as for Fe@Ni and Ir@Ni core-shell nanoparticles, their catalytic activities are still unsatisfactory compared to the active metal Ru. In addition, in order to further explain the synergistic effect of bimetallic core-shell nanoparticles, the partial density of states were also calculated. The results show that d-band electrons provided by the core metal are the main factors affecting the entire catalytic process.
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Li, Zhipeng; Liu, Feng; You, Hong; Ding, Yi; Yao, Jie; Jin, Chao
2018-04-01
This paper investigated the performance of the combined system of catalytic ozonation and the gas-liquid-solid internal circulating fluidized bed reactor for the advanced treatment of biologically pretreated coal chemical industry wastewater (CCIW). The results indicated that with ozonation alone for 60min, the removal efficiency of chemical oxygen demand (COD) could reach 34%. The introduction of activated carbon, pumice, γ-Al 2 O 3 carriers improved the removal performance of COD, and the removal efficiency was increased by 8.6%, 4.2%, 2%, respectively. Supported with Mn, the catalytic performance of activated carbon and γ-Al 2 O 3 were improved significantly with COD removal efficiencies of 46.5% and 41.3%, respectively; however, the promotion effect of pumice supported with Mn was insignificant. Activated carbon supported with Mn had the best catalytic performance. The catalytic ozonation combined system of MnO X /activated carbon could keep ozone concentration at a lower level in the liquid phase, and promote the transfer of ozone from the gas phase to the liquid phase to improve ozonation efficiency.
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NASA Astrophysics Data System (ADS)
Shen, Meng; Han, Ali; Wang, Xijun; Ro, Yun Goo; Kargar, Alireza; Lin, Yue; Guo, Hua; Du, Pingwu; Jiang, Jun; Zhang, Jingyu; Dayeh, Shadi A.; Xiang, Bin
2015-02-01
Catalysts play a significant role in clean renewable hydrogen fuel generation through water splitting reaction as the surface of most semiconductors proper for water splitting has poor performance for hydrogen gas evolution. The catalytic performance strongly depends on the atomic arrangement at the surface, which necessitates the correlation of the surface structure to the catalytic activity in well-controlled catalyst surfaces. Herein, we report a novel catalytic performance of simple-synthesized porous NiO nanowires (NWs) as catalyst/co-catalyst for the hydrogen evolution reaction (HER). The correlation of catalytic activity and atomic/surface structure is investigated by detailed high resolution transmission electron microscopy (HRTEM) exhibiting a strong dependence of NiO NW photo- and electrocatalytic HER performance on the density of exposed high-index-facet (HIF) atoms, which corroborates with theoretical calculations. Significantly, the optimized porous NiO NWs offer long-term electrocatalytic stability of over one day and 45 times higher photocatalytic hydrogen production compared to commercial NiO nanoparticles. Our results open new perspectives in the search for the development of structurally stable and chemically active semiconductor-based catalysts for cost-effective and efficient hydrogen fuel production at large scale.
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NASA Astrophysics Data System (ADS)
Gao, Zhiyong; Liu, Xiao; Chang, Jiuli; Wu, Dapeng; Xu, Fang; Zhang, Lingcui; Du, Weimin; Jiang, Kai
2017-01-01
Graphene incorporated, N doped activated carbons (GNACs) are synthesized by alkali activation of graphene-polypyrrole composite (G-PPy) at different temperatures for application as electrode materials of supercapacitors. Under optimal activation temperature of 700 °C, the resultant samples, labeled as GNAC700, owns hierarchically porous texture with high specific surface area and efficient ions diffusion channels, N, O functionalized surface with apparent pseudocapacitance contribution and high wettability, thus can deliver a moderate capacitance, a high rate capability and a good cycleability when used as supercapacitor electrode. Additionally, the GNAC700 electrode demonstrates high catalytic activity for the redox reaction of pyrocatechol/o-quinone pair in H2SO4 electrolyte, thus enables a high pseudocapacitance from electrolyte. Under optimal pyrocatechol concentration in H2SO4 electrolyte, the electrode capacitance of GNAC700 increases by over 4 folds to 512 F g-1 at 1 A g-1, an excellent cycleability is also achieved simultaneously. Pyridinic- N is deemed to be responsible for the high catalytic activity. This work provides a promising strategy to ameliorate the capacitive performances of supercapacitors via the synergistic interaction between redox-active electrolyte and catalytic electrodes.
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A dynamic mechanism for allosteric activation of Aurora kinase A by activation loop phosphorylation.
Ruff, Emily F; Muretta, Joseph M; Thompson, Andrew R; Lake, Eric W; Cyphers, Soreen; Albanese, Steven K; Hanson, Sonya M; Behr, Julie M; Thomas, David D; Chodera, John D; Levinson, Nicholas M
2018-02-21
Many eukaryotic protein kinases are activated by phosphorylation on a specific conserved residue in the regulatory activation loop, a post-translational modification thought to stabilize the active DFG-In state of the catalytic domain. Here we use a battery of spectroscopic methods that track different catalytic elements of the kinase domain to show that the ~100 fold activation of the mitotic kinase Aurora A (AurA) by phosphorylation occurs without a population shift from the DFG-Out to the DFG-In state, and that the activation loop of the activated kinase remains highly dynamic. Instead, molecular dynamics simulations and electron paramagnetic resonance experiments show that phosphorylation triggers a switch within the DFG-In subpopulation from an autoinhibited DFG-In substate to an active DFG-In substate, leading to catalytic activation. This mechanism raises new questions about the functional role of the DFG-Out state in protein kinases. © 2018, Ruff et al.
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NASA Astrophysics Data System (ADS)
Almeida, T. S.; Palma, L. M.; Leonello, P. H.; Morais, C.; Kokoh, K. B.; De Andrade, A. R.
2012-10-01
The aim of this work was to perform a systematic study of the parameters that can influence the composition, morphology, and catalytic activity of PtSn/C nanoparticles and compare two different methods of nanocatalyst preparation, namely microwave-assisted heating (MW) and thermal decomposition of polymeric precursors (DPP). An investigation of the effects of the reducing and stabilizing agents on the catalytic activity and morphology of Pt75Sn25/C catalysts prepared by microwave-assisted heating was undertaken for optimization purposes. The effect of short-chain alcohols such as ethanol, ethylene glycol, and propylene glycol as reducing agents was evaluated, and the use of sodium acetate and citric acid as stabilizing agents for the MW procedure was examined. Catalysts obtained from propylene glycol displayed higher catalytic activity compared with catalysts prepared in ethylene glycol. Introduction of sodium acetate enhanced the catalytic activity, but this beneficial effect was observed until a critical acetate concentration was reached. Optimization of the MW synthesis allowed for the preparation of highly dispersed catalysts with average sizes lying between 2.0 and 5.0 nm. Comparison of the best catalyst prepared by MW with a catalyst of similar composition prepared by the polymeric precursors method showed that the catalytic activity of the material can be improved when a proper condition for catalyst preparation is achieved.
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Xue, Teng; Lin, Zhaoyang; Chiu, Chin-Yi; ...
2017-01-06
Metallic nanoparticles are emerging as an exciting class of heterogeneous catalysts with the potential advantages of exceptional activity, stability, recyclability, and easier separation than homogeneous catalysts. The traditional colloid nanoparticle syntheses usually involve strong surface binding ligands that could passivate the surface active sites and result in poor catalytic activity. The subsequent removal of surface ligands could reactivate the surface but often leads to metal ion leaching and/or severe Ostwald ripening with diminished catalytic activity or poor stability. Molecular ligand engineering represents a powerful strategy for the design of homogeneous molecular catalysts but is insufficiently explored for nanoparticle catalysts tomore » date. We report a systematic investigation on molecular ligand modulation of palladium (Pd) nanoparticle catalysts. Our studies show that β-functional groups of butyric acid ligand on Pd nanoparticles can significantly modulate the catalytic reaction process to modify the catalytic activity and stability for important aerobic reactions. With a β-hydroxybutyric acid ligand, the Pd nanoparticle catalysts exhibit exceptional catalytic activity and stability with an unsaturated turnover number (TON) >3000 for dehydrogenative oxidation of cyclohexenone to phenol, greatly exceeding that of homogeneous Pd(II) catalysts (TON, ~30). This study presents a systematic investigation of molecular ligand modulation of nanoparticle catalysts and could open up a new pathway toward the design and construction of highly efficient and robust heterogeneous catalysts through molecular ligand engineering.« less
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Sun, Qi; Aguila, Briana; Perman, Jason; Nguyen, Nicholas; Ma, Shengqian
2016-12-07
The combination of two or more reactive centers working in concert on a substrate to facilitate the reaction is now considered state of the art in catalysis, yet there still remains a tremendous challenge. Few heterogeneous systems of this sort have been exploited, as the active sites spatially separated within the rigid framework are usually difficult to cooperate. It is now shown that this roadblock can be surpassed. The underlying principle of the strategy presented here is the integration of catalytic components with excellent flexibility and porous heterogeneous catalysts, as demonstrated by the placement of linear ionic polymers in close proximity to surface Lewis acid active sites anchored on the walls of a covalent organic framework (COF). Using the cycloaddition of the epoxides and CO 2 as a model reaction, dramatic activity improvements have been achieved for the composite catalysts in relation to the individual catalytic component. Furthermore, they also clearly outperform the benchmark catalytic systems formed by the combination of the molecular organocatalysts and heterogeneous Lewis acid catalysts, while affording additional recyclability. The extraordinary flexibility and enriched concentration of the catalytically active moieties on linear polymers facilitate the concerted catalysis, thus leading to superior catalytic performance. This work therefore uncovers an entirely new strategy for designing bifunctional catalysts with double-activation behavior and opens a new avenue in the design of multicapable systems that mimic biocatalysis.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Fatimah, Is
Preparation of zeolite supported TiO{sub 2}, ZnO and ZrO{sub 2} and their catalytic activity was studied. Activated natural zeolite from Indonesia was utilized for the preparation and catalytic activity test on NO{sub x} reduction by NH{sub 3} and also 1-pentanol dehydration were examined. Physicochemical characterization of materials was studied by x-ray diffraction (XRD) measurement, scanning electron microscope, solid acidity determination and also gas sorption analysis. The results confirmed that the preparation gives some improvements on physicochemical characters suitable for catalysis mechanism in those reactions. Solid acidity and specific surface area contributed significantly to the activity.
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Detection of damaged DNA bases by DNA glycosylase enzymes.
Friedman, Joshua I; Stivers, James T
2010-06-22
A fundamental and shared process in all forms of life is the use of DNA glycosylase enzymes to excise rare damaged bases from genomic DNA. Without such enzymes, the highly ordered primary sequences of genes would rapidly deteriorate. Recent structural and biophysical studies are beginning to reveal a fascinating multistep mechanism for damaged base detection that begins with short-range sliding of the glycosylase along the DNA chain in a distinct conformation we call the search complex (SC). Sliding is frequently punctuated by the formation of a transient "interrogation" complex (IC) where the enzyme extrahelically inspects both normal and damaged bases in an exosite pocket that is distant from the active site. When normal bases are presented in the exosite, the IC rapidly collapses back to the SC, while a damaged base will efficiently partition forward into the active site to form the catalytically competent excision complex (EC). Here we review the unique problems associated with enzymatic detection of rare damaged DNA bases in the genome and emphasize how each complex must have specific dynamic properties that are tuned to optimize the rate and efficiency of damage site location.
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Atkinson, Nicky; Leitão, Nuno; Orr, Douglas J; Meyer, Moritz T; Carmo-Silva, Elizabete; Griffiths, Howard; Smith, Alison M; McCormick, Alistair J
2017-04-01
Introducing components of algal carbon concentrating mechanisms (CCMs) into higher plant chloroplasts could increase photosynthetic productivity. A key component is the Rubisco-containing pyrenoid that is needed to minimise CO 2 retro-diffusion for CCM operating efficiency. Rubisco in Arabidopsis was re-engineered to incorporate sequence elements that are thought to be essential for recruitment of Rubisco to the pyrenoid, namely the algal Rubisco small subunit (SSU, encoded by rbcS) or only the surface-exposed algal SSU α-helices. Leaves of Arabidopsis rbcs mutants expressing 'pyrenoid-competent' chimeric Arabidopsis SSUs containing the SSU α-helices from Chlamydomonas reinhardtii can form hybrid Rubisco complexes with catalytic properties similar to those of native Rubisco, suggesting that the α-helices are catalytically neutral. The growth and photosynthetic performance of complemented Arabidopsis rbcs mutants producing near wild-type levels of the hybrid Rubisco were similar to those of wild-type controls. Arabidopsis rbcs mutants expressing a Chlamydomonas SSU differed from wild-type plants with respect to Rubisco catalysis, photosynthesis and growth. This confirms a role for the SSU in influencing Rubisco catalytic properties. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.
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Effects of surfactants on lipase structure, activity, and inhibition.
Delorme, Vincent; Dhouib, Rabeb; Canaan, Stéphane; Fotiadu, Frédéric; Carrière, Frédéric; Cavalier, Jean-François
2011-08-01
Lipase inhibitors are the main anti-obesity drugs prescribed these days, but the complexity of their mechanism of action is making it difficult to develop new molecules for this purpose. The efficacy of these drugs is known to depend closely on the physico-chemistry of the lipid-water interfaces involved and on the unconventional behavior of the lipases which are their target enzymes. The lipolysis reaction which occurs at an oil-water interface involves complex equilibria between adsorption-desorption processes, conformational changes and catalytic mechanisms. In this context, surfactants can induce significant changes in the partitioning of the enzyme and the inhibitor between the water phase and lipid-water interfaces. Surfactants can be found at the oil-water interface where they compete with lipases for adsorption, but also in solution in the form of micellar aggregates and monomers that may interact with hydrophobic parts of lipases in solution. These various interactions, combined with the emulsification and dispersion of insoluble substrates and inhibitors, can either promote or decrease the activity and the inhibition of lipases. Here, we review some examples of the various effects of surfactants on lipase structure, activity and inhibition, which show how complex the various equilibria involved in the lipolysis reaction tend to be.
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NASA Astrophysics Data System (ADS)
Mao, Bao-Hua; Liu, Chang-Hai; Gao, Xu; Chang, Rui; Liu, Zhi; Wang, Sui-Dong
2013-10-01
The room-temperature ionic liquid assisted sputtering method is utilized to achieve the Pd-nanoparticle (NP)-graphene hybrid. The supported Pd NPs possess uniformly small sizes of 1-2 nm, which create huge surface area with ultralow Pd consumption and high NP stability. The Pd-NP-graphene hybrid is in situ characterized by the ambient pressure X-ray photoelectron spectroscopy using synchrotron radiation, and the results demonstrate high catalytic activity of the hybrid for CO oxidation. The catalytic behavior is reproducible for several catalytic cycles. The present simple and clean approach is promising to produce metal-NP-based high-efficiency catalysts for CO oxidation.
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HIGH-THROUGHPUT IDENTIFICATION OF CATALYTIC REDOX-ACTIVE CYSTEINE RESIDUES
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...
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Domènech, Berta; Ziegler, Kharla K; Carrillo, Fernando; Muñoz, Maria; Muraviev, Dimitri N; Macanás, Jorge
2013-05-16
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.
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Composite ceria-coated aerogels and methods of making the same
Eyring, Edward M; Ernst, Richard D; Turpin, Gregory C; Dunn, Brian C
2013-05-07
Ceria-coated aerogels can include an aerogel support material having a stabilized ceria coating thereon. The ceria coating can be formed by solution or vapor deposition of alcogels or aerogels. Additional catalytic metal species can also be incorporated into the coating to form multi-metallic compounds having improved catalytic activity. Further, the ceria coated aerogels retain high surface areas at elevated temperatures. Thus, improvements in catalytic activity and thermal stability can be achieved using these ceria-coated composite aerogels.
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NASA Astrophysics Data System (ADS)
Guzman Blas, Rolando Pedro
This thesis is focused on fuel cells using hydrogen, methanol and ethanol as fuel. Also, in the method of preparation of catalytic material for the anode: Supercritical Fluid Deposition (SFD) and impregnation method using ethylenediaminetetraacetic acid (EDTA) as a chelating agent. The first part of the thesis describes the general knowledge about Hydrogen Polymer Exchange Membrane Fuel Cell (HPEMFC),Direct Methanol Fuel Cell (DMFC) and Direct Ethanol Fuel Cell (DEFC), as well as the properties of Cerium and CeO2 (Ceria). The second part of the thesis describes the preparation of catalytic material by Supercritical Fluid Deposition (SFD). SFD was utilized to deposit Pt and ceria simultaneously onto gas diffusion layers. The Pt-ceria catalyst deposited by SFD exhibited higher methanol oxidation activity compared to the platinum catalyst alone. The linear sweep traces of the cathode made for the methanol cross over study indicate that Pt-Ceria/C as the anode catalyst, due to its better activity for methanol, improves the fuel utilization, minimizing the methanol permeation from anode to cathode compartment. The third and fourth parts of the thesis describe the preparation of material catalytic material Carbon-Platinum-Cerium by a simple and cheap impregnation method using EDTA as a chelating agent to form a complex with cerium (III). This preparation method allows the mass production of the material catalysts without additional significant cost. Fuel cell polarization and power curves experiments showed that the Carbon-Platinum-Cerium anode materials exhibited better catalytic activity than the only Vulcan-Pt catalysts for DMFC, DEFC and HPEMFC. In the case of Vulcan-20%Pt-5%w Cerium, this material exhibits better catalytic activity than the Vulcan-20%Pt in DMFC. In the case of Vulcan-40% Pt-doped Cerium, this material exhibits better catalytic activity than the Vulcan-40% Pt in DMFC, DEFC and HPEMFC. Finally, I propose a theory that explains the reason why the carbon-platinum-cerium has better catalytic activity than platinum-carbon. Due to the hybridization behavior of C and Ce could arise charge transfer, both carbon and cerium to the Platinum. Ce-C→Pt charge transfer could occur at the Ce-C/Pt interface. Thus, results in an increase in the catalytic activity of platinum-cerium-carbon when compared with carbon-platinum.
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Chen, Bang-Bao; Ma, De-Kun; Ke, Qing-Ping; Chen, Wei; Huang, Shao-Ming
2016-03-07
Edges often play a role as active centers for catalytic reactions in some nanomaterials. Therefore it is highly desirable to enhance catalytic activity of a material through modulating the microstructure of the edges. However, the study associated with edge engineering is less investigated and still at its preliminary stage. Here we report that Cu2MoS4 nanosheets with indented edges can be fabricated through a simple chemical etching route at room temperature, using Cu2MoS4 nanosheets with flat ones as sacrifice templates. Taking the electrocatalytic hydrogen evolution reaction (HER), photocatalytic degradation of rhodamine B (RhB) and conversion of benzyl alcohol as examples, the catalytic activity of Cu2MoS4 indented nanosheets (INSs) obtained through edge engineering was comparatively studied with those of Cu2MoS4 flat nanosheets (FNSs) without any modification. The photocatalytic tests revealed that the catalytic active sites of Cu2MoS4 nanosheets were associated with their edges rather than basal planes. Cu2MoS4 INSs were endowed with larger electrochemically active surface area (ECSA), more active edges and better hydrophilicity through the edge engineering. As a result, the as-fabricated Cu2MoS4 INSs exhibited an excellent HER activity with a small Tafel slope of 77 mV dec(-1), which is among the best records for Cu2MoS4 catalysts. The present work demonstrated the validity of adjusting catalytic activity of the material through edge engineering and provided a new strategy for designing and developing highly efficient catalysts.
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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.
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Williams, D M; Pieken, W A; Eckstein, F
1992-01-01
The importance of the 2'-hydroxyl group of several guanosine residues for the catalytic efficiency of a hammerhead ribozyme has been investigated. Five ribozymes in which single guanosine residues were substituted with 2'-amino-, 2'-fluoro-, or 2'-deoxyguanosine were chemically synthesized. The comparison of the catalytic activity of the three 2' modifications at a specific position allows conclusions about the functional role of the parent 2'-hydroxyl group. Substitutions of nonconserved nucleotides within the ribozyme caused little alteration in the catalytic activity relative to that obtained with the unmodified ribozyme. In contrast, when either of the guanosines within the single-stranded loop between stem I and stem II of the ribozyme was replaced by 2'-deoxyguanosine or 2'-fluoro-2'-deoxyguanosine, the catalytic activities of the resulting ribozymes were reduced by factors of at least 150. The catalytic activities of the corresponding ribozymes containing 2'-amino-2'-deoxyguanosine substitutions at these positions, however, were both reduced by factors of 15. These effects resulted from decreases in the respective kcat values, whereas variations in the Km values were comparatively small. A different pattern of reactivity of the three 2' modifications was observed at the guanosine immediately 3' to stem II of the ribozyme. Whereas both 2'-deoxyguanosine and 2'-amino-2'-deoxyguanosine at this position showed catalytic activity similar to that of the unmodified ribozyme, the activity of the corresponding 2'-fluoro-2'-deoxyguanosine-containing ribozyme was reduced by a factor of 15. The implications of these substitution-specific reactivities on the functional role of the native 2'-hydroxyl groups are discussed. Images PMID:1736306
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De la Fuente, Ildefonso M.; Cortes, Jesus M.; Perez-Pinilla, Martin B.; Ruiz-Rodriguez, Vicente; Veguillas, Juan
2011-01-01
Background Experimental observations and numerical studies with dissipative metabolic networks have shown that cellular enzymatic activity self-organizes spontaneously leading to the emergence of a metabolic core formed by a set of enzymatic reactions which are always active under all environmental conditions, while the rest of catalytic processes are only intermittently active. The reactions of the metabolic core are essential for biomass formation and to assure optimal metabolic performance. The on-off catalytic reactions and the metabolic core are essential elements of a Systemic Metabolic Structure which seems to be a key feature common to all cellular organisms. Methodology/Principal Findings In order to investigate the functional importance of the metabolic core we have studied different catalytic patterns of a dissipative metabolic network under different external conditions. The emerging biochemical data have been analysed using information-based dynamic tools, such as Pearson's correlation and Transfer Entropy (which measures effective functionality). Our results show that a functional structure of effective connectivity emerges which is dynamical and characterized by significant variations of bio-molecular information flows. Conclusions/Significance We have quantified essential aspects of the metabolic core functionality. The always active enzymatic reactions form a hub –with a high degree of effective connectivity- exhibiting a wide range of functional information values being able to act either as a source or as a sink of bio-molecular causal interactions. Likewise, we have found that the metabolic core is an essential part of an emergent functional structure characterized by catalytic modules and metabolic switches which allow critical transitions in enzymatic activity. Both, the metabolic core and the catalytic switches in which also intermittently-active enzymes are involved seem to be fundamental elements in the self-regulation of the Systemic Metabolic Structure. PMID:22125607
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Bowen, Anthony; Wear, Maggie P; Cordero, Radames J B; Oscarson, Stefan; Casadevall, Arturo
2017-01-13
Studies in the 1980s first showed that some natural antibodies were "catalytic" and able to hydrolyze peptide or phosphodiester bonds in antigens. Many naturally occurring catalytic antibodies have since been isolated from human sera and associated with positive and negative outcomes in autoimmune disease and infection. The function and prevalence of these antibodies, however, remain unclear. A previous study suggested that the 18B7 monoclonal antibody against glucuronoxylomannan (GXM), the major component of the Cryptococcus neoformans polysaccharide capsule, hydrolyzed a peptide antigen mimetic. Using mass spectrometry and Förster resonance energy transfer techniques, we confirm and characterize the hydrolytic activity of 18B7 against peptide mimetics and show that 18B7 is able to hydrolyze an oligosaccharide substrate, providing the first example of a naturally occurring catalytic antibody for polysaccharides. Additionally, we show that the catalytic 18B7 antibody increases release of capsular polysaccharide from fungal cells. A serine protease inhibitor blocked peptide and oligosaccharide hydrolysis by 18B7, and a putative serine protease-like active site was identified in the light chain variable region of the antibody. An algorithm was developed to detect similar sites present in unique antibody structures in the Protein Data Bank. The putative site was found in 14 of 63 (22.2%) catalytic antibody structures and 119 of 1602 (7.4%) antibodies with no annotation of catalytic activity. The ability of many antibodies to cleave antigen, albeit slowly, supports the notion that this activity is an important immunoglobulin function in host defense. The discovery of GXM hydrolytic activity suggests new therapeutic possibilities for polysaccharide-binding antibodies. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.
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Preparation of immobilized coating Fenton-like catalyst for high efficient degradation of phenol.
Wang, Jiankang; Yao, Zhongping; Wang, Yajing; Xia, Qixing; Chu, Huiya; Jiang, Zhaohua
2017-05-01
In this study, solid acid amorphous Fe 3 O 4 /SiO 2 ceramic coating decorated with sulfur on Q235 carbon steel as Fenton-like catalyst for phenol degradation was successfully prepared by plasma electrolytic oxidation (PEO) in silicate electrolyte containing Na 2 S 2 O 8 as sulfur source. The surface morphology and phase composition were characterized by SEM, EDS, XRD and XPS analyses. NH 3 -TPD was used to evaluate surface acidity of PEO coating. The results indicated that sulfur decorated amorphous Fe 3 O 4 /SiO 2 ceramic coatings with porous structure and higher acid strength had the similar pore size and the surface became more and more uneven with the increase of Na 2 S 2 O 8 in the silicate electrolyte. The Fenton-like catalytic activity of sulfur decorated PEO coatings was also evaluated. In contrast to negligible catalytic activity of sulfur undecorated PEO coating, catalytic activity of sulfur decorated PEO coating was excellent and PEO coating prepared with 3.0 g Na 2 S 2 O 8 had the highest catalytic activity which could degrade 99% of phenol within 8 min under circumneutral pH. The outstanding performance of sulfur decorated PEO coating was attributed to strong acidic microenvironment and more Fe 2+ on the surface. The strong acid sites played a key factor in determining catalytic activity of catalyst. In conclusion, rapid phenol removal under circumneutral pH and easier separation endowed it potential application in wastewater treatment. In addition, this strategy of preparing immobilized solid acid coating could provide guidance for designing Fenton-like catalyst with excellent catalytic activity and easier separation. Copyright © 2017 Elsevier Ltd. All rights reserved.
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Influence of active site location on catalytic activity in de novo-designed zinc metalloenzymes.
Zastrow, Melissa L; Pecoraro, Vincent L
2013-04-17
While metalloprotein design has now yielded a number of successful metal-bound and even catalytically active constructs, the question of where to put a metal site along a linear, repetitive sequence has not been thoroughly addressed. Often several possibilities in a given sequence may exist that would appear equivalent but may in fact differ for metal affinity, substrate access, or protein dynamics. We present a systematic variation of active site location for a hydrolytically active ZnHis3O site contained within a de novo-designed three-stranded coiled coil. We find that the maximal rate, substrate access, and metal-binding affinity are dependent on the selected position, while catalytic efficiency for p-nitrophenyl acetate hydrolysis can be retained regardless of the location of the active site. This achievement demonstrates how efficient, tailor-made enzymes which control rate, pKa, substrate and solvent access (and selectivity), and metal-binding affinity may be realized. These findings may be applied to the more advanced de novo design of constructs containing secondary interactions, such as hydrogen-bonding channels. We are now confident that changes to location for accommodating such channels can be achieved without location-dependent loss of catalytic efficiency. These findings bring us closer to our ultimate goal of incorporating the secondary interactions we believe will be necessary in order to improve both active site properties and the catalytic efficiency to be competitive with the native enzyme, carbonic anhydrase.
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Graciani, J.; Stacchiola, D.; Yang, F.; ...
2015-09-09
Nanostructured RuO x/TiO 2(110) catalysts have a remarkable catalytic activity for CO oxidation at temperatures in the range of 350–375 K. Furthermore, the RuO 2(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 RuO 2(110) to 0.66 eV in RuO x/TiO 2(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 COmore » and O species to give CO 2 (the main barrier for the CO oxidation reaction) passing from around 0.7 eV in RuO 2(110) to 0.55 eV in RuO x/TiO 2(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
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Expansion of chemical space for natural products by uncommon P450 reactions.
Zhang, Xingwang; Li, Shengying
2017-08-30
Covering: 2000 to 2017Cytochrome P450 enzymes (P450s) are the most versatile biocatalysts in nature. The catalytic competence of these extraordinary hemoproteins is broadly harnessed by numerous chemical defenders such as bacteria, fungi, and plants for the generation of diverse and complex natural products. Rather than the common tailoring reactions (e.g. hydroxylation and epoxidation) mediated by the majority of biosynthetic P450s, in this review, we will focus on the unusual P450 enzymes in relation to new chemistry, skeleton construction, and structure re-shaping via their own unique catalytic power or the intriguing protein-protein interactions between P450s and other proteins. These uncommon P450 reactions lead to a higher level of chemical space expansion for natural products, through which a broader spectrum of bioactivities can be gained by the host organisms.
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Sheng, Gang; Zhao, Hongtu; Wang, Jiuyu; Rao, Yu; Tian, Wenwen; Swarts, Daan C.; van der Oost, John; Patel, Dinshaw J.; Wang, Yanli
2014-01-01
We report on crystal structures of ternary Thermus thermophilus Argonaute (TtAgo) complexes with 5′-phosphorylated guide DNA and a series of DNA targets. These ternary complex structures of cleavage-incompatible, cleavage-compatible, and postcleavage states solved at improved resolution up to 2.2 Å have provided molecular insights into the orchestrated positioning of catalytic residues, a pair of Mg2+ cations, and the putative water nucleophile positioned for in-line attack on the cleavable phosphate for TtAgo-mediated target cleavage by a RNase H-type mechanism. In addition, these ternary complex structures have provided insights into protein and DNA conformational changes that facilitate transition between cleavage-incompatible and cleavage-compatible states, including the role of a Glu finger in generating a cleavage-competent catalytic Asp-Glu-Asp-Asp tetrad. Following cleavage, the seed segment forms a stable duplex with the complementary segment of the target strand. PMID:24374628
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Calmodulin fishing with a structurally disordered bait triggers CyaA catalysis
O’Brien, Darragh P.; Durand, Dominique; Voegele, Alexis; Hourdel, Véronique; Davi, Marilyne; Chamot-Rooke, Julia; Vachette, Patrice; Brier, Sébastien; Ladant, Daniel
2017-01-01
Once translocated into the cytosol of target cells, the catalytic domain (AC) of the adenylate cyclase toxin (CyaA), a major virulence factor of Bordetella pertussis, is potently activated by binding calmodulin (CaM) to produce supraphysiological levels of cAMP, inducing cell death. Using a combination of small-angle X-ray scattering (SAXS), hydrogen/deuterium exchange mass spectrometry (HDX-MS), and synchrotron radiation circular dichroism (SR-CD), we show that, in the absence of CaM, AC exhibits significant structural disorder, and a 75-residue-long stretch within AC undergoes a disorder-to-order transition upon CaM binding. Beyond this local folding, CaM binding induces long-range allosteric effects that stabilize the distant catalytic site, whilst preserving catalytic loop flexibility. We propose that the high enzymatic activity of AC is due to a tight balance between the CaM-induced decrease of structural flexibility around the catalytic site and the preservation of catalytic loop flexibility, allowing for fast substrate binding and product release. The CaM-induced dampening of AC conformational disorder is likely relevant to other CaM-activated enzymes. PMID:29287065
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DOE Office of Scientific and Technical Information (OSTI.GOV)
He, Yongqiang; Huang, Guanbo, E-mail: gbhuang2007@hotmail.com; Pan, Zeng
2015-10-15
Highlights: • A simple route for the in situ preparation of Ag nanoparticles has been developed. • The Ag loaded hydrogel showed catalytic activity for reduction of 4-nitrophenol. • The catalyst can be recovered by simple separation and showed good recyclability. - Abstract: A simple route for the in situ preparation of catalytically active Ag nanoparticles (NPs) in hydrogel networks has been developed. The electronegativity of the amide and carboxyl groups on the poly(acrylamide-co-acryl acid) chains caused strong binding of the Ag{sup +} ions which made the ions distribute uniformly inside the hydrogels. When the Ag{sup +} loaded hydrogels weremore » immersed in NaBH{sub 4} solution, the Ag{sup +} ions on the polymer networks were reduced to Ag NPs. The resultant hydrogel showed good catalytic activity for the reduction of a common organic pollutant, 4-nitrophenol, with sodium borohydride. A kinetic study of the catalytic reaction was carried out and a possible reason for the decline of the catalytic performance with reuse is proposed.« less
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NASA Astrophysics Data System (ADS)
Tang, Tiantian; Li, Kan; Shen, Zhemin; Sun, Tonghua; Wang, Yalin; Jia, Jinping
2016-01-01
Polypyrrole functionalized nickel foam is facilely prepared through the potentiostatic electrodeposition. The PPy-functionalized Ni foam functions as a hydrogen-evolution cathode in a rotating disk photocatalytic fuel cell, in which hydrogen energy and electric power are generated by consuming organic wastes. The PPy-functionalized Ni foam cathode exhibits stable catalytic activities after thirteen continuous runs. Compared with net or plate structure, the Ni foam with a unique three-dimensional reticulate structure is conducive to the electrodeposition of PPy. Compared with Pt-group electrode, PPy-coated Ni foam shows a satisfactory catalytic performance for the H2 evolution. The combination of PPy and Ni forms a synergistic effect for the rapid trapping and removal of proton from solution and the catalytic reduction of proton to hydrogen. The PPy-functionalized Ni foam could be applied in photocatalytic and photoelectrochemical generation of H2. In all, we report a low cost, high efficient and earth abundant PPy-functionalized Ni foam with a satisfactory catalytic activities comparable to Pt for the practical application of poly-generation of hydrogen and electricity.
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Catalytic Ethanol Dehydration over Different Acid-activated Montmorillonite Clays.
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.
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Huang, Yuanxing; Cui, Chenchen; Zhang, Daofang; Li, Liang; Pan, Ding
2015-01-01
Iron-loaded activated carbon was prepared and used as catalyst in heterogeneous catalytic ozonation of dibutyl phthalate (DBP). The catalytic activity of iron-loaded activated carbon was investigated under various conditions and the mechanisms of DBP removal were deduced. Characterization of catalyst indicated that the iron loaded on activated carbon was mainly in the form of goethite, which reduced its surface area, pore volume and pore diameter. The presence of metals on activated carbon positively contributed to its catalytic activity in ozonation of DBP. Iron loading content of 15% and initial water pH of 8 achieved highest DBP removal among all the tried conditions. Catalyst dosage of 10 mg L(-1) led to approximately 25% of increase in DBP (initial concentration 2 mg L(-1)) removal in 60 min as compared with ozone alone, and when catalyst dosage increased to 100 mg L(-1), the DBP removal was further improved by 46%. Based on a comparison of reaction rates for direct and indirect transformation of DBP, the increased removal of DBP in this study likely occurred via transformation of ozone into hydroxyl radicals on the catalyst surface. Copyright © 2014 Elsevier Ltd. All rights reserved.
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2004-01-01
The nucleotide pyrophosphatases/phosphodiesterases NPP1 and NPP2/autotaxin are structurally related eukaryotic ecto-enzymes, but display a very different substrate specificity. NPP1 releases nucleoside 5′-monophosphates from various nucleotides, whereas NPP2 mainly functions as a lysophospholipase D. We have used a domain-swapping approach to map substrate-specifying determinants of NPP1 and NPP2. The catalytic domain of NPP1 fused to the N- and C-terminal domains of NPP2 was hyperactive as a nucleotide phosphodiesterase, but did not show any lysophospholipase D activity. In contrast, chimaeras of the catalytic domain of NPP2 and the N- and/or C-terminal domains of NPP1 were completely inactive. These data indicate that the catalytic domain as well as both extremities of NPP2 contain lysophospholipid-specifying sequences. Within the catalytic domain of NPP1 and NPP2, we have mapped residues close to the catalytic site that determine the activities towards nucleotides and lysophospholipids. We also show that the conserved Gly/Phe-Xaa-Gly-Xaa-Xaa-Gly (G/FXGXXG) motif near the catalytic site is required for metal binding, but is not involved in substrate-specification. Our data suggest that the distinct activities of NPP1 and NPP2 stem from multiple differences throughout the polypeptide chain. PMID:15096095
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Patel, Parth; Parmar, Bhavesh; Kureshy, Rukhsana I; Khan, Noor-Ul H; Suresh, Eringathodi
2018-06-19
Herein, a zinc(ii)-based 3D mixed ligand metal organic framework (MOF) was synthesized via versatile routes including green mechanochemical synthesis. The MOF {[Zn(ATA)(L)·H2O]}n (ZnMOF-1-NH2) has been characterized by various physico-chemical techniques, including SCXRD, and composed of the bipyridyl-based Schiff base (E)-N'-(pyridin-4-ylmethylene)isonicotinohydrazide (L) and 2-aminoterephthalic acid (H2ATA) ligands as linkers. The MOF material has been explored as a multifunctional heterogeneous catalyst for the cycloaddition of alkyl and aryl epoxides with CO2 and sulfoxidation reactions of aryl sulfides. The influence of various reaction parameters is examined to optimize the performance of the catalytic reactions. It is found that solvent-free catalytic reaction conditions offer good catalytic conversion in the case of cyclic carbonates, and for sulfoxide, good conversion and selectivity are achieved in the presence of DCM as a solvent medium under ambient reaction conditions. The chemical and thermal stability of the catalyst are excellent and it is active for up to four catalytic cycles without significant loss in activity. Furthermore, based on the catalytic activity and structural evidence, a plausible mechanism for both catalytic reactions is proposed.
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Dong, Liang; Zou, Hechang; Yuan, Chong; Hong, Yu H.; Kuklev, Dmitry V.; Smith, William L.
2016-01-01
Prostaglandin endoperoxide H synthases (PGHSs), also called cyclooxygenases (COXs), convert arachidonic acid (AA) to PGH2. PGHS-1 and PGHS-2 are conformational heterodimers, each composed of an (Eallo) and a catalytic (Ecat) monomer. Previous studies suggested that the binding to Eallo of saturated or monounsaturated fatty acids (FAs) that are not COX substrates differentially regulate PGHS-1 versus PGHS-2. Here, we substantiate and expand this concept to include polyunsaturated FAs known to modulate COX activities. Non-substrate FAs like palmitic acid bind Eallo of PGHSs stimulating human (hu) PGHS-2 but inhibiting huPGHS-1. We find the maximal effects of non-substrate FAs on both huPGHSs occurring at the same physiologically relevant FA/AA ratio of ∼20. This inverse allosteric regulation likely underlies the ability of PGHS-2 to operate at low AA concentrations, when PGHS-1 is effectively latent. Unlike FAs tested previously, we observe that C-22 FAs, including ω-3 fish oil FAs, have higher affinities for Ecat than Eallo subunits of PGHSs. Curiously, C-20 ω-3 eicosapentaenoate preferentially binds Ecat of huPGHS-1 but Eallo of huPGHS-2. PGE2 production decreases 50% when fish oil consumption produces tissue EPA/AA ratios of ≥0.2. However, 50% inhibition of huPGHS-1 itself is only seen with ω-3 FA/AA ratios of ≥5.0. This suggests that fish oil-enriched diets disfavor AA oxygenation by altering the composition of the FA pool in which PGHS-1 functions. The distinctive binding specificities of PGHS subunits permit different combinations of non-esterified FAs, which can be manipulated dietarily, to regulate AA binding to Eallo and/or Ecat thereby controlling COX activities. PMID:26703471
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Patel, Disha; Antwi, Janet; Koneru, Pratibha C; Serrao, Erik; Forli, Stefano; Kessl, Jacques J; Feng, Lei; Deng, Nanjie; Levy, Ronald M; Fuchs, James R; Olson, Arthur J; Engelman, Alan N; Bauman, Joseph D; Kvaratskhelia, Mamuka; Arnold, Eddy
2016-11-04
HIV-1 integrase (IN) is essential for virus replication and represents an important multifunctional therapeutic target. Recently discovered quinoline-based allosteric IN inhibitors (ALLINIs) potently impair HIV-1 replication and are currently in clinical trials. ALLINIs exhibit a multimodal mechanism of action by inducing aberrant IN multimerization during virion morphogenesis and by competing with IN for binding to its cognate cellular cofactor LEDGF/p75 during early steps of HIV-1 infection. However, quinoline-based ALLINIs impose a low genetic barrier for the evolution of resistant phenotypes, which highlights a need for discovery of second-generation inhibitors. Using crystallographic screening of a library of 971 fragments against the HIV-1 IN catalytic core domain (CCD) followed by a fragment expansion approach, we have identified thiophenecarboxylic acid derivatives that bind at the CCD-CCD dimer interface at the principal lens epithelium-derived growth factor (LEDGF)/p75 binding pocket. The most active derivative (5) inhibited LEDGF/p75-dependent HIV-1 IN activity in vitro with an IC 50 of 72 μm and impaired HIV-1 infection of T cells at an EC 50 of 36 μm The identified lead compound, with a relatively small molecular weight (221 Da), provides an optimal building block for developing a new class of inhibitors. Furthermore, although structurally distinct thiophenecarboxylic acid derivatives target a similar pocket at the IN dimer interface as the quinoline-based ALLINIs, the lead compound, 5, inhibited IN mutants that confer resistance to quinoline-based compounds. Collectively, our findings provide a plausible path for structure-based development of second-generation ALLINIs. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.
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Zhang, Hao; Xu, Xiaobin; Lin, Haifeng; Ud Din, Muhammad Aizaz; Wang, Haiqing; Wang, Xun
2017-09-14
Ultrathin nanocrystals generally provide a remarkable catalytic performance due to their high specific surface area and exposure of certain active sites. However, deactivation caused by growth and gathering limits the catalytic application of ultrathin nanocrystals. Here we report Ag nanocrystal-decorated polyoxometalate (Ag-POM) single-walled nanotubes assembled via a concise, surfactant-free soaking method as a new kind of well-defined core-sheath nanoreactor. The diameter of Ag nanocrystals inside polyoxometalate nanotubes can be controlled via simply adjusting the reactant concentration. Ag-POM provided outstanding oxidative desulfurization (ODS) catalytic performance for aromatic sulfocompounds at room temperature. It was suggested that Ag nanocrystals decorated on the inner surface played a key role in adjusting the electronic distribution and enhancing the catalytic activity. The as-prepared Ag-POM nanotubes are promising candidate catalysts with enhanced performance for practical catalytic applications in the gasoline desulfurization industry.
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Engineering New Catalysts for In-Process Elimination of Tars
DOE Office of Scientific and Technical Information (OSTI.GOV)
Felix, Larry G.
2012-09-30
The key objective of this project was to develop a new and more efficient methodology for engineering and economically producing optimized robust catalysts for the reduction or elimination of tars in biomass gasification. Whereas current catalyst technology typically disposes thin layers of catalytically-active material onto rigid supports via wet chemistry-based methods, this project investigated novel thermal methods for directly incorporating catalytically active materials onto robust supports as well as novel approaches for incorporating catalytically active materials on and/or within an otherwise inert refractory support material which is then subsequently formed and processed to create a catalytically-active material on all exposedmore » surfaces. Specifically, the focus of this engineered catalyst development was on materials which were derived from, or otherwise related to, olivine-like minerals, due to the inherent attrition resistance and moderate catalytic properties exhibited by natural olivine when used in a fluidized bed biomass gasifier. Task 1 of this project successfully demonstrated the direct thermal impregnation of catalytically-active materials onto an olivine substrate, with the production of a Ni-olivine catalyst. Nickel and nickel oxide were thermally impregnated onto an olivine substrate and when reduced were shown to demonstrate improved catalytic activity over the baseline olivine material and equal the tar-decomposing performance of Ni-olivine catalysts prepared by conventional wet impregnation. Task 2 involved coordination with our subcontracted project partners to further develop and characterize catalyst formulations and to optimize activity and production methods. Within this task, several significant new materials were developed. NexTech Materials developed a sintered ceramic nickel-magnesium-silicate catalyst that demonstrated superb catalytic activity and high resistance to deactivation by H2S. Alfred University developed both supported and integrated (bulk) catalysts via a glass-ceramic processing route which were shown to exhibit excellent catalytic activity and superior resistance to attrition deactivation. With the discovery of these active, robust, glass-based catalysts, and with the permission of the project officer, the investigation of waste-based materials as originally proposed for Task 3 and pilot-scale testing proposed in Task 5 were deferred indefinitely in favor of further investigation of the glass-ceramic based catalyst materials. This choice was justified in part because during FY 2006 and through FY 2007, funding restrictions imposed by congressional budget choices significantly reduced funding for DOE biomass-related projects. Funding for this project was limited to what had been authorized which slowed the pace of project work at GTI so that our project partners could continue in their work. Thereafter, project work was allowed to resume and with restored funding, the project continued and concentrated on the development and testing of glass-ceramic catalysts in bulk or supported formats. Work concluded with a final development devoted to increasing the surface area of glass-ceramic catalysts in the form of microspheres. Following that development, project reporting was completed and the project was concluded.« less
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Liu, Di Jia; Shui, Jianglan; Chen, Chen
2016-05-24
A nanofibrous catalyst and method of manufacture. A precursor solution of a transition metal based material is formed into a plurality of interconnected nanofibers by electro-spinning the precursor solution with the nanofibers converted to a catalytically active material by a heat treatment. Selected subsequent treatments can enhance catalytic activity.
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Dual Active Site in the Endolytic Transglycosylase gp144 of Bacteriophage phiKZ.
Chertkov, O V; Armeev, G A; Uporov, I V; Legotsky, S A; Sykilinda, N N; Shaytan, A K; Klyachko, N L; Miroshnikov, K A
2017-01-01
Lytic transglycosylases are abundant peptidoglycan lysing enzymes that degrade the heteropolymers of bacterial cell walls in metabolic processes or in the course of a bacteriophage infection. The conventional catalytic mechanism of transglycosylases involves only the Glu or Asp residue. Endolysin gp144 of Pseudomonas aeruginosa bacteriophage phiKZ belongs to the family of Gram-negative transglycosylases with a modular composition and C -terminal location of the catalytic domain. Glu115 of gp144 performs the predicted role of a catalytic residue. However, replacement of this residue does not completely eliminate the activity of the mutant protein. Site-directed mutagenesis has revealed the participation of Tyr197 in the catalytic mechanism, as well as the presence of a second active site involving Glu178 and Tyr147. The existence of the dual active site was supported by computer modeling and monitoring of the molecular dynamics of the changes in the conformation and surface charge distribution as a consequence of point mutations.
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NASA Astrophysics Data System (ADS)
Shi, Wenwu; Wang, Zhiguo; Qing Fu, Yong
2017-10-01
This paper reports a new design methodology to improve catalytic activities of catalysts based on 2D transition metal dichalcogenides through elemental doping which induces structural transformations. Effects of rhenium (Re) doping on structural stability/phase transformation and catalytic activity of mono-layered trigonal prismatic (2H) MoS2 were investigated using density functional theory as one example. Results show that 2H-Mo1-x Re x S2 transforms into 1T‧-Mo1-x Re x S2MoS2 as the value of x is larger than 0.4, and the transfer of the electron from Re to Mo is identified as the main reason for this structural transformation. The 1T‧-Mo1-x Re x S2 shows a good catalytic activity for the hydrogen evolution reaction when 0.75 ⩽ x ⩽ 0.94.
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Supercritical CO{sub 2} mediated synthesis and catalytic activity of graphene/Pd nanocomposites
DOE Office of Scientific and Technical Information (OSTI.GOV)
Tang, Lulu; Nguyen, Van Hoa; Department of Chemistry, Nha Trang University, 2 Nguyen Dinh Chieu, Nha Trang
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 electronmore » 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.« less
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Catalytic conversion of methane to methanol using Cu-zeolites.
Alayon, Evalyn Mae C; Nachtegaal, Maarten; Ranocchiari, Marco; van Bokhoven, Jeroen A
2012-01-01
The conversion of methane to value-added liquid chemicals is a promising answer to the imminent demand for fuels and chemical synthesis materials in the advent of a dwindling petroleum supply. Current technology requires high energy input for the synthesis gas production, and is characterized by low overall selectivity, which calls for alternative reaction routes. The limitation to achieve high selectivity is the high C-H bond strength of methane. High-temperature reaction systems favor gas-phase radical reactions and total oxidation. This suggests that the catalysts for methane activation should be active at low temperatures. The enzymatic-inspired metal-exchanged zeolite systems apparently fulfill this need, however, methanol yield is low and a catalytic process cannot yet be established. Homogeneous and heterogeneous catalytic systems have been described which stabilize the intermediate formed after the first C-H activation. The understanding of the reaction mechanism and the determination of the active metal sites are important for formulating strategies for the upgrade of methane conversion catalytic technologies.
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Yao, Xin-Qiu; Cato, M Claire; Labudde, Emily; Beyett, Tyler S; Tesmer, John J G; Grant, Barry J
2017-09-29
G protein-coupled receptors (GPCRs) are essential for transferring extracellular signals into carefully choreographed intracellular responses controlling diverse aspects of cell physiology. The duration of GPCR-mediated signaling is primarily regulated via GPCR kinase (GRK)-mediated phosphorylation of activated receptors. Although many GRK structures have been reported, the mechanisms underlying GRK activation are not well-understood, in part because it is unknown how these structures map to the conformational landscape available to this enzyme family. Unlike most other AGC kinases, GRKs rely on their interaction with GPCRs for activation and not phosphorylation. Here, we used principal component analysis of available GRK and protein kinase A crystal structures to identify their dominant domain motions and to provide a framework that helps evaluate how close each GRK structure is to being a catalytically competent state. Our results indicated that disruption of an interface formed between the large lobe of the kinase domain and the regulator of G protein signaling homology domain (RHD) is highly correlated with establishment of the active conformation. By introducing point mutations in the GRK5 RHD-kinase domain interface, we show with both in silico and in vitro experiments that perturbation of this interface leads to higher phosphorylation activity. Navigation of the conformational landscape defined by this bioinformatics-based study is likely common to all GPCR-activated GRKs. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.
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Massey, V; Ghisla, S; Kieschke, K
1980-04-10
L-Lactate oxidase from Mycobacterium smegmatis catalyzes the oxidative decarboxylation of glycollate, with formate, CO2, and H2O as the major products. In addition, some "uncoupling" of the normal reaction occurs, with glyoxylate and H2O adition, some "uncoupling" of the normal reaction occurs, with glyoxylate and H2O2 as products. Glyoxylate is also a substrate (presumably as its hydrate); in this case, the reaction products are oxalate and H2O2. Evidence is presented that the enzyme recognizes glycollate as a prochiral substrate, differentiating between the Re- and Si-faces of the alpha carbon atom. Two highly fluorescent species are formed concomitantly from the reaction with glycollate; they are proposed to be covalent alpha-glycollyl adducts to the reduced flavin position N(5). One of these adducts is labile and in rapid equilibrium with oxidized enzyme and glycollate, and with the complex of reduced enzyme and glyoxylate; this adduct is a catalytically competent intermediate. The other adduct is comparatively stable (t 1/2 for decay = 20 min at 25 degrees C) and does not react with O2. It is formed at a rate approximately 1% that of the catalytic adduct, but because of its lack of reaction with O2 and its stability, it gradually accumulates during catalytic turnover, resulting in catalytically incompetent enzyme. An isotope effect of approximately 4 is found in the reduction of oxidized enzyme flavin and in the formation of the labile fluorescent adduct, when alpha-2H2-glycollate or (R)-glycollate-2-d is used, but not with the (S)-glycollate-2-d enantiomer. It is concluded that the catalytic adduct is formed by hydrogen abstraction from the Re-face of glycollate.
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Yang, Li; Zhou, Huang; Qin, Xin; Guo, Xiaodong; Cui, Guanwei; Asiri, Abdullah M; Sun, Xuping
2018-02-22
Co(hydro)oxides show unsatisfactory catalytic activity for the hydrogen evolution reaction (HER) in alkaline media, and it is thus highly desirable but still remains a challenge to design and develop Co(hydro)oxide derived materials as superb hydrogen-evolving catalysts using a facile, rapid and less energy-intensive method. Here, we propose a cathodic electrochemical activation strategy toward greatly boosted HER activity of a Co 3 O 4 nanoarray via room-temperature cathodic polarization in sodium hypophosphite solution. After activation, the overpotential significantly decreases from 260 to 73 mV to drive a geometrical catalytic current density of 10 mA cm -2 in 1.0 M KOH. Notably, this activated electrode also shows strong long-term electrochemical durability with the retention of its catalytic activity at 100 mA cm -2 for at least 40 h.
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Wu, Yi-Xin; Sato, Eiji; Kimura, Wataru; Miura, Naoyuki
2013-09-01
Baicalin and scutellarin are the major active principal flavonoids extracted from the Chinese herbal medicines Scutellaria baicalensis and Erigeron breviscapus (Vant.) Hand-Mazz. It has recently been reported that baicalin and scutellarin have antitumor activity. However, the mechanisms of action are unknown. We previously reported that some flavonoids have a specific role in the inhibition of the activity of proteasome subunits and induced apoptosis in tumor cells. To further investigate these pharmacological effects, we examined the inhibitory activity of baicalin and scutellarin on the extracted proteasomes from mice and cancer cells. Using fluorogenic substrates for proteasome catalytic subunits, we found that baicalin and scutellarin specifically inhibited chymotrypsin-like activity but did not inhibit trypsin-like and peptidyl-glutamyl peptide hydrolyzing activities. These data suggested that baicalin and scutellarin specifically inhibit chymotrypsin-like catalytic activity in the proteasome. Copyright © 2012 John Wiley & Sons, Ltd.
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Impact of active phase chemical composition and dispersity on catalytic behavior in PROX reaction
NASA Astrophysics Data System (ADS)
Cherkezova-Zheleva, Z.; Paneva, D.; Todorova, S.; Kolev, H.; Shopska, M.; Yordanova, I.; Mitov, I.
2014-04-01
Iron and iron-platinum catalysts supported on activated carbon have been successfully synthesized by wet impregnation method and low-temperature treatment in inert atmosphere. The content of the supported phases corresponds to 10 wt % Fe and 0.5 wt % Pt. Four catalytic samples were synthesized: Sample A—activated carbon impregnated with Fe nitrate; Sample B—activated carbon impregnated with Pt salt; Sample C—activated carbon impregnated consequently with Fe and Pt salts; Sample D—activated carbon impregnated simultaneously with Fe and Pt salts. The as-prepared materials were characterized by Mössbauer spectroscopy, X-ray diffraction, infrared and X-ray photoelectron spectroscopy. The spectra show that the activated carbon support and the preparation procedure give rise to the synthesis of isolated metal Pt ions and ultradispersed Fe and Pt oxide species. Probably the presence of different functional groups of activated carbon gives rise to registered very high dispersion of loaded species on support. The catalytic tests were carried out in PROX reaction. A lower activity of bimetallic Pt-Fe samples was explained with the increase in surface oxygen species as a result of predomination of iron oxide on the support leading to the increase in selectivity to the H2 oxidation. Partial agglomeration of supported iron oxide phase was registered after catalytic tests.
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Recent progress in asymmetric bifunctional catalysis using multimetallic systems.
Shibasaki, Masakatsu; Kanai, Motomu; Matsunaga, Shigeki; Kumagai, Naoya
2009-08-18
The concept of bifunctional catalysis, wherein both partners of a bimolecular reaction are simultaneously activated, is very powerful for designing efficient asymmetric catalysts. Catalytic asymmetric processes are indispensable for producing enantiomerically enriched compounds in modern organic synthesis, providing more economical and environmentally benign results than methods requiring stoichiometric amounts of chiral reagents. Extensive efforts in this field have produced many asymmetric catalysts, and now a number of reactions can be rendered asymmetric. We have focused on the development of asymmetric catalysts that exhibit high activity, selectivity, and broad substrate generality under mild reaction conditions. Asymmetric catalysts based on the concept of bifunctional catalysis have emerged as a particularly effective class, enabling simultaneous activation of multiple reaction components. Compared with conventional catalysts, bifunctional catalysts generally exhibit enhanced catalytic activity and higher levels of stereodifferentiation under milder reaction conditions, attracting much attention as next-generation catalysts for prospective practical applications. In this Account, we describe recent advances in enantioselective catalysis with bifunctional catalysts. Since our identification of heterobimetallic rare earth-alkali metal-BINOL (REMB) complexes, we have developed various types of bifunctional multimetallic catalysts. The REMB catalytic system is effective for catalytic asymmetric Corey-Chaykovsky epoxidation and cyclopropanation. A dinucleating Schiff base has emerged as a suitable multidentate ligand for bimetallic catalysts, promoting catalytic syn-selective nitro-Mannich, anti-selective nitroaldol, and Mannich-type reactions. The sugar-based ligand GluCAPO provides a suitable platform for polymetallic catalysts; structural elucidation revealed that their higher order polymetallic structures are a determining factor for their function in the catalytic asymmetric Strecker reaction. Rational design identified a related ligand, FujiCAPO, which exhibits superior performance in catalytic asymmetric conjugate addition of cyanide to enones and a catalytic asymmetric Diels-Alder-type reaction. The combination of an amide-based ligand with a rare earth metal constitutes a unique catalytic system: the ligand-metal association is in equilibrium because of structural flexibility. These catalytic systems are effective for asymmetric amination of highly coordinative substrate as well as for Mannich-type reaction of alpha-cyanoketones, in which hydrogen bonding cooperatively contributes to substrate activation and stereodifferentiation. Most of the reactions described here generate stereogenic tetrasubstituted carbons or quaternary carbons, noteworthy accomplishments even with modern synthetic methods. Several reactions have been incorporated into the asymmetric synthesis of therapeutics (or their candidate molecules) such as Tamiflu, AS-3201 (ranirestat), GRL-06579A, and ritodrine, illustrating the usefulness of bifunctional asymmetric catalysis.
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Oracko, Troy; Jaquish, Rigel; Losovyj, Yaroslav B; Morgan, David Gene; Pink, Maren; Stein, Barry D; Doluda, Valentin Yu; Tkachenko, Olga P; Shifrina, Zinaida B; Grigoriev, Maxim E; Sidorov, Alexander I; Sulman, Esther M; Bronstein, Lyudmila M
2017-10-04
Here, we report on the development of novel Zn-, Zn-Cr-, and Zn-Cu-containing catalysts using magnetic silica (Fe 3 O 4 -SiO 2 ) as the support. Transmission electron microscopy, powder X-ray diffraction, and X-ray photoelectron spectroscopy (XPS) showed that the iron oxide nanoparticles are located in mesoporous silica pores and the magnetite (spinel) structure remains virtually unchanged despite the incorporation of Zn and Cr. According to XPS data, the Zn and Cr species are intermixed within the magnetite structure. In the case of the Zn-Cu-containing catalysts, a separate Cu 2 O phase was also observed along with the spinel structure. The catalytic activity of these catalysts was tested in methanol synthesis from syngas (CO + H 2 ). The catalytic experiments showed an improved catalytic performance of Zn- and Zn-Cr-containing magnetic silicas compared to that of the ZnO-SiO 2 catalyst. The best catalytic activity was obtained for the Zn-Cr-containing magnetic catalyst prepared with 1 wt % Zn and Cr each. X-ray absorption spectroscopy demonstrated the presence of oxygen vacancies near Fe and Zn in Zn-containing, and even more in Zn-Cr-containing, magnetic silica (including oxygen vacancies near Cr ions), revealing a correlation between the catalytic properties and oxygen vacancies. The easy magnetic recovery, robust synthetic procedure, and high catalytic activity make these catalysts promising for practical applications.
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Enhancement in the catalytic activity of Pd/USY in the heck reaction induced by H2 bubbling.
Okumura, Kazu; Tomiyama, Takuya; Moriyama, Sayaka; Nakamichi, Ayaka; Niwa, Miki
2010-12-24
Pd was loaded on ultra stable Y (USY) zeolites prepared by steaming NH(4)-Y zeolite under different conditions. Heck reactions were carried out over the prepared Pd/USY. We found that H₂ bubbling was effective in improving not only the catalytic activity of Pd/USY, but also that of other supported Pd catalysts and Pd(OAc)₂. Moreover, the catalytic activity of Pd/USY could be optimized by choosing appropriate steaming conditions for the preparation of the USY zeolites; Pd loaded on USY prepared at 873 K with 100% H₂O gave the highest activity (TOF = 61,000 h⁻¹), which was higher than that of Pd loaded on other kinds of supports. The prepared Pd/USY catalysts were applicable to the Heck reactions using various kinds of substrates including bromo- and chloro-substituted aromatic and heteroaromatic compounds. Characterization of the acid properties of the USY zeolites revealed that the strong acid site (OH(strong)) generated as a result of steaming had a profound effect on the catalytic activity of Pd.
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Electro-catalytic degradation of sulfisoxazole by using graphene anode.
Wang, Yanyan; Liu, Shuan; Li, Ruiping; Huang, Yingping; Chen, Chuncheng
2016-05-01
Graphite and graphene electrodes were prepared by using pure graphite as precursor. The electrode materials were characterized by a scanning electron microscope (SEM), X-ray diffraction (XRD) and cyclic voltammetry (CV) measurements. The electro-catalytic activity for degradation of sulfisoxazole (SIZ) was investigated by using prepared graphene or graphite anode. The results showed that the degradation of SIZ was much more rapid on the graphene than that on the graphite electrode. Moreover, the graphene electrode exhibited good stability and recyclability. The analysis on the intermediate products and the measurement of active species during the SIZ degradation demonstrated that indirect oxidation is the dominant mechanism, involving the electro-catalytic generation of OH and O2(-) as the main active oxygen species. This study implies that graphene is a promising potential electrode material for long-term application to electro-catalytic degradation of organic pollutants. Copyright © 2015. Published by Elsevier B.V.
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Simple size-controlled synthesis of Au nanoparticles and their size-dependent catalytic activity
DOE Office of Scientific and Technical Information (OSTI.GOV)
Suchomel, Petr; Kvitek, Libor; Prucek, Robert
The controlled preparation of Au nanoparticles (NPs) in the size range of 6 to 22 nm is explored in this study. The Au NPs were prepared by the reduction of tetrachloroauric acid using maltose in the presence of nonionic surfactant Tween 80 at various concentrations to control the size of the resulting Au NPs. With increasing concentration of Tween 80 a decrease in the size of produced Au NPs was observed, along with a significant decrease in their size distribution. The size-dependent catalytic activity of the synthesized Au NPs was tested in the reduction of 4-nitrophenol with sodium borohydride, resultingmore » in increasing catalytic activity with decreasing size of the prepared nanoparticles. Eley-Rideal catalytic mechanism emerges as the more probable, in contrary to the Langmuir-Hinshelwood mechanism reported for other noble metal nanocatalysts.« less
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Simple size-controlled synthesis of Au nanoparticles and their size-dependent catalytic activity
Suchomel, Petr; Kvitek, Libor; Prucek, Robert; ...
2018-03-15
The controlled preparation of Au nanoparticles (NPs) in the size range of 6 to 22 nm is explored in this study. The Au NPs were prepared by the reduction of tetrachloroauric acid using maltose in the presence of nonionic surfactant Tween 80 at various concentrations to control the size of the resulting Au NPs. With increasing concentration of Tween 80 a decrease in the size of produced Au NPs was observed, along with a significant decrease in their size distribution. The size-dependent catalytic activity of the synthesized Au NPs was tested in the reduction of 4-nitrophenol with sodium borohydride, resultingmore » in increasing catalytic activity with decreasing size of the prepared nanoparticles. Eley-Rideal catalytic mechanism emerges as the more probable, in contrary to the Langmuir-Hinshelwood mechanism reported for other noble metal nanocatalysts.« less
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NASA Astrophysics Data System (ADS)
Carette, Noëlle; Engelkamp, Hans; Akpa, Eric; Pierre, Sebastien J.; Cameron, Neil R.; Christianen, Peter C. M.; Maan, Jan C.; Thies, Jens C.; Weberskirch, Ralf; Rowan, Alan E.; Nolte, Roeland J. M.; Michon, Thierry; van Hest, Jan C. M.
2007-04-01
Virus particles are probably the most precisely defined nanometre-sized objects that can be formed by protein self-assembly. Although their natural function is the storage and transport of genetic material, they have more recently been applied as scaffolds for mineralization and as containers for the encapsulation of inorganic compounds. The reproductive power of viruses has been used to develop versatile analytical methods, such as phage display, for the selection and identification of (bio)active compounds. To date, the combined use of self-assembly and reproduction has not been used for the construction of catalytic systems. Here we describe a self-assembled system based on a plant virus that has its coat protein genetically modified to provide it with a lipase enzyme. Using single-object and bulk catalytic studies, we prove that the virus-anchored lipase molecules are catalytically active. This anchored biocatalyst, unlike man-made supported catalysts, has the capability to reproduce itself in vivo, generating many independent catalytically active copies.
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Lee, Hyosun; Lim, Juhyung; Lee, Changhwan; Back, Seoin; An, Kwangjin; Shin, Jae Won; Ryoo, Ryong; Jung, Yousung; Park, Jeong Young
2018-06-08
Despite numerous studies, the origin of the enhanced catalytic performance of bimetallic nanoparticles (NPs) remains elusive because of the ever-changing surface structures, compositions, and oxidation states of NPs under reaction conditions. An effective strategy for obtaining critical clues for the phenomenon is real-time quantitative detection of hot electrons induced by a chemical reaction on the catalysts. Here, we investigate hot electrons excited on PtCo bimetallic NPs during H 2 oxidation by measuring the chemicurrent on a catalytic nanodiode while changing the Pt composition of the NPs. We reveal that the presence of a CoO/Pt interface enables efficient transport of electrons and higher catalytic activity for PtCo NPs. These results are consistent with theoretical calculations suggesting that lower activation energy and higher exothermicity are required for the reaction at the CoO/Pt interface.
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Hu, Ling-Ya; Chen, Li-Xian; Liu, Meng-Ting; Wang, Ai-Jun; Wu, Lan-Ju; Feng, Jiu-Ju
2017-05-01
Theophylline as a naturally alkaloid is commonly employed to treat asthma and chronic obstructive pulmonary disorder. Herein, a facile theophylline-assisted green approach was firstly developed for synthesis of PtAu nanospheres/reduced graphene oxide (PtAu NSs/rGO), without any surfactant, polymer, or seed involved. The obtained nanocomposites were applied for the catalytic reduction and removal of highly toxic chromium (VI) using formic acid as a model reductant at 50°C, showing the significantly enhanced catalytic activity and improved recyclability when compared with commercial Pt/C (50%) and home-made Au nanocrystals supported rGO (Au NCs/rGO). It demonstrates great potential applications of the catalyst in wastewater treatment and environmental protection. The eco-friendly route provides a new platform to fabricate other catalysts with enhanced catalytic activity. Copyright © 2016 Elsevier Inc. All rights reserved.
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Low Pt content direct methanol fuel cell anode catalyst: nanophase PtRuNiZr
NASA Technical Reports Server (NTRS)
Whitacre, Jay F. (Inventor); Narayanan, Sekharipuram R. (Inventor)
2010-01-01
A method for the preparation of a metallic material having catalytic activity that includes synthesizing a material composition comprising a metal content with a lower Pt content than a binary alloy containing Pt but that displays at least a comparable catalytic activity on a per mole Pt basis as the binary alloy containing Pt; and evaluating a representative sample of the material composition to ensure that the material composition displays a property of at least a comparable catalytic activity on a per mole Pt basis as a representative binary alloy containing Pt. Furthermore, metallic compositions are disclosed that possess substantial resistance to corrosive acids.
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Wang, Qiu-lin; Huang, Qun-xing; Wu, Hui-fan; Lu, Sheng-yong; Wu, Hai-long; Li, Xiao-dong; Yan, Jian-hua
2016-02-01
Gaseous 1,2-dichlorobenzene (1,2-DCBz) was catalytically decomposed in a fixed-bed catalytic reactor using composite copper-based titanium oxide (CuOx/TiO2) catalysts with different copper ratios. Carbon nanotubes (CNTs) were introduced to produce novel CuOx/TiO2-CNTs catalysts by the sol-gel method. The catalytic performances of CuOx/TiO2 and CuOx/TiO2-CNTs on 1,2-DCBz oxidative destruction under different temperatures (150-350 °C) were experimentally examined and the correlation between catalyst structure and catalytic activity was characterized and the role of oxygen in catalytic reaction was discussed. Polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs) generation during 1,2-DCBz catalytic oxidation by CuOx/TiO2-CNTs composite catalyst was also examined. Results indicate that the 1,2-DCBz destruction/removal efficiencies of CuOx (4 wt%)/TiO2 catalyst at 150 °C and 350 °C with a GHSV of 3400 h(-1) are 59% and 94% respectively and low-temperature (150 °C) catalytic activity of CuOx/TiO2 on 1,2-DCBz oxidation can be improved from 59 to 77% when CNTs are introduced. Furthermore, oxygen either in catalyst or from reaction atmosphere is indispensible in reaction. The former is offered to activate and oxidize the 1,2-DCBz adsorbed on catalyst, thus can be generally consumed during reaction and the oxygen content in catalyst is observed lost from 39.9 to 35.0 wt% after reacting under inert atmosphere; the latter may replenish the vacancy in catalyst created by the consumed oxygen thus extends the catalyst life and raises the destruction/removal efficiency. The introduction of CNTs also increases the Cu(2+)/Cu(+) ratio, chemisorbed oxygen concentration and surface lattice oxygen binding energy which are closely related with catalytic activity. PCDD/Fs is confirmed to be formed when 1,2-DCBz catalytically oxidized by CuOx/TiO2-CNTs composite catalyst with sufficient oxygen (21%), proper temperature (350 °C) and high concentration of 1,2-DCBz feed (120 ppm). Copyright © 2015 Elsevier Ltd. All rights reserved.
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Lü, Jianhua; Yang, Yu; Gao, Junfang; Duan, Haichao; Lü, Changli
2018-06-19
A series of novel well-defined 8-hydroxyquinoline (HQ)-containing thermo-responsive amphiphilic diblock copolymers poly(styrene-co-5-(2-methacryloylethyloxy- methyl)-8-quinolinol)-b-poly(N-isopropylacrylamide) P(St-co-MQ)-b-PNIPAm (P1,2), P(NIPAm- co-MQ)-b-PSt (P3,4) and triblock copolymer poly(N-isopropylacrylamide)-b-poly(methyl- methacrylate-co-5-(2-methacryloylethyloxymethyl)-8-quinolinol)-b-polystyrene PNIPAm-b- P(MMA-co-MQ)-b-PSt (P5) were prepared by reversible addition fragmentation chain transfer (RAFT) polymerization, and their self-assembly behaviors were studied. The block copolymers P1-P5 stabilized gold nanoparticles (Au@P1-Au@P5) with small size and narrow distribution were obtained through in situ reduction of gold precursors in aqueous solution of polymer micelles with HQ as the coordination groups. The resulting Au@P nanohybrids possessed excellent catalytic activities for the reduction of nitrophenols using NaBH4. The size, morphology and surface chemistry of Au NPs could be controlled by adjusting the structure of block polymers with HQ in different block positions, which plays an important role in the catalytic properties. It was found that longer chain length of hydrophilic or hydrophobic segments of block copolymers were beneficial to elevate the catalytic activity of Au NPs for the reduction of nitrophenols, and the spherical nanoparticles (Au@P5) stabilized with triblock copolymer exhibit higher catalytic performance. Surprisingly, the gold nanowires (Au@P4) produced with P4 have a highest catalytic activity due to large abundance of grain boundaries. Excellent thermo-responsive behaviors for catalytic reaction make the as-prepared Au@P hybrids become an environmentally responsive nano-catalytic materials.
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NASA Astrophysics Data System (ADS)
Fang, Ruimei; Huang, Haibao; Huang, Wenjun; Ji, Jian; Feng, Qiuyu; Shu, Yajie; Zhan, Yujie; Liu, Gaoyuan; Xie, Ruijie
2017-10-01
Coal based activated carbon (AC) was pretreated by peracetic acid solution and used for supporting Mn catalyst towards oxidation of gaseous benzene by catalytic ozonation. The as-obtained activated carbon was characterized by XPS, BET, SEM, and TG technologies. It indicates that peracetic acid solution modification not only raised the quantity of chemisorbed oxygen or water, and hydroxyl group on activated carbon material surface, but also increased the specific surface area and benzene adsorption capacity of activated carbon. Benzene could be completely removed in 300 min and CO2 selectivity reached to 61.9% over Mn/AC-modified catalyst. A possible catalytic ozonation mechanism of activated carbon which was treated by peracetic acid solution supported Mn catalyst for oxidation of benzene was proposed.
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NASA Astrophysics Data System (ADS)
Lu, Qiang; Zhang, Zhen-xi; Wang, Xin; Guo, Hao-qiang; Cui, Min-shu; Yang, Yong-ping
2018-02-01
A new technique was proposed to co-produce phenol and activated carbon (AC) from catalytic fast pyrolysis of biomass impregnated with K3PO4 in a hydrogen atmosphere, followed by activation of the pyrolytic solid residues. Lab-scale catalytic fast pyrolysis experiments were performed to quantitatively determine the pyrolytic product distribution, as well as to investigate the effects of several factors on the phenol production, including pyrolysis atmosphere, catalyst type, biomass type, catalytic pyrolysis temperature, and catalyst impregnation content. In addition, the pyrolytic solid residues were activated to prepare ACs with high specific surface areas. The results indicated that phenol could be obtained due to the synergistic effects of K3PO4 and hydrogen atmosphere, with the yield and selectivity reaching 5.3 wt% and 17.8% from catalytic fast pyrolysis of poplar wood with 8 wt% K3PO4 at 550 oC in a hydrogen atmosphere. This technique was adaptable to different woody materials for phenol production. Moreover, gas product generated from the pyrolysis process was feasible to be recycled to provide the hydrogen atmosphere, instead of extra hydrogen supply. In addition, the pyrolytic solid residue was suitable for AC preparation, using CO2 activation method, the specific surface area was as high as 1605 m2/g.
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Martínez-Araya, Jorge I; Glossman-Mitnik, Daniel
2018-01-18
Ten functionals were used to assess their capability to compute a local reactivity descriptor coming from the Conceptual Density Functional Theory on a group of iron-based organometallic compounds that have been synthesized by Zohuri, G.H. et al. in 2010; these compounds bear the following substituent groups: H-, O 2 N- and CH 3 O- at the para position of the pyridine ring and their catalytic activities were experimentally measured by these authors. The present work involved a theoretical analysis applied on the aforementioned iron-based compounds thus leading to suggest a new 2,6-bis(imino)pyridine catalyst based on iron(II) bearing a fluorine atom whose possible catalytic activity is suggested to be near the catalytic activity of the complex bearing a hydrogen atom as a substituent group by means of the so called local hyper-softness (LHS) thus opening a chance to estimate a possible value of catalytic activity for a new catalyst that has not been synthesized yet without simulating the entire process of ethylene polymerization. Since Conceptual DFT is not a predictive theory, but rather interpretative, an analysis of the used reactivity descriptor and its dependence upon the level of theory was carried in the present work, thus revealing that care should be taken when DFT calculations are used for these purposes.
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Structural insights into the catalytic mechanism of a family 18 exo-chitinase
van Aalten, D. M. F.; Komander, D.; Synstad, B.; Gåseidnes, S.; Peter, M. G.; Eijsink, V. G. H.
2001-01-01
Chitinase B (ChiB) from Serratia marcescens is a family 18 exo-chitinase whose catalytic domain has a TIM-barrel fold with a tunnel-shaped active site. We have solved structures of three ChiB complexes that reveal details of substrate binding, substrate-assisted catalysis, and product displacement. The structure of an inactive ChiB mutant (E144Q) complexed with a pentameric substrate (binding in subsites −2 to +3) shows closure of the “roof” of the active site tunnel. It also shows that the sugar in the −1 position is distorted to a boat conformation, thus providing structural evidence in support of a previously proposed catalytic mechanism. The structures of the active enzyme complexed to allosamidin (an analogue of a proposed reaction intermediate) and of the active enzyme soaked with pentameric substrate show events after cleavage of the glycosidic bond. The latter structure shows reopening of the roof of the active site tunnel and enzyme-assisted product displacement in the +1 and +2 sites, allowing a water molecule to approach the reaction center. Catalysis is accompanied by correlated structural changes in the core of the TIM barrel that involve conserved polar residues whose functions were hitherto unknown. These changes simultaneously contribute to stabilization of the reaction intermediate and alternation of the pKa of the catalytic acid during the catalytic cycle. PMID:11481469
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Lu, Qiang; Zhang, Zhen-xi; Wang, Xin; Guo, Hao-qiang; Cui, Min-shu; Yang, Yong-ping
2018-01-01
A new technique was proposed to co-produce phenol and activated carbon (AC) from catalytic fast pyrolysis of biomass impregnated with K3PO4 in a hydrogen atmosphere, followed by activation of the pyrolytic solid residues. Lab-scale catalytic fast pyrolysis experiments were performed to quantitatively determine the pyrolytic product distribution, as well as to investigate the effects of several factors on the phenol production, including pyrolysis atmosphere, catalyst type, biomass type, catalytic pyrolysis temperature, and catalyst impregnation content. In addition, the pyrolytic solid residues were activated to prepare ACs with high specific surface areas. The results indicated that phenol could be obtained due to the synergistic effects of K3PO4 and hydrogen atmosphere, with the yield and selectivity reaching 5.3 wt% and 17.8% from catalytic fast pyrolysis of poplar wood with 8 wt% K3PO4 at 550°C in a hydrogen atmosphere. This technique was adaptable to different woody materials for phenol production. Moreover, gas product generated from the pyrolysis process was feasible to be recycled to provide the hydrogen atmosphere, instead of extra hydrogen supply. In addition, the pyrolytic solid residue was suitable for AC preparation, using CO2 activation method, the specific surface area was as high as 1,605 m2/g. PMID:29515994
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Lu, Qiang; Zhang, Zhen-Xi; Wang, Xin; Guo, Hao-Qiang; Cui, Min-Shu; Yang, Yong-Ping
2018-01-01
A new technique was proposed to co-produce phenol and activated carbon (AC) from catalytic fast pyrolysis of biomass impregnated with K 3 PO 4 in a hydrogen atmosphere, followed by activation of the pyrolytic solid residues. Lab-scale catalytic fast pyrolysis experiments were performed to quantitatively determine the pyrolytic product distribution, as well as to investigate the effects of several factors on the phenol production, including pyrolysis atmosphere, catalyst type, biomass type, catalytic pyrolysis temperature, and catalyst impregnation content. In addition, the pyrolytic solid residues were activated to prepare ACs with high specific surface areas. The results indicated that phenol could be obtained due to the synergistic effects of K 3 PO 4 and hydrogen atmosphere, with the yield and selectivity reaching 5.3 wt% and 17.8% from catalytic fast pyrolysis of poplar wood with 8 wt% K 3 PO 4 at 550°C in a hydrogen atmosphere. This technique was adaptable to different woody materials for phenol production. Moreover, gas product generated from the pyrolysis process was feasible to be recycled to provide the hydrogen atmosphere, instead of extra hydrogen supply. In addition, the pyrolytic solid residue was suitable for AC preparation, using CO 2 activation method, the specific surface area was as high as 1,605 m 2 /g.
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Hocharoen, Lalintip; Joyner, Jeff C; Cowan, J A
2013-12-27
The N- and C-terminal domains of human somatic angiotensin I converting enzyme (sACE-1) demonstrate distinct physiological functions, with resulting interest in the development of domain-selective inhibitors for specific therapeutic applications. Herein, the activity of lisinopril-coupled transition metal chelates was tested for both reversible binding and irreversible catalytic inactivation of each domain of sACE-1. C/N domain binding selectivity ratios ranged from 1 to 350, while rates of irreversible catalytic inactivation of the N- and C-domains were found to be significantly greater for the N-domain, suggesting a more optimal orientation of M-chelate-lisinopril complexes within the active site of the N-domain of sACE-1. Finally, the combined effect of binding selectivity and inactivation selectivity was assessed for each catalyst (double-filter selectivity factors), and several catalysts were found to cause domain-selective catalytic inactivation. The results of this study demonstrate the ability to optimize the target selectivity of catalytic metallopeptides through both binding and catalytic factors (double-filter effect).
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Zhong, Hong; Su, Yanqing; Chen, Xingwei; Li, Xiaoju; Wang, Ruihu
2017-12-22
CO 2 adsorption and concomitant catalytic conversion into useful chemicals are promising approaches to alleviate the energy crisis and effects of global warming. This is highly desirable for developing new types of heterogeneous catalytic materials containing CO 2 -philic groups and catalytic active sites for CO 2 chemical transformation. Here, we present an imidazolium- and triazine-based porous organic polymer with counter chloride anion (IT-POP-1). The porosity and CO 2 affinity of IT-POP-1 may be modulated at the molecular level through a facile anion-exchange strategy. Compared with the post-modified polymers with iodide and hexafluorophosphate anions, IT-POP-1 possesses the highest surface area and the best CO 2 uptake capacity with excellent adsorption selectivity over N 2 . The roles of the task-specific components such as triazine, imidazolium, hydroxyl, and counter anions in CO 2 absorption and catalytic performance were illustrated. IT-POP-1 exhibits the highest catalytic activity and excellent recyclability in solvent- and additive-free cycloaddition reaction of CO 2 with epoxides. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
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Azad, Md Abul Kalam; Sawa, Yoshihiro; Ishikawa, Takahiro; Shibata, Hitoshi
2006-11-30
The holoenzyme of protein phosphatase (PP) from tulip petals was purified by using hydrophobic interaction, anion exchange and microcystin affinity chromatography to analyze activity towards p-nitrophenyl phosphate (p-NPP). The catalytic subunit of PP was released from its endogenous regulatory subunits by ethanol precipitation and further purified. Both preparations were characterized by immunological and biochemical approaches to be PP2A. On SDS-PAGE, the final purified holoenzyme preparation showed three protein bands estimated at 38, 65, and 75 kDa while the free catalytic subunit preparation showed only the 38 kDa protein. In both preparations, the 38 kDa protein was identified immunologically as the catalytic subunit of PP2A by using a monoclonal antibody against the PP2A catalytic subunit. The final 623- and 748- fold purified holoenzyme and the free catalytic preparations, respectively, exhibited high sensitivity to inhibition by 1 nM okadaic acid when activity was measured with p-NPP. The holoenzyme displayed higher stimulation in the presence of ammonium sulfate than the free catalytic subunit did by protamine, thereby suggesting different enzymatic behaviors.
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NASA Astrophysics Data System (ADS)
Ko, Younji; Kim, Donghee; Kwon, Cheong Hoon; Cho, Jinhan
2018-04-01
In this study, we introduce hydrophobic and hydrophilic graphene oxide nanosheet (GON) catalysts prepared by consecutive ligand replacement of hydrophobically stabilized magnetic and catalytic nanoparticles (NPs); it exhibits high catalytic activity, fast magnetic response, and good dispersion in both nonpolar and aqueous media, allowing high loading amount of magnetic and catalytic NPs onto GON sheets. More specifically, these GON catalysts showed a high product yield of 66-99% and notable recyclability (93% of the initial product yield after 10 reaction cycles) in a Suzuki-Miyaura reaction in nonpolar media, outperforming the performance of the conventional hydrophilic GON catalysts. Additional coating of a hydrophilic layer onto GON catalysts also showed the notable performance (product yield ∼99%) in catalytic reactions performed in aqueous media. Given that ligand-controlled catalytic NPs adsorbed onto 2D nanosheets can be used as hydrophobic and hydrophilic stabilizers as well as catalysts, our approach can provide a tool for developing and designing 2D-nanosheet catalysts with high performance in nonpolar and polar media.
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[Catalytic performance of Ce/Zr series catalysts on soot combustion].
Zhu, Ling; Wang, Xue-Zhong; Hao, Zheng-Ping
2005-09-01
Catalytic performances of Ce/Zr series catalysts (Ce(x)Zr(1-x)O2) on soot combustion and the influence of feed gas were investigated by TG and TPO. The catalytic activity is high, and affects by the Ce/Zr ratio. The concentration of O2 affects the speed-limited step during the process of soot combustion. H2O showed no effect on the catalytic activity for soot combustion on Ce(0.5)Zr(0.5)O2. NO could promote soot combustion by presenting NO2, a more powerful oxidant than O2, and the ignition temperature of soot decreased 30 degrees C. Results of TG and TPO show that the beta species oxygen on the catalyst take part in the combustion process.
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Gold nanoparticle-catalyzed environmentally benign deoxygenation of epoxides to alkenes.
Noujima, Akifumi; Mitsudome, Takato; Mizugaki, Tomoo; Jitsukawa, Koichiro; Kaneda, Kiyotomi
2011-09-28
We have developed a highly efficient and green catalytic deoxygenation of epoxides to alkenes using gold nanoparticles (NPs) supported on hydrotalcite [HT: Mg(6)Al(2)CO(3)(OH)(16)] (Au/HT) with alcohols, CO/H(2)O or H(2) as the reducing reagent. Various epoxides were selectively converted to the corresponding alkenes. Among the novel metal NPs on HT, Au/HT was found to exhibit outstanding catalytic activity for the deoxygenation reaction. Moreover, Au/HT can be separated from the reaction mixture and reused with retention of its catalytic activity and selectivity. The high catalytic performance of Au/HT was attributed to the selective formation of Au-hydride species by the cooperative effect between Au NPs and HT.
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Biocatalytically active silCoat-composites entrapping viable Escherichia coli.
Findeisen, A; Thum, O; Ansorge-Schumacher, M B
2014-02-01
Application of whole cells in industrial processes requires high catalytic activity, manageability, and viability under technical conditions, which can in principle be accomplished by appropriate immobilization. Here, we report the identification of carrier material allowing exceptionally efficient adsorptive binding of Escherichia coli whole cells hosting catalytically active carbonyl reductase from Candida parapsilosis (CPCR2). With the immobilizates, composite formation with both hydrophobic and hydrophilized silicone was achieved, yielding advanced silCoat-material and HYsilCoat-material, respectively. HYsilCoat-whole cells were viable preparations with a cell loading up to 400 mg(E. coli) · g(-1)(carrier) and considerably lower leaching than native immobilizates. SilCoat-whole cells performed particularly well in neat substrate exhibiting distinctly increased catalytic activity.
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Active anatase (0 0 1)-like surface of hydrothermally synthesized titania nanotubes
NASA Astrophysics Data System (ADS)
Chen, Qiang; Mogilevsky, Gregory; Wagner, George W.; Forstater, Jacob; Kleinhammes, Alfred; Wu, Yue
2009-11-01
Using 31P and 13C NMR with DFT calculations we demonstrate the exposed surface of titania nanotubes (TiNTs) is a stable, unterminated anatase (0 0 1)-like surface and is catalytically active under ambient conditions. We find that methanol dissociatively adsorbs on the surface of TiNTs agreeing with the predicted activity of surface dissociation of organic molecules on the crystalline (0 0 1)-anatase surface. We further examined the catalytic activity of anatase power, TiNT, and nanosheets in catalytic hydrolysis of S-[2-(diisopropylamino)ethyl]- O-ethyl methylphosphonothioate (VX) via 31P NMR and demonstrate that titanate-like nanosheets are inactive in the reaction owing to their hydroxylated (0 0 1) surface.
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NASA Astrophysics Data System (ADS)
Mohanapriya, S.; Renuka devi, R.; Raj, V.
2018-02-01
Mesoporous Nickel has been prepared by electrodeposition using non-ionic surfactant based liquid crystalline template under optimized processing conditions. Physico-chemical properties of mesoporous nickel is systematically characterized through XRD, SEM and AFM analyses. Comparison of electrocatalytic activity of mesoporous nickel with smooth nickel was interrogated using cyclic voltammetry (CV), chronoamperometry (CA) and electrochemical impedance spectroscopy (EIS) analyses. Distinctly enhanced electrocatalytic activity with improved surface poisoning resistance related to mesoporous nickel electrode towards methanol oxidation stems from unique mesoporous morphology. This mesoporous morphology with high surface to volume ratio is highly beneficial to promote active catalytic centers to offer readily accessible Pt catalytic sites for MOR, through facilitating mass and electron transports.
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The catalytic activity of CoMo/USY on deoxygenation reaction of anisole in a batch reactor
NASA Astrophysics Data System (ADS)
Nugrahaningtyas, K. D.; Putri, I. F.; Heraldy, E.; Hidayat, Y.
2018-04-01
The catalytic hydrodeoxigenation of the bio oil model compounds (biomass pyrolysis results) typically uses sulphide catalysts. In this study, we studied the activity of non-sulphide catalyst, the effect of temperature and reaction time on anisole deoxygenation. The catalytic activity was performed in a batch reactor, using N2 gas at 1 bar of pressure. The product was analyzed by gas chromatography (GC) and gas chromatography-mass spectrometry (GC-MS). The result showed that the Co-Mo/USY catalyst perform a highest activity and produce pentamethylbenzene, an oxygen free products, when reaction time is 2 hours. The Co-Mo/USY catalysts has the value of the total yield of the product increased with time increase drastically.
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NASA Astrophysics Data System (ADS)
Kim, Il Hee; Lee, Hyerim; Yu, Areum; Jeong, Jae Hwan; Lee, Youngmi; Kim, Myung Hwa; Lee, Chongmok; Dok Kim, Young
2018-04-01
NiO/NiCo2O4 nanotubes with a diameter of approximately 100 nm are synthesized using Ni and Co precursors via electro-spinning and subsequent calcination processes. The tubular structure is confirmed via transmission electron microscopy imaging, whereas the structures and elemental compositions of the nanotubes are determined using x-ray diffraction, energy dispersive x-ray spectroscopy, and x-ray photoelectron spectroscopy. N2 adsorption isotherm data reveal that the surface of the nanotubes consists of micropores, thereby resulting in a significantly higher surface area (˜20 m2 g-1) than expected for a flat-surface structure (<15 m2 g-1). Herein, we present a study of the catalytic activity of our novel NiO/NiCo2O4 nanotubes for CO and acetaldehyde oxidation. The catalytic activity of NiO/NiCo2O4 is superior to Pt below 100 °C for CO oxidation. For acetaldehyde oxidation, the total oxidation activity of NiO/NiCo2O4 for acetaldehyde is comparable with that of Pt. Coexistence of many under-coordinated Co and Ni active sites in our structure is suggested be related to the high catalytic activity. It is suggested that our novel NiO/NiCo2O4 tubular structures with surface microporosity can be of interest for a variety of applications, including the catalytic oxidation of harmful gases.
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Kim, Il Hee; Lee, Hyerim; Yu, Areum; Jeong, Jae Hwan; Lee, Youngmi; Kim, Myung Hwa; Lee, Chongmok; Kim, Young Dok
2018-04-27
NiO/NiCo 2 O 4 nanotubes with a diameter of approximately 100 nm are synthesized using Ni and Co precursors via electro-spinning and subsequent calcination processes. The tubular structure is confirmed via transmission electron microscopy imaging, whereas the structures and elemental compositions of the nanotubes are determined using x-ray diffraction, energy dispersive x-ray spectroscopy, and x-ray photoelectron spectroscopy. N 2 adsorption isotherm data reveal that the surface of the nanotubes consists of micropores, thereby resulting in a significantly higher surface area (∼20 m 2 g -1 ) than expected for a flat-surface structure (<15 m 2 g -1 ). Herein, we present a study of the catalytic activity of our novel NiO/NiCo 2 O 4 nanotubes for CO and acetaldehyde oxidation. The catalytic activity of NiO/NiCo 2 O 4 is superior to Pt below 100 °C for CO oxidation. For acetaldehyde oxidation, the total oxidation activity of NiO/NiCo 2 O 4 for acetaldehyde is comparable with that of Pt. Coexistence of many under-coordinated Co and Ni active sites in our structure is suggested be related to the high catalytic activity. It is suggested that our novel NiO/NiCo 2 O 4 tubular structures with surface microporosity can be of interest for a variety of applications, including the catalytic oxidation of harmful gases.
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Qi, Wei; Yan, Pengqiang; Su, Dang Sheng
2018-03-20
Sustainable and environmentally benign catalytic processes are vital for the future to supply the world population with clean energy and industrial products. The replacement of conventional metal or metal oxide catalysts with earth abundant and renewable nonmetallic materials has attracted considerable research interests in the field of catalysis and material science. The stable and efficient catalytic performance of nanocarbon materials was discovered at the end of last century, and these materials are considered as potential alternatives for conventional metal-based catalysts. With its rapid development in the past 20 years, the research field of carbon catalysis has been experiencing a smooth transition from the discovery of novel nanocarbon materials or related new reaction systems to the atomistic-level mechanistic understanding on the catalytic process and the subsequent rational design of the practical catalytic reaction systems. In this Account, we summarize the recent progress in the kinetic and mechanistic studies on nanocarbon catalyzed alkane oxidative dehydrogenation (ODH) reactions. The paper attempts to extract general concepts and basic regularities for carbon catalytic process directing us on the way for rational design of novel efficient metal-free catalysts. The nature of the active sites for ODH reactions has been revealed through microcalorimetric analysis, ambient pressure X-ray photoelectron spectroscopy (XPS) measurement, and in situ chemical titration strategies. The detailed kinetic analysis and in situ catalyst structure characterization suggests that carbon catalyzed ODH reactions involve the redox cycles of the ketonic carbonyl-hydroxyl pairs, and the key physicochemical parameters (activation energy, reaction order, and rate/equilibrium constants, etc.) of the carbon catalytic systems are proposed and compared with conventional transition metal oxide catalysts. The proposal of the intrinsic catalytic activity (TOF) provides the possibility for the fair comparisons of different nanocarbon catalysts and the consequent structure-function relation regularity. Surface modification and heteroatom doping are proved as the most effective strategies to adjust the catalytic property (activity and product selectivity etc.) of the nanocarbon catalysts. Nanocarbon is actually a proper candidate platform helping us to understand the classical catalytic reaction mechanism better, since there is no lattice oxygen and all the catalytic process happens on nanocarbon surface. This Account also exhibits the importance of the in situ structural characterizations for heterogeneous nanocarbon catalysis. The research strategy and methods proposed for carbon catalysts may also shed light on other complicated catalytic systems or fields concerning the applications of nonmetallic materials, such as energy storage and environment protection etc.
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Investigating Catalytic Properties of Composite Nanoparticle Assemblies
2001-11-01
electrode surfaces, were found to be catalytically active towards electrooxidation of CO and MeOH upon activation. The activation involved partial removal...to proceed under stirring at room temperature for 4 hours. producing a dark-brown solution of DT-encapsulated nanoparticles that was then cleaned in... ethanol or used in the heating treatment. Processing. Highly-monodispersed Au particles (5.3 ±0.3 nm) were prepared by thermally activated treatment of
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Catalytic oxidation of VOCs over Mn/TiO2/activated carbon under 185 nm VUV irradiation.
Shu, Yajie; Xu, Yin; Huang, Haibao; Ji, Jian; Liang, Shimin; Wu, Muyan; Leung, Dennis Y C
2018-06-04
Volatile organic compounds (VOCs) are regarded as the major contributors to air pollution, and should be strictly regulated. Photocatalytic oxidation (PCO) is of great interest for the removal of VOCs owing to its strong oxidation capability. However, its application is greatly limited by catalytic deactivation. Vacuum Ultraviolet (VUV) irradiation provides a novel way to improve the photocatalytic activity while much O 3 will be generated which may cause secondary pollution. In this study, a multi-functional catalyst of Mn/TiO 2 /activated carbon (AC) was developed to eliminate and utilize O 3 , as well as enhance catalytic oxidation of VOC degradation via ozone-assisted catalytic oxidation (OZCO). The results indicate that Mn modified TiO 2 /AC (i.e. 0.1%Mn/20%TiO 2 /AC) achieved a toluene removal efficiency of nearly 86% with 100% elimination rate of O 3 . With the help of Mn/TiO 2 /AC catalyst, O 3 was catalytically decomposed and transformed into active species of O ( 1 D) and OH, thus enhancing toluene removal. The combination of VUV irradiation with multi-functional catalyst provides a novel and efficient way for the degradation of VOCs. Copyright © 2018 Elsevier Ltd. All rights reserved.
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Nanoparticle mediated micromotor motion
NASA Astrophysics Data System (ADS)
Liu, Mei; Liu, Limei; Gao, Wenlong; Su, Miaoda; Ge, Ya; Shi, Lili; Zhang, Hui; Dong, Bin; Li, Christopher Y.
2015-03-01
In this paper, we report the utilization of nanoparticles to mediate the motion of a polymer single crystal catalytic micromotor. Micromotors have been fabricated by directly self-assembling functional nanoparticles (platinum and iron oxide nanoparticles) onto one or both sides of two-dimensional polymer single crystals. We show that the moving velocity of these micromotors in fluids can be readily tuned by controlling the nanoparticles' surface wettability and catalytic activity. A 3 times velocity increase has been achieved for a hydrophobic micromotor as opposed to the hydrophilic ones. Furthermore, we demonstrate that the catalytic activity of platinum nanoparticles inside the micromotor can be enhanced by their synergetic interactions with iron oxide nanoparticles and an electric field. Both strategies lead to dramatically increased moving velocities, with the highest value reaching ~200 μm s-1. By decreasing the nanoparticles' surface wettability and increasing their catalytic activity, a maximum of a ~10-fold increase in the moving speed of the nanoparticle based micromotor can be achieved. Our results demonstrate the advantages of using nanoparticles in micromotor systems.In this paper, we report the utilization of nanoparticles to mediate the motion of a polymer single crystal catalytic micromotor. Micromotors have been fabricated by directly self-assembling functional nanoparticles (platinum and iron oxide nanoparticles) onto one or both sides of two-dimensional polymer single crystals. We show that the moving velocity of these micromotors in fluids can be readily tuned by controlling the nanoparticles' surface wettability and catalytic activity. A 3 times velocity increase has been achieved for a hydrophobic micromotor as opposed to the hydrophilic ones. Furthermore, we demonstrate that the catalytic activity of platinum nanoparticles inside the micromotor can be enhanced by their synergetic interactions with iron oxide nanoparticles and an electric field. Both strategies lead to dramatically increased moving velocities, with the highest value reaching ~200 μm s-1. By decreasing the nanoparticles' surface wettability and increasing their catalytic activity, a maximum of a ~10-fold increase in the moving speed of the nanoparticle based micromotor can be achieved. Our results demonstrate the advantages of using nanoparticles in micromotor systems. Electronic supplementary information (ESI) available: Fig. S1-S5 and Video S1-S3. See DOI: 10.1039/c4nr07558g
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NASA Astrophysics Data System (ADS)
Ivashkina, Elena; Nazarova, Galina; Shafran, Tatyana; Stebeneva, Valeriya
2017-08-01
The effect of the feedstock composition and the process conditions on the current catalyst activity in catalytic cracking technology using a mathematical model is performed in this research. The mathematical model takes into account the catalyst deactivation by coke for primary and secondary cracking reactions. The investigation results have shown that the feedstock has significant effect on the yield and the content of coke on the catalyst. Thus, the relative catalyst activity is significantly reduced by 7.5-10.7 %. With increasing the catalytic cracking temperature due to the catalyst flow temperature rising, the coke content and the yield per feedstock increase and the catalyst activity decreases by 5.3-7.7%. Rising the process temperature together with the catalyst circulation ratio contributes to increase of the coke yield per feedstock in the catalytic cracking and decrease of the coke content on the catalyst. It is connected with the catalyst flow rising to the riser and the contact time decreasing in the reaction zone. Also, the catalyst activity decreases in the range of 3.8-5.5% relatively to the regenerated catalyst activity (83 %).
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The ability of different nano-sized materials (NSM) to effectively act as active photo-catalytic surfaces has been described for the mineralization/inactivation of many different aqueous pollutants. The reason for their enhanced ability over larger catalytic surfaces owes muc...
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Open-mouthed hybrid microcapsules with elevated enzyme loading and enhanced catalytic activity.
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.
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Method of maintaining activity of hydrogen-sensing platinum electrode
NASA Technical Reports Server (NTRS)
Harman, J. N., III
1968-01-01
Three-electrode hydrogen sensor containing a platinum electrode maintained in a highly catalytic state, operates with a minimal response time and maximal sensitivity to the hydrogen gas being sensed. Electronic control and readout circuitry reactivates the working electrode of the sensor to a state of maximal catalytic activity.
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Catalytic and reactive polypeptides and methods for their preparation and use
Schultz, Peter
1994-01-01
Catalytic and reactive polypeptides include a binding site specific for a reactant or reactive intermediate involved in a chemical reaction of interest. The polypeptides further include at least one active functionality proximate the binding site, where the active functionality is capable of catalyzing or chemically participating in the chemical reaction in such a way that the reaction rate is enhanced. Methods for preparing the catalytic peptides include chemical synthesis, site-directed mutagenesis of antibody and enzyme genes, covalent attachment of the functionalities through particular amino acid side chains, and the like.
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Choi, Isaac; Chung, Hyunho; Park, Jang Won; Chung, Young Keun
2016-11-04
A cobalt-rhodium heterobimetallic nanoparticle-catalyzed reductive cyclization of 2-(2-nitroaryl)acetonitriles to indoles has been achieved. The tandem reaction proceeds without any additives under the mild conditions (1 atm H 2 and 25 °C). This procedure could be scaled up to the gram scale. The catalytic system is significantly stable under these reaction conditions and could be reused more than ten times without loss of catalytic activity.
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Mita, Tsuyoshi; Sugawara, Masumi; Saito, Keisuke; Sato, Yoshihiro
2014-06-06
A catalytic enantioselective silylation of N-tert-butylsulfonylimines using a Cu-secondary diamine complex was demonstrated. The resulting optically active α-amino silanes could be carboxylated under a CO2 atmosphere (1 atm) to afford the corresponding α-amino acids in a stereoretentive manner. This two-step sequence provides a new synthetic protocol for optically active α-amino acids from gaseous CO2 and imines in the presence of a catalytic amount of a chiral source.
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Evolutionary game theory: molecules as players.
Bohl, Katrin; Hummert, Sabine; Werner, Sarah; Basanta, David; Deutsch, Andreas; Schuster, Stefan; Theissen, Günter; Schroeter, Anja
2014-12-01
In this and an accompanying paper we review the use of game theoretical concepts in cell biology and molecular biology. This review focuses on the subcellular level by considering viruses, genes, and molecules as players. We discuss in which way catalytic RNA can be treated by game theory. Moreover, genes can compete for success in replication and can have different strategies in interactions with other genetic elements. Also transposable elements, or "jumping genes", can act as players because they usually bear different traits or strategies. Viruses compete in the case of co-infecting a host cell. Proteins interact in a game theoretical sense when forming heterodimers. Finally, we describe how the Shapley value can be applied to enzymes in metabolic pathways. We show that game theory can be successfully applied to describe and analyse scenarios at the molecular level resulting in counterintuitive conclusions.
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SABER: A computational method for identifying active sites for new reactions
Nosrati, Geoffrey R; Houk, K N
2012-01-01
A software suite, SABER (Selection of Active/Binding sites for Enzyme Redesign), has been developed for the analysis of atomic geometries in protein structures, using a geometric hashing algorithm (Barker and Thornton, Bioinformatics 2003;19:1644–1649). SABER is used to explore the Protein Data Bank (PDB) to locate proteins with a specific 3D arrangement of catalytic groups to identify active sites that might be redesigned to catalyze new reactions. As a proof-of-principle test, SABER was used to identify enzymes that have the same catalytic group arrangement present in o-succinyl benzoate synthase (OSBS). Among the highest-scoring scaffolds identified by the SABER search for enzymes with the same catalytic group arrangement as OSBS were l-Ala d/l-Glu epimerase (AEE) and muconate lactonizing enzyme II (MLE), both of which have been redesigned to become effective OSBS catalysts, demonstrated by experiments. Next, we used SABER to search for naturally existing active sites in the PDB with catalytic groups similar to those present in the designed Kemp elimination enzyme KE07. From over 2000 geometric matches to the KE07 active site, SABER identified 23 matches that corresponded to residues from known active sites. The best of these matches, with a 0.28 Å catalytic atom RMSD to KE07, was then redesigned to be compatible with the Kemp elimination using RosettaDesign. We also used SABER to search for potential Kemp eliminases using a theozyme predicted to provide a greater rate acceleration than the active site of KE07, and used Rosetta to create a design based on the proteins identified. PMID:22492397
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Yu, Deyang; Peng, Ying; Ayaz-Guner, Serife; Gregorich, Zachery R.; Ge, Ying
2015-01-01
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 has 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. PMID:26489410
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Probing the Catalytic Mechanism of Vibrio harveyi GH20 β-N-Acetylglucosaminidase by Chemical Rescue
Meekrathok, Piyanat; Suginta, Wipa
2016-01-01
Background Vibrio harveyi GH20 β-N-acetylglucosaminidase (VhGlcNAcase) is a chitinolytic enzyme responsible for the successive degradation of chitin fragments to GlcNAc monomers, activating the onset of the chitin catabolic cascade in marine Vibrios. Methods Two invariant acidic pairs (Asp303-Asp304 and Asp437-Glu438) of VhGlcNAcase were mutated using a site-directed mutagenesis strategy. The effects of these mutations were examined and the catalytic roles of these active-site residues were elucidated using a chemical rescue approach. Enhancement of the enzymic activity of the VhGlcNAcase mutants was evaluated by a colorimetric assay using pNP-GlcNAc as substrate. Results Substitution of Asp303, Asp304, Asp437 or Glu438 with Ala/Asn/Gln produced a dramatic loss of the GlcNAcase activity. However, the activity of the inactive D437A mutant was recovered in the presence of sodium formate. Our kinetic data suggest that formate ion plays a nucleophilic role by mimicking the β-COO-side chain of Asp437, thereby stabilizing the reaction intermediate during both the glycosylation and the deglycosylation steps. Conclusions Chemical rescue of the inactive D437A mutant of VhGlcNAcase by an added nucleophile helped to identify Asp437 as the catalytic nucleophile/base, and hence its acidic partner Glu438 as the catalytic proton donor/acceptor. General Significance Identification of the catalytic nucleophile of VhGlcNAcases supports the proposal of a substrate-assisted mechanism of GH20 GlcNAcases, requiring the catalytic pair Asp437-Glu438 for catalysis. The results suggest the mechanistic basis of the participation of β-N-acetylglucosaminidase in the chitin catabolic pathway of marine Vibrios. PMID:26870945
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Maggi, Maristella; Chiarelli, Laurent R; Valentini, Giovanna; Scotti, Claudia
2015-01-01
Bacterial L-asparaginases have been used as anti-cancer drugs for over 4 decades though presenting, along with their therapeutic efficacy, several side effects due to their bacterial origin and, seemingly, to their secondary glutaminase activity. Helicobacter pylori type II L-asparaginase possesses interesting features, among which a reduced catalytic efficiency for L-GLN, compared to the drugs presently used in therapy. In the present study, we describe some enzyme variants with catalytic and in vitro cytotoxic activities different from the wild type enzyme. Particularly, replacements on catalytic threonines (T16D and T95E) deplete the enzyme of both its catalytic activities, once more underlining the essential role of such residues. One serendipitous mutant, M121C/T169M, had a preserved efficiency vs L-asparagine but was completely unable to carry out L-glutamine hydrolysis. Interestingly, this variant did not exert any cytotoxic effect on HL-60 cells. The M121C and T169M single mutants had reduced catalytic activities (nearly 2.5- to 4-fold vs wild type enzyme, respectively). Mutant Q63E, endowed with a similar catalytic efficiency versus asparagine and halved glutaminase efficiency with respect to the wild type enzyme, was able to exert a cytotoxic effect comparable to, or higher than, the one of the wild type enzyme when similar asparaginase units were used. These findings may be relevant to determine the role of glutaminase activity of L-asparaginase in the anti-proliferative effect of the drug and to shed light on how to engineer the best asparaginase/glutaminase combination for an ever improved, patients-tailored therapy.
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Maggi, Maristella; Chiarelli, Laurent R.; Valentini, Giovanna; Scotti, Claudia
2015-01-01
Bacterial L-asparaginases have been used as anti-cancer drugs for over 4 decades though presenting, along with their therapeutic efficacy, several side effects due to their bacterial origin and, seemingly, to their secondary glutaminase activity. Helicobacter pylori type II L-asparaginase possesses interesting features, among which a reduced catalytic efficiency for L-GLN, compared to the drugs presently used in therapy. In the present study, we describe some enzyme variants with catalytic and in vitro cytotoxic activities different from the wild type enzyme. Particularly, replacements on catalytic threonines (T16D and T95E) deplete the enzyme of both its catalytic activities, once more underlining the essential role of such residues. One serendipitous mutant, M121C/T169M, had a preserved efficiency vs L-asparagine but was completely unable to carry out L-glutamine hydrolysis. Interestingly, this variant did not exert any cytotoxic effect on HL-60 cells. The M121C and T169M single mutants had reduced catalytic activities (nearly 2.5- to 4-fold vs wild type enzyme, respectively). Mutant Q63E, endowed with a similar catalytic efficiency versus asparagine and halved glutaminase efficiency with respect to the wild type enzyme, was able to exert a cytotoxic effect comparable to, or higher than, the one of the wild type enzyme when similar asparaginase units were used. These findings may be relevant to determine the role of glutaminase activity of L-asparaginase in the anti-proliferative effect of the drug and to shed light on how to engineer the best asparaginase/glutaminase combination for an ever improved, patients-tailored therapy. PMID:25664771
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Investigation of the Origin of Catalytic Activity in Oxide-Supported Nanoparticle Gold
DOE Office of Scientific and Technical Information (OSTI.GOV)
Harrison, Ian
Since Haruta’s discovery in 1987 of the surprising catalytic activity of supported Au nanoparticles, we have seen a very large number of experimental and theoretical efforts to explain this activity and to fully understand the nature of the behavior of the responsible active sites. In 2011, we discovered that a dual catalytic site at the perimeter of ~3nm diameter Au particles supported on TiO 2 is responsible for oxidative catalytic activity. O 2 molecules bind with Au atoms and Ti4+ ions in the TiO 2 support and the weakened O-O bond dissociates at low temperatures, proceeding to produce O atomsmore » which act as oxidizing agents for the test molecule, CO. The papers supported by DOE have built on this finding and have been concerned with two aspects of the behavior of Au/TiO 2 catalysts: (1). Mechanistic behavior of dual catalytic sites in the oxidation of organic molecules such as ethylene and acetic acid; (2). Studies of the electronic properties of the TiO 2 (110) single crystal in relation to its participation in charge transfer at the occupied dual catalytic site. A total of 20 papers have been produced through DOE support of this work. The papers combine IR spectroscopic investigations of Au/TiO 2 catalysts with surface science on the TiO 2(110) and TiO 2 nanoparticle surfaces with modern density functional modeling. The primary goals of the work were to investigate the behavior of the dual Au/Ti 4+ site for the partial oxidation of alcohols to acids, the hydrogenation of aldehydes and ketones to alcohols, and the condensation of oxygenate intermediates- all processes related to the utilization of biomass in the production of useful chemical energy sources.« less
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Characterization of a chitinase from the cellulolytic actinomycete Thermobifida fusca.
Gaber, Yasser; Mekasha, Sophanit; Vaaje-Kolstad, Gustav; Eijsink, Vincent G H; Fraaije, Marco W
2016-09-01
Thermobifida fusca is a well-known cellulose-degrading actinomycete, which produces various glycoside hydrolases for this purpose. However, despite the presence of putative chitinase genes in its genome, T. fusca has not been reported to grow on chitin as sole carbon source. In this study, a gene encoding a putative membrane-anchored GH18 chitinase (Tfu0868) from T. fusca has been cloned and overexpressed in Escherichia coli. The protein was produced as SUMO fusion protein and, upon removal of the SUMO domain, soluble pure TfChi18A was obtained with yields typically amounting to 150mg per litre of culture. The enzyme was found to be relatively thermostable (apparent Tm=57.5°C) but not particularly thermoactive, the optimum temperature being 40-45°C. TfChi18A bound to α- and β-chitin and degraded both these substrates. Interestingly, activity towards colloidal chitin was minimal and in this case, substrate inhibition was observed. TfChi18A also cleaved soluble chito-oligosaccharides and showed a clear preference for substrates having five sugars or more. While these results show that TfChi18A is a catalytically competent GH18 chitinase, the observed catalytic rates were low compared to those of well-studied GH18 chitinases. This suggests that TfChi18A is not a true chitinase and not likely to endow T. fusca with the ability to grow on chitin. Copyright © 2016 Elsevier B.V. All rights reserved.
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Suarez, Javier; Ranguelova, Kalina; Jarzecki, Andrzej A.; Manzerova, Julia; Krymov, Vladimir; Zhao, Xiangbo; Yu, Shengwei; Metlitsky, Leonid; Gerfen, Gary J.; Magliozzo, Richard S.
2009-01-01
A mechanism accounting for the robust catalase activity in catalase-peroxidases (KatG) presents a new challenge in heme protein enzymology. In Mycobacterium tuberculosis, KatG is the sole catalase and is also responsible for peroxidative activation of isoniazid, an anti-tuberculosis pro-drug. Here, optical stopped-flow spectrophotometry, rapid freeze-quench EPR spectroscopy both at the X-band and at the D-band, and mutagenesis are used to identify catalase reaction intermediates in M. tuberculosis KatG. In the presence of millimolar H2O2 at neutral pH, oxyferrous heme is formed within milliseconds from ferric (resting) KatG, whereas at pH 8.5, low spin ferric heme is formed. Using rapid freeze-quench EPR at X-band under both of these conditions, a narrow doublet radical signal with an 11 G principal hyperfine splitting was detected within the first milliseconds of turnover. The radical and the unique heme intermediates persist in wild-type KatG only during the time course of turnover of excess H2O2 (1000-fold or more). Mutation of Met255, Tyr229, or Trp107, which have covalently linked side chains in a unique distal side adduct (MYW) in wild-type KatG, abolishes this radical and the catalase activity. The D-band EPR spectrum of the radical exhibits a rhombic g tensor with dual gx values (2.00550 and 2.00606) and unique gy (2.00344) and gz values (2.00186) similar to but not typical of native tyrosyl radicals. Density functional theory calculations based on a model of an MYW adduct radical built from x-ray coordinates predict experimentally observed hyperfine interactions and a shift in g values away from the native tyrosyl radical. A catalytic role for an MYW adduct radical in the catalase mechanism of KatG is proposed. PMID:19139099
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White, Mark D; Kamps, Jos J A G; East, Samuel; Taylor Kearney, Leah J; Flashman, Emily
2018-05-30
Group VII Ethylene Response Factors (ERF-VIIs) regulate transcriptional adaptation to flooding-induced hypoxia in plants. ERF-VII stability is controlled in an O 2 -dependent manner by the Cys/Arg branch of the N-end rule pathway, whereby oxidation of a conserved N-terminal cysteine residue initiates target degradation. This oxidation is catalyzed by Plant Cysteine Oxidases (PCOs) which use O 2 as co-substrate to generate Cys-sulfinic acid. The PCOs directly link O2 availability to ERF-VII stability and anaerobic adaptation leading to the suggestion that they act as plant O 2 sensors. However, their ability to respond to fluctuations in O 2 concentration has not been established. Here, we investigated the steady-state kinetics of Arabidopsis thaliana PCOs 1-5 to ascertain whether their activities are sensitive to O 2 levels. We found that the most catalytically competent isoform is AtPCO4, in terms of both responding to O 2 , and oxidizing At RAP2.2 and 2.12, two of the primary hypoxic response activating ERF-VIIs; these data suggest that AtPCO4 plays a central role in ERF-VII regulation. Furthermore, we found that AtPCO activity is susceptible to decreases in pH and that the hypoxia-inducible AtPCOs 1/2 and the non-inducible AtPCOs 4/5 have discrete AtERF-VII substrate preferences. Pertinently, the AtPCOs had K m app (O 2 ) values in a physiologically relevant range, which should enable them to sensitively react to changes in O 2 availability. This work validates an O 2 -sensing role for the PCOs and suggests that differences in expression pattern, ERF-VII selectivity and catalytic capability may enable the different isoforms to have distinct biological functions. Individual PCOs could therefore be targeted to manipulate ERF-VII levels and improve stress tolerance in plants. Published under license by The American Society for Biochemistry and Molecular Biology, Inc.
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Contrasting Sensitivities of Escherichia coli Aconitases A and B to Oxidation and Iron Depletion
Varghese, Shery; Tang, Yue; Imlay, James A.
2003-01-01
Superoxide damages dehydratases that contain catalytic [4Fe-4S]2+ clusters. Aconitases are members of that enzyme family, and previous work showed that most aconitase activity is lost when Escherichia coli is exposed to superoxide stress. More recently it was determined that E. coli synthesizes at least two isozymes of aconitase, AcnA and AcnB. Synthesis of AcnA, the less-abundant enzyme, is positively controlled by SoxS, a protein that is activated in the presence of superoxide-generating chemicals. We have determined that this arrangement exists because AcnA is resistant to superoxide in vivo. Surprisingly, purified AcnA is extremely sensitive to superoxide and other chemical oxidants unless it is combined with an uncharacterized factor that is present in cell extracts. In contrast, AcnB is highly sensitive to a variety of chemical oxidants in vivo, in extracts, and in its purified form. Thus, the induction of AcnA during oxidative stress provides a mechanism to circumvent a block in the tricarboxylic acid cycle. AcnA appears to be as catalytically competent as AcnB, so the retention of the latter as the primary housekeeping enzyme must provide some other advantage. We observed that the [4Fe-4S] cluster of AcnB is in dynamic equilibrium with the surrounding iron pool, so that AcnB is rapidly demetallated when intracellular iron pools drop. AcnA and other dehydratases do not show this trait. Demetallated AcnB is known to bind its cognate mRNA. The absence of AcnB activity also causes the accumulation and excretion of citrate, an iron chelator for which E. coli synthesizes a transport system. Thus, AcnB may be retained as the primary aconitase because the lability of its exposed cluster allows E. coli to sense and respond to iron depletion. PMID:12486059
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Lu, Yanan; Zhao, Shulin; Yang, Rui; Xu, Dongdong; Yang, Jing; Lin, Yue; Shi, Nai-En; Dai, Zhihui; Bao, Jianchun; Han, Min
2018-03-07
Development of cheap, highly active, and robust bimetallic nanocrystal (NC)-based nanohybrid (NH) electrocatalysts for oxygen reduction reaction (ORR) is helpful for advancing fuel cells or other renewable energy technologies. Here, four kinds of well-coupled Mn x Pd y (MnPd 3 , MnPd-Pd, Mn 2 Pd 3 , Mn 2 Pd 3 -Mn 11 Pd 21 )/C NHs have been synthesized by in situ integration of Mn x Pd y NCs with variable component ratios on pretreated Vulcan XC-72 C using the solvothermal method accompanied with annealing under Ar/H 2 atmosphere and used as electrocatalysts for ORR. Among them, the MnPd 3 /C NHs possess the unique "half-embedded and half-encapsulated" interfaces and exhibit the highest catalytic activity, which can compete with some currently reported non-Pt catalysts (e.g., Ag-Co nanoalloys, Pd 2 NiAg NCs, PdCo/N-doped porous C, G-Cu 3 Pd nanocomposites, etc.), and close to commercial Pt/C. Electrocatalytic dynamic measurements disclose that their ORR mechanism abides by the direct 4e - pathway. Moreover, their durability and methanol-tolerant capability are much higher than that of Pt/C. As revealed by spectroscopic and electrochemical analyses, the excellent catalytic performance of MnPd 3 /C NHs results from the proper component ratio of Mn and Pd and the strong interplay of their constituents, which not only facilitate to optimize the d-band center or the electronic structure of Pd but also induce the phase transformation of MnPd 3 active components and enhance their conductivity or interfacial electron transfer dynamics. This work demonstrates that MnPd 3 /C NHs are promising methanol-tolerant cathode electrocatalysts that may be employed in fuel cells or other renewable energy option.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Wiedner, Eric S.; Brown, Houston J.; Helm, Monte L.
2016-01-20
The hydrogen production electrocatalyst Ni(PPh2NPh2)22+ (1) is capable of traversing multiple electrocatalytic pathways. When using dimethylformamidium, DMF(H)+, the mechanism of formation of H2 catalyzed by 1 changes from an ECEC to an EECC mechanism as the potential approaches the Ni(I/0) couple. Two recent electrochemical methods, current-potential analysis and foot-of-the-wave analysis (FOWA), were performed on 1 to measure the detailed chemical kinetics of the competing ECEC and EECC pathways. A sensitivity analysis was performed on the electrochemical methods using digital simulations to gain a better understanding of their strengths and limitations. Notably, chemical rate constants were significantly underestimated when not accountingmore » for electron transfer kinetics, even when electron transfer was fast enough to afford a reversible non-catalytic wave. The EECC pathway of 1 was found to be faster than the ECEC pathway under all conditions studied. Using buffered DMF: DMF(H)+ mixtures led to an increase in the catalytic rate constant (kobs) of the EECC pathway, but kobs for the ECEC pathway did not change when using buffered acid. Further kinetic analysis of the ECEC path revealed that added base increases the rate of isomerization of the exo-protonated Ni(0) isomers to the catalytically active endo-isomers, but decreases the net rate of protonation of Ni(I). FOWA on 1 did not provide accurate rate constants due to incomplete reduction of the exo-protonated Ni(I) intermediate at the foot of the wave, but FOWA could be used to estimate the reduction potential of this previously undetected intermediate. This research was supported as part of the Center for Molecular Electrocatalysis, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences. Pacific Northwest National Laboratory is operated by Battelle for the U.S. Department of Energy.« less
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Gross, Elad; Shu, Xing-Zhong; Alayoglu, Selim; Bechtel, Hans A; Martin, Michael C; Toste, F Dean; Somorjai, Gabor A
2014-03-05
Analysis of catalytic organic transformations in flow reactors and detection of short-lived intermediates are essential for optimization of these complex reactions. In this study, spectral mapping of a multistep catalytic reaction in a flow microreactor was performed with a spatial resolution of 15 μm, employing micrometer-sized synchrotron-based IR and X-ray beams. Two nanometer sized Au nanoclusters were supported on mesoporous SiO2, packed in a flow microreactor, and activated toward the cascade reaction of pyran formation. High catalytic conversion and tunable products selectivity were achieved under continuous flow conditions. In situ synchrotron-sourced IR microspectroscopy detected the evolution of the reactant, vinyl ether, into the primary product, allenic aldehyde, which then catalytically transformed into acetal, the secondary product. By tuning the residence time of the reactants in a flow microreactor a detailed analysis of the reaction kinetics was performed. An in situ micrometer X-ray absorption spectroscopy scan along the flow reactor correlated locally enhanced catalytic conversion, as detected by IR microspectroscopy, to areas with high concentration of Au(III), the catalytically active species. These results demonstrate the fundamental understanding of the mechanism of catalytic reactions which can be achieved by the detailed mapping of organic transformations in flow reactors.
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NASA Astrophysics Data System (ADS)
Wang, Tehua; Chong, Siying; Wang, Tongtong; Lu, Huiyi; Ji, Min
2018-01-01
In order to correlate the physicochemical properties of carbon-covered alumina (CCA) materials with their catalytic performance for oxidative dehydrogenation of ethylbenzene with CO2 (CO2-ODEB), a series of CCA materials with diverse carbon contents (8.7-31.3 wt%) and pyrolysis temperatures (600-800 °C), which were synthesized via an impregnation method followed by pyrolysis, were applied. These catalytic materials were characterized by TGA, N2 physisorption, XRD, Raman spectroscopy and XPS techniques. It was found that the catalytic performance of these CCA materials highly depended on their physicochemical properties, and the optimum CCA catalyst exhibited much better catalytic stability than conventional hydroxyl carbon nanotubes. Below an optimum value of carbon content, the CCA catalyst preserved the main pore characteristics of the Al2O3 support and its catalytic activity increased with the carbon content. Excessive carbon loading resulted in significant textural alterations and thereby decreased both the ethylbenzene conversion and styrene selectivity. On the other hand, high pyrolysis temperature was detrimental to the ordered graphitic structure of the carbon species within the Al2O3 pore. The decreased ordered graphitic degree was found to be associated with the loss of the surface active carbonyl groups, consequently hampering the catalytic efficiency of the CCA catalyst.
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NASA Astrophysics Data System (ADS)
Tong, H.; Snow, G. C.; Chu, E. K.; Chang, R. L. S.; Angwin, M. J.; Pessagno, S. L.
1981-09-01
Durable catalytic reactors for advanced gas turbine engines were developed. Objectives were: to evaluate furnace aging as a cost effective catalytic reactor screening test, measure reactor degradation as a function of furnace aging, demonstrate 1,000 hours of combustion durability, and define a catalytic reactor system with a high probability of successful integration into an automotive gas turbine engine. Fourteen different catalytic reactor concepts were evaluated, leading to the selection of one for a durability combustion test with diesel fuel for combustion conditions. Eight additional catalytic reactors were evaluated and one of these was successfully combustion tested on propane fuel. This durability reactor used graded cell honeycombs and a combination of noble metal and metal oxide catalysts. The reactor was catalytically active and structurally sound at the end of the durability test.
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NASA Technical Reports Server (NTRS)
Tong, H.; Snow, G. C.; Chu, E. K.; Chang, R. L. S.; Angwin, M. J.; Pessagno, S. L.
1981-01-01
Durable catalytic reactors for advanced gas turbine engines were developed. Objectives were: to evaluate furnace aging as a cost effective catalytic reactor screening test, measure reactor degradation as a function of furnace aging, demonstrate 1,000 hours of combustion durability, and define a catalytic reactor system with a high probability of successful integration into an automotive gas turbine engine. Fourteen different catalytic reactor concepts were evaluated, leading to the selection of one for a durability combustion test with diesel fuel for combustion conditions. Eight additional catalytic reactors were evaluated and one of these was successfully combustion tested on propane fuel. This durability reactor used graded cell honeycombs and a combination of noble metal and metal oxide catalysts. The reactor was catalytically active and structurally sound at the end of the durability test.
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Ribeiro, António J M; Holliday, Gemma L; Furnham, Nicholas; Tyzack, Jonathan D; Ferris, Katherine; Thornton, Janet M
2018-01-04
M-CSA (Mechanism and Catalytic Site Atlas) is a database of enzyme active sites and reaction mechanisms that can be accessed at www.ebi.ac.uk/thornton-srv/m-csa. Our objectives with M-CSA are to provide an open data resource for the community to browse known enzyme reaction mechanisms and catalytic sites, and to use the dataset to understand enzyme function and evolution. M-CSA results from the merging of two existing databases, MACiE (Mechanism, Annotation and Classification in Enzymes), a database of enzyme mechanisms, and CSA (Catalytic Site Atlas), a database of catalytic sites of enzymes. We are releasing M-CSA as a new website and underlying database architecture. At the moment, M-CSA contains 961 entries, 423 of these with detailed mechanism information, and 538 with information on the catalytic site residues only. In total, these cover 81% (195/241) of third level EC numbers with a PDB structure, and 30% (840/2793) of fourth level EC numbers with a PDB structure, out of 6028 in total. By searching for close homologues, we are able to extend M-CSA coverage of PDB and UniProtKB to 51 993 structures and to over five million sequences, respectively, of which about 40% and 30% have a conserved active site. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.
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Atomic-Scale Principles of Combustion Nanocatalysis
2014-05-19
of Combustion Nanocatalysts: Structures, Electronic Characteristics and Catalytic Pathways MURI FINAL REPORT Reporting Period: June 1, 2008 to...properties of nanoscale materials to be employed for catalytic combustion of fuels and propellants. Furthermore the research program seeks to establish... catalytic cycle. Both the carbon– hydrogen bond activation and the subsequent desorption of the ethylene product molecule require cooperative action
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Competing endogenous RNA and interactome bioinformatic analyses on human telomerase.
Arancio, Walter; Pizzolanti, Giuseppe; Genovese, Swonild Ilenia; Baiamonte, Concetta; Giordano, Carla
2014-04-01
We present a classic interactome bioinformatic analysis and a study on competing endogenous (ce) RNAs for hTERT. The hTERT gene codes for the catalytic subunit and limiting component of the human telomerase complex. Human telomerase reverse transcriptase (hTERT) is essential for the integrity of telomeres. Telomere dysfunctions have been widely reported to be involved in aging, cancer, and cellular senescence. The hTERT gene network has been analyzed using the BioGRID interaction database (http://thebiogrid.org/) and related analysis tools such as Osprey (http://biodata.mshri.on.ca/osprey/servlet/Index) and GeneMANIA (http://genemania.org/). The network of interaction of hTERT transcripts has been further analyzed following the competing endogenous (ce) RNA hypotheses (messenger [m] RNAs cross-talk via micro [mi] RNAs) using the miRWalk database and tools (www.ma.uni-heidelberg.de/apps/zmf/mirwalk/). These analyses suggest a role for Akt, nuclear factor-κB (NF-κB), heat shock protein 90 (HSP90), p70/p80 autoantigen, 14-3-3 proteins, and dynein in telomere functions. Roles for histone acetylation/deacetylation and proteoglycan metabolism are also proposed.
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Metal active site elasticity linked to activation of homocysteine in methionine synthases
DOE Office of Scientific and Technical Information (OSTI.GOV)
Koutmos, Markos; Pejchal, Robert; Bomer, Theresa M.
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 uponmore » 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.« less
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Synthesis of urease hybrid nanoflowers and their enhanced catalytic properties.
Somturk, Burcu; Yilmaz, Ismail; Altinkaynak, Cevahir; Karatepe, Aslıhan; Özdemir, Nalan; Ocsoy, Ismail
2016-05-01
Increasing numbers of materials have been extensively used as platforms for enzyme immobilization to enhance catalytic activity and stability. Although stability of enzyme was accomplished with immobilization approaches, activity of the most of the enzymes was declined after immobilization. Herein, we synthesize the flower shaped-hybrid nanomaterials called hybrid nanoflower (HNF) consisting of urease enzyme and copper ions (Cu(2+)) and report a mechanistic elucidation of enhancement in both activity and stability of the HNF. We demonstrated how experimental factors influence morphology of the HNF. We proved that the HNF (synthesized from 0.02mgmL(-1) urease in 10mM PBS (pH 7.4) at +4°C) exhibited the highest catalytic activity of ∼2000% and ∼4000% when stored at +4°C and RT, respectively compared to free urease. The highest stability was also achieved by this HNF by maintaining 96.3% and 90.28% of its initial activity within storage of 30 days at +4°C and RT, respectively. This dramatically enhanced activity is attributed to high surface area, nanoscale-entrapped urease and favorable urease conformation of the HNF. The exceptional catalytic activity and stability properties of HNF can be taken advantage of to use it in fields of biomedicine and chemistry. Copyright © 2015 Elsevier Inc. All rights reserved.
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NASA Astrophysics Data System (ADS)
Wang, Shan; Gao, Shasha; Tang, Yakun; Wang, Lei; Jia, Dianzeng; Liu, Lang
2018-04-01
Coal-based activated carbons (AC) were acted as the support, Cu/AC catalysts were synthesized by a facile solid-state reaction combined with subsequent heat treatment. In Cu/AC composites, highly dispersed Cu nanospheres were anchored on AC. The catalytic activity for 4-nitrophenol (4-NP) was investigated, the effects of activation temperature and copper loading on the catalytic performance were studied. The catalysts exhibited very high catalytic activity and moderate chemical stability due to the unique characteristics of the particle-assembled nanostructures, the high surface area and the porous structure of coal-based AC and the good dispersion of metal particles. Design and preparation of non-noble metal composite catalysts provide a new direction for improving the added value of coal.
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Catalytic activity of platinum on ruthenium electrodes with modified (electro)chemical states.
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.
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Solution structure of the catalytic domain of RICH protein from goldfish.
Kozlov, Guennadi; Denisov, Alexey Y; Pomerantseva, Ekaterina; Gravel, Michel; Braun, Peter E; Gehring, Kalle
2007-03-01
Regeneration-induced CNPase homolog (RICH) is an axonal growth-associated protein, which is induced in teleost fish upon optical nerve injury. RICH consists of a highly acidic N-terminal domain, a catalytic domain with 2',3'-cyclic nucleotide 3'-phosphodiesterase (CNPase) activity and a C-terminal isoprenylation site. In vitro RICH and mammalian brain CNPase specifically catalyze the hydrolysis of 2',3'-cyclic nucleotides to produce 2'-nucleotides, but the physiologically relevant in vivo substrate remains unknown. Here, we report the NMR structure of the catalytic domain of goldfish RICH and describe its binding to CNPase inhibitors. The structure consists of a twisted nine-stranded antiparallel beta-sheet surrounded by alpha-helices on both sides. Despite significant local differences mostly arising from a seven-residue insert in the RICH sequence, the active site region is highly similar to that of human CNPase. Likewise, refinement of the catalytic domain of rat CNPase using residual dipolar couplings gave improved agreement with the published crystal structure. NMR titrations of RICH with inhibitors point to a similar catalytic mechanism for RICH and CNPase. The results suggest a functional importance for the evolutionarily conserved phosphodiesterase activity and hint of a link with pre-tRNA splicing.
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A novel 3D Ag(I)-MOF: Surfactant-directed syntheses and catalytic degradation of o/m/p-Nitrophenol
DOE Office of Scientific and Technical Information (OSTI.GOV)
Wu, Xue-Qian; Wen, Guo-Xuan; Wu, Ya-Pan
2016-10-15
For the first time, sodium caprylate has been investigated to direct the crystal growth of 3D Ag-MOF, [Ag{sub 2}(ddcba)(4,4′-bipy){sub 2}] (1), constructing from 3,5-(di(2′,5′-dicarboxylphenyl)benozoic acid and 4,4′-bipy. The single crystal diffraction analyses shows that complex 1 possess 3D neutral framework with a three-connected ThSi{sub 2} (10{sup 3}-b) topology. Compound 1 exhibits predominant catalytic activity towards the degradation of o-Nitrophenol (ONP), m-Nitrophenol (MNP) and p-Nitrophenol (PNP) in aqueous solution. The kinetics of such catalytic degradation reactions was also studied. - Graphical abstract: A novel 3D Ag(I)-MOF with ThSi{sub 2} (10{sup 3}-b) topology exhibits predominant catalytic activity towards the degradation of o-Nitrophenolmore » (ONP), m-Nitrophenol (MNP) and p-Nitrophenol (PNP) in aqueous solution. - Highlights: • A novel 3D Ag(I)-MOF with ThSi{sub 2} (10{sup 3}-b) topology. • Surfactant as additive for directing the crystal growth. • Predominant catalytic activities for the degradation of o/m/p-nitrophenol.« less
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Ye, Weichun; Shi, Xuezhao; Zhang, Yane; Hong, Chenghui; Wang, Chunming; Budzianowski, Wojciech M; Xue, Desheng
2016-02-10
Palladium-cobalt alloy nanoparticles were synthesized and dispersed on carbon black support, aiming to have a less expensive catalyst. Catalytic behaviors of PdCo/C catalyst for the oxidation of hydroquinone (HQ) with H2O2 in aqueous solution were evaluated using high-performance liquid chromatography (HPLC). The results revealed that PdCo/C catalyst had better catalytic activity than an equal amount of commercial Pd/C and Co/C catalysts because of the d-band hybridization between Pd and Co. The effects of pH value, solvent, and various interferents including inorganic and organic compounds on the efficiency of HQ oxidation were further investigated. Furthermore, on the basis of mixed potential theory, comprehensive electrochemical measurements such as the open-circuit potential-time (OCP-t) technique and Tafel plot were efficient to assess the catalytic activity of the catalyst, and the results obtained were consistent with those of HPLC measurements. The efficient HQ oxidation was closely associated with the catalytic activity of PdCo nanoparticles because they accelerated the electron-transfer process and facilitated the generation of OH radicals.
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Basak, Papri; Maitra-Majee, Susmita; Das, Jayanta Kumar; Mukherjee, Abhishek; Ghosh Dastidar, Shubhra; Pal Choudhury, Pabitra
2017-01-01
A molecular evolutionary analysis of a well conserved protein helps to determine the essential amino acids in the core catalytic region. Based on the chemical properties of amino acid residues, phylogenetic analysis of a total of 172 homologous sequences of a highly conserved enzyme, L-myo-inositol 1-phosphate synthase or MIPS from evolutionarily diverse organisms was performed. This study revealed the presence of six phylogenetically conserved blocks, out of which four embrace the catalytic core of the functional protein. Further, specific amino acid modifications targeting the lysine residues, known to be important for MIPS catalysis, were performed at the catalytic site of a MIPS from monocotyledonous model plant, Oryza sativa (OsMIPS1). Following this study, OsMIPS mutants with deletion or replacement of lysine residues in the conserved blocks were made. Based on the enzyme kinetics performed on the deletion/replacement mutants, phylogenetic and structural comparison with the already established crystal structures from non-plant sources, an evolutionarily conserved peptide stretch was identified at the active pocket which contains the two most important lysine residues essential for catalytic activity. PMID:28950028
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Zou, Min, E-mail: zoumin3362765@163.com; Wang, Xin, E-mail: wangx@mail.njust.edu.cn; Jiang, Xiaohong, E-mail: jxh0668@sina.com
2014-05-01
Catalyzed thermal decomposition process of ammonium perchlorate (AP) over neodymium oxide (Nd{sub 2}O{sub 3}) was investigated. Catalytic performances of nanometer-sized Nd{sub 2}O{sub 3} and micrometer-sized Nd{sub 2}O{sub 3} were evaluated by differential scanning calorimetry (DSC). In contrast to universal concepts, catalysts in different sizes have nearly similar catalytic activities. Based on structural and morphological variation of the catalysts during the reaction, combined with mass spectrum analyses and studies of unmixed style, a new understanding of this catalytic process was proposed. We believed that the newly formed chloride neodymium oxide (NdOCl) was the real catalytic species in the overall thermal decompositionmore » of AP over Nd{sub 2}O{sub 3}. Meanwhile, it was the “self-distributed” procedure which occurred within the reaction that also worked for the improvement of overall catalytic activities. This work is of great value in understanding the roles of micrometer-sized catalysts used in heterogeneous reactions, especially the solid–solid reactions which could generate a large quantity of gaseous species. - Graphical abstract: In-situ and self-distributed reaction process in thermal decomposition of AP catalyzed by Nd{sub 2}O{sub 3}. - Highlights: • Micro- and nano-Nd{sub 2}O{sub 3} for catalytic thermal decomposition of AP. • No essential differences on their catalytic performances. • Structural and morphological variation of catalysts digs out catalytic mechanism. • This catalytic process is “in-situ and self-distributed” one.« less
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An Iron Reservoir to the Catalytic Metal
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
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Zhang, Jing; Nie, Huagui; Wu, Zhan; Yang, Zhi; Zhang, Lijie; Xu, Xiangju; Huang, Shaoming
2014-01-21
A simple and sensitive gap-electrical biosensor based on self-catalytic growth of unmodified gold nanoparticles (AuNPs) as conductive bridges has been developed for amplifying DNA hybridization events. In this strategy, the signal amplification degree of such conductive bridges is closely related to the variation of the glucose oxidase (GOx)-like catalytic activity of AuNPs upon interaction with single- and double-stranded DNA (ssDNA and dsDNA), respectively. In the presence of target DNA, the obtained dsDNA product cannot adsorb onto the surface of AuNPs due to electrostatic interaction, which makes the unmodified AuNPs exhibit excellent GOx-like catalytic activity. Such catalytic activity can enlarge the diameters of AuNPs in the glucose and HAuCl4 solution and result in a connection between most of the AuNPs and a conductive gold film formation with a dramatically increased conductance. For the control sample, the catalytic activity sites of AuNPs are fully blocked by ssDNA due to the noncovalent interaction between nucleotide bases and AuNPs. Thus, the growth of the assembled AuNPs will not happen and the conductance between microelectrodes will be not changed. Under the optimal experimental conditions, the developed strategy exhibited a sensitive response to target DNA with a high signal-to-noise ratio. Moreover, this strategy was also demonstrated to provide excellent differentiation ability for single-nucleotide polymorphism. Such performances indicated the great potential of this label-free electrical strategy for clinical diagnostics and genetic analysis under real biological sample separation.
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Zhang, Junshuai; Yao, Tongjie; Zhang, Hui; Zhang, Xiao; Wu, Jie
2016-11-10
In this manuscript, we have introduced a novel method to improve the catalytic activity of metal nanoparticles via optimizing the support structure. To this end, raspberry-like γ-Fe 2 O 3 /crackled nitrogen-doped carbon (CNC) capsules were prepared by a two-step method. Compared with traditional magnetic capsules, in γ-Fe 2 O 3 /CNC capsules, the γ-Fe 2 O 3 nanoparticles were embedded in a CNC shell; therefore, they neither occupied the anchoring sites for metal nanoparticles nor came into contact with them, which was beneficial for increasing the metal nanoparticle loading. Numerous tiny cracks appeared on the porous CNC shell, which effectively improved the mass diffusion and transport in catalytic reactions. Additionally, the coordination interaction could be generated between the precursor metal ions and doped-nitrogen atoms in the capsule shell. With the help of these structural merits, γ-Fe 2 O 3 /CNC capsules were ideal supports for Pd nanoparticles, because they were beneficial for improving the Pd loading, reducing the nanoparticle size, increasing their dispersity and maximizing the catalytic performance of Pd nanoparticles anchored on the inner shell surface. As expected, γ-Fe 2 O 3 /CNC@Pd catalysts exhibited a dramatically enhanced catalytic activity towards hydrophilic 4-nitrophenol and hydrophobic nitrobenzene. The reaction rate constant k was compared with recent work and the corresponding reference samples. Moreover, they could be easily recycled by using a magnet and reused without an obvious loss of catalytic activity.
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Ozone-Activated Nanoporous Gold: A Stable and Storable Material for Catalytic Oxidation
Personick, Michelle L.; Zugic, Branko; Biener, Monika M.; ...
2015-05-28
We report a new method for facile and reproducible activation of nanoporous gold (npAu) materials of different forms for the catalytic selective partial oxidation of alcohols under ambient pressure, steady flow conditions. This method, based on the surface cleaning of npAu ingots with ozone to remove carbon documented in ultrahigh vacuum conditions, produces active npAu catalysts from ingots, foils, and shells by flowing an ozone/dioxygen mixture over the catalyst at 150 °C, followed by a temperature ramp from 50 to 150 °C in a flowing stream of 10% methanol and 20% oxygen. With this treatment, all three materials (ingots, foils,more » and shells) can be reproducibly activated, despite potential carbonaceous poisons resulting from their synthesis, and are highly active for the selective oxidation of primary alcohols over prolonged periods of time. The npAu materials activated in this manner exhibit catalytic behavior substantially different from those activated under different conditions previously reported. Once activated in this manner, they can be stored and easily reactivated by flow of reactant gases at 150 °C for a few hours. They possess improved selectivity for the coupling of higher alcohols, such as 1-butanol, and are not active for carbon monoxide oxidation. As a result, this ozone-treated npAu is a functionally new catalytic material.« less
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Ozone-Activated Nanoporous Gold: A Stable and Storable Material for Catalytic Oxidation
DOE Office of Scientific and Technical Information (OSTI.GOV)
Personick, Michelle L.; Zugic, Branko; Biener, Monika M.
We report a new method for facile and reproducible activation of nanoporous gold (npAu) materials of different forms for the catalytic selective partial oxidation of alcohols under ambient pressure, steady flow conditions. This method, based on the surface cleaning of npAu ingots with ozone to remove carbon documented in ultrahigh vacuum conditions, produces active npAu catalysts from ingots, foils, and shells by flowing an ozone/dioxygen mixture over the catalyst at 150 °C, followed by a temperature ramp from 50 to 150 °C in a flowing stream of 10% methanol and 20% oxygen. With this treatment, all three materials (ingots, foils,more » and shells) can be reproducibly activated, despite potential carbonaceous poisons resulting from their synthesis, and are highly active for the selective oxidation of primary alcohols over prolonged periods of time. The npAu materials activated in this manner exhibit catalytic behavior substantially different from those activated under different conditions previously reported. Once activated in this manner, they can be stored and easily reactivated by flow of reactant gases at 150 °C for a few hours. They possess improved selectivity for the coupling of higher alcohols, such as 1-butanol, and are not active for carbon monoxide oxidation. As a result, this ozone-treated npAu is a functionally new catalytic material.« less
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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.
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Binding of (/sup 3/H)Forskolin to rat brain membranes
DOE Office of Scientific and Technical Information (OSTI.GOV)
Seamon, K.B.; Vaillancourt, R.; Edwards, M.
1984-08-01
(12-/sup 3/H)Forskolin (27 Ci/mmol) has been used to study binding sites in rat brain tissue by using both centrifugation and filtration assays. The binding isotherm measured in the presence of 5 mM MgCl/sub 2/ by using the centrifugation assay is described best by a two-site model: K/sub d1/ = 15 nM, B/sub max/sub 1// (maximal binding) = 270 fmol/mg of protein; K/sub d2/ = 1.1 ..mu..M; B/sub max/sub 2// = 4.2 pmol/mg of protein. Only the high-affinity binding sites are detected when the binding is determined by using a filtration assay; K/sub d/ = 26 nM, B/sub max/ = 400more » fmol/mg of protein. Analogs of forskolin that do not activate adenylate cyclase (EC 4.6.1.1) do not compete effectively for (/sup 3/H)forskolin binding sites. Analogs of forskolin that are less potent than forskolin in activating adenylate cyclase are also less potent in competing for forskolin binding sites. The presence of 5 mM MgCl/sub 2/ or MnCl/sub 2/ was found to enhance binding. In the presence of 1 mM EDTA the amount of high-affinity binding is reduced to 110 fmol/mg of protein with no change in K/sub d/. There is no effect of CaCl/sub 2/ (20 mM) or NaCl (100 mM) on the binding. No high-affinity binding can be detected in membranes from ram sperm, which contains an adenylate cyclase that is not activated by forskolin. It is proposed that the high-affinity binding sites for forskolin are associated with the activated complex of catalytic subunit and stimulatory guanine nucleotide binding protein. 23 references, 5 figures, 2 tables.« less
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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 efficiencies towards target reactions.
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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 efficiencies towards target reactions. PMID:27243223
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The influence of desilication on high-silica MFI and its catalytic performance for N2O decomposition
NASA Astrophysics Data System (ADS)
Shen, Qun; Wu, Minfang; Wang, Hui; Sun, Nannan; He, Chi; Wei, Wei
2018-05-01
A series of MFI zeolites with different Si/Al ratios were pretreated by a basic solution and their catalytic activity was evaluated in N2O decomposition after iron exchange. The performance of Fe-ZSM-5 catalysts could be improved by alkaline pretreatment. Among these samples, the activity curve of Fe-Z5-250-S sample could move to low temperature by >100 °C with a good preservation of hydrothermal stability. It is found that with the meso-microporous hybrid structure, the content of iron as active metal is significantly increased. Additionally, well preservation of the chemical environment around the tetrahedral aluminum and the site accessibility probably may be the other important factors to influence the catalytic activity.
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Wang, Liang; Wang, Hong; Rice, Andrew E; Zhang, Wei; Li, Xiaokun; Chen, Mingshu; Meng, Xiangju; Lewis, James P; Xiao, Feng-Shou
2015-06-18
A synergistic effect between individual components is crucial for increasing the activity of metal/metal oxide catalysts. The greatest challenge is how to control the synergistic effect to obtain enhanced catalytic performance. Through density functional theory calculations of model Au/TiO2 catalysts, it is suggested that there is strong interaction between Au nanoparticles and Ti species at the edge/corner sites of anatase, which is favorable for the formation of stable oxygen vacancies. Motivated by this theoretical analysis, we have rationally prepared Au nanoparticles attached to edge/corner sites of anatase support (Au/TiO2-EC), confirmed by their HR-TEM images. As expected, this strong interaction is well characterized by Raman, UV-visible, and XPS techniques. Very interestingly, compared with conventional Au catalysts, Au/TiO2-EC exhibits superior catalytic activity in the oxidations using O2. Our approach to controlling Au nanoparticle positioning on anatase to obtain enhanced catalytic activity offers an efficient strategy for developing more novel supported metal catalysts.
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Catalytic hydrolysis of ammonia borane via cobalt palladium nanoparticles.
Sun, Daohua; Mazumder, Vismadeb; Metin, Önder; Sun, Shouheng
2011-08-23
Monodisperse 8 nm CoPd nanoparticles (NPs) with controlled compositions were synthesized by the reduction of cobalt acetylacetonate and palladium bromide in the presence of oleylamine and trioctylphosphine. These NPs were active catalysts for hydrogen generation from the hydrolysis of ammonia borane (AB), and their activities were composition dependent. Among the 8 nm CoPd catalysts tested for the hydrolysis of AB, the Co(35)Pd(65) NPs exhibited the highest catalytic activity and durability. Their hydrolysis completion time and activation energy were 5.5 min and 27.5 kJ mol(-1), respectively, which were comparable to the best Pt-based catalyst reported. The catalytic performance of the CoPd/C could be further enhanced by a preannealing treatment at 300 °C under air for 15 h with the hydrolysis completion time reduced to 3.5 min. This high catalytic performance of Co(35)Pd(65) NP catalyst makes it an exciting alternative in pursuit of practical implementation of AB as a hydrogen storage material for fuel cell applications. © 2011 American Chemical Society
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NASA Astrophysics Data System (ADS)
Vijselaar, Wouter; Westerik, Pieter; Veerbeek, Janneke; Tiggelaar, Roald M.; Berenschot, Erwin; Tas, Niels R.; Gardeniers, Han; Huskens, Jurriaan
2018-03-01
A solar-driven photoelectrochemical cell provides a promising approach to enable the large-scale conversion and storage of solar energy, but requires the use of Earth-abundant materials. Earth-abundant catalysts for the hydrogen evolution reaction, for example nickel-molybdenum (Ni-Mo), are generally opaque and require high mass loading to obtain high catalytic activity, which in turn leads to parasitic light absorption for the underlying photoabsorber (for example silicon), thus limiting production of hydrogen. Here, we show the fabrication of a highly efficient photocathode by spatially and functionally decoupling light absorption and catalytic activity. Varying the fraction of catalyst coverage over the microwires, and the pitch between the microwires, makes it possible to deconvolute the contributions of catalytic activity and light absorption to the overall device performance. This approach provided a silicon microwire photocathode that exhibited a near-ideal short-circuit photocurrent density of 35.5 mA cm-2, a photovoltage of 495 mV and a fill factor of 62% under AM 1.5G illumination, resulting in an ideal regenerative cell efficiency of 10.8%.
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Soot Combustion over Nanostructured Ceria with Different Morphologies
Zhang, Wen; Niu, Xiaoyu; Chen, Liqiang; Yuan, Fulong; Zhu, Yujun
2016-01-01
In this study, nano-structure ceria with three different morphologies (nanorod, nanoparticle and flake) have been prepared by hydrothermal and solvothermal methods. The ceria samples were deeply characterized by XRD, SEM, TEM, H2-TPR, XPS and in-situ DRIFTS, and tested for soot combustion in absence/presence NO atmospheres under loose and tight contact conditions. The prepared ceria samples exhibit excellent catalytic activities, especially, the CeO2 with nanorod (Ce-R) shows the best catalytic activity, for which the peak temperature of soot combustion (Tm) is about 500 and 368 °C in loose and tight contact conditions, respectively. The catalytic activity for Ce-R is higher than that of the reported CeO2 catalysts and reaches a level that of precious metals. The characterization results reveal that the maximal amounts of adsorbed oxygen species on the surface of the nanostructure Ce-R catalyst should be the crucial role to decide the catalytic soot performance. High BET surface area may also be a positive effect on soot oxidation activity under loose contact conditions. PMID:27353143
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Bian, J; Xiao, M; Wang, S J; Lu, Y X; Meng, Y Z
2009-06-01
Novel Cu-Ni bimetallic catalysts supported on thermally expanded graphite (TEG) were prepared as an example to show the particular characteristics of TEG as a carbon support material. The structures of TEG and the synthesized Cu-Ni/TEG catalysts were characterized using BET, FTIR, TG, SEM, TEM, XRD and TPR techniques. The catalytic activities of the prepared catalysts were investigated by performing micro-reaction in the direct synthesis of dimethyl carbonate (DMC) from CH3OH and CO2. The experimental results indicated that the prepared Cu-Ni/TEG catalysts exhibited highly catalytic activity. Under the optimal catalytic conditions at 100 degrees C and under 1.2 MPa, the highest conversion of CH3OH of 4.97% and high selectivity of DMC of 89.3% can be achieved. The highly catalytic activity of Cu-Ni/TEG in DMC synthesis can be attributed to the synergetic effects of metal Cu, Ni and Cu-Ni alloy in the activation of CH3OH and CO2 and the particular characteristics of TEG as a carbon support material.
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Enzymatic Detoxication, Conformational Selection, and the Role of Molten Globule Active Sites*
Honaker, Matthew T.; Acchione, Mauro; Zhang, Wei; Mannervik, Bengt; Atkins, William M.
2013-01-01
The role of conformational ensembles in enzymatic reactions remains unclear. Discussion concerning “induced fit” versus “conformational selection” has, however, ignored detoxication enzymes, which exhibit catalytic promiscuity. These enzymes dominate drug metabolism and determine drug-drug interactions. The detoxication enzyme glutathione transferase A1–1 (GSTA1–1), exploits a molten globule-like active site to achieve remarkable catalytic promiscuity wherein the substrate-free conformational ensemble is broad with barrierless transitions between states. A quantitative index of catalytic promiscuity is used to compare engineered variants of GSTA1–1 and the catalytic promiscuity correlates strongly with characteristics of the thermodynamic partition function, for the substrate-free enzymes. Access to chemically disparate transition states is encoded by the substrate-free conformational ensemble. Pre-steady state catalytic data confirm an extension of the conformational selection model, wherein different substrates select different starting conformations. The kinetic liability of the conformational breadth is minimized by a smooth landscape. We propose that “local” molten globule behavior optimizes detoxication enzymes. PMID:23649628
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Piñeiro, Yolanda; Buceta, David; Calvo, Javier; Huseyinova, Shahana; Cuerva, Miguel; Pérez, Ángel; Domínguez, Blanca; López-Quintela, M Arturo
2015-07-01
Clusters are stable catalytic species, which are produced during the synthesis of nanoparticles (NPs). Their existence contradicts the thermodynamic principles used to explain the formation of NPs by the classical nucleation and growth theories (NGTs). Using chemical and electrochemical methods we will show that depending on the experimental conditions one can produce either Ag clusters or Ag NPs. Moreover, using already prepared Ag clusters one can observe the disappearance of the usual induction period observed for the kinetics of NP formation, indicating that clusters catalyze the formation of NPs. Taking these data together with some previous examples of cluster-catalyzed anisotropic growth, we derived a qualitative approach to include the catalytic activities of clusters into the formation of NPs, which is incorporated into the NGT. Some qualitative conclusions about the main experimental parameters, which affect the formation of clusters versus NPs, as well as the catalytic mechanism versus the non-catalytic one, are also described. Copyright © 2015 Elsevier Inc. All rights reserved.
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NASA Astrophysics Data System (ADS)
Kulsi, Chiranjit; Ghosh, Amrita; Mondal, Anup; Kargupta, Kajari; Ganguly, Saibal; Banerjee, Dipali
2017-01-01
Bismuth selenide (Bi2Se3) and nickel (Ni) doped Bi2Se3 were prepared by a solvothermal approach to explore the photo-catalytic performance of the materials in degradation of malachite green (MG). The presence of nickel was confirmed by X-ray photoelectron spectroscopy (XPS) measurement in doped Bi2Se3. The results showed that the nickel doping played an important role in microstructure and photo-catalytic activity of the samples. Nickel doped Bi2Se3 sample exhibited higher photo-catalytic activity than that of the pure Bi2Se3 sample under visible-light irradiation. The photo-catalytic degradation followed first-order reaction kinetics. Fast degradation kinetics and complete (100% in 5 min of visible light irradiation) removal of MG was achieved by nickel doped Bi2Se3 in presence of hydrogen peroxide (H2O2) due to modification of band gap energies leading to suppression of photo-generated electron-hole recombination.
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Ristanović, Zoran; Kerssens, Marleen M; Kubarev, Alexey V; Hendriks, Frank C; Dedecker, Peter; Hofkens, Johan; Roeffaers, Maarten B J; Weckhuysen, Bert M
2015-02-02
Fluid catalytic cracking (FCC) is a major process in oil refineries to produce gasoline and base chemicals from crude oil fractions. The spatial distribution and acidity of zeolite aggregates embedded within the 50-150 μm-sized FCC spheres heavily influence their catalytic performance. Single-molecule fluorescence-based imaging methods, namely nanometer accuracy by stochastic chemical reactions (NASCA) and super-resolution optical fluctuation imaging (SOFI) were used to study the catalytic activity of sub-micrometer zeolite ZSM-5 domains within real-life FCC catalyst particles. The formation of fluorescent product molecules taking place at Brønsted acid sites was monitored with single turnover sensitivity and high spatiotemporal resolution, providing detailed insight in dispersion and catalytic activity of zeolite ZSM-5 aggregates. The results point towards substantial differences in turnover frequencies between the zeolite aggregates, revealing significant intraparticle heterogeneities in Brønsted reactivity. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Kumaran, D.; Eswaramoorthy, S; Furey, W
2009-01-01
Clostridium botulinum produces seven antigenically distinct neurotoxins [C. botulinum neurotoxins (BoNTs) A-G] sharing a significant sequence homology. Based on sequence and functional similarity, it was believed that their three-dimensional structures will also be similar. Indeed, the crystal structures of BoNTs A and B exhibit similar fold and domain association where the translocation domain is flanked on either side by binding and catalytic domains. Here, we report the crystal structure of BoNT E holotoxin and show that the domain association is different and unique, although the individual domains are similar to those of BoNTs A and B. In BoNT E, bothmore » the binding domain and the catalytic domain are on the same side of the translocation domain, and all three have mutual interfaces. This unique association may have an effect on the rate of translocation, with the molecule strategically positioned in the vesicle for quick entry into cytosol. Botulism, the disease caused by BoNT E, sets in faster than any other serotype because of its speedy internalization and translocation, and the present structure offers a credible explanation. We propose that the translocation domain in other BoNTs follows a two-step process to attain translocation-competent conformation as in BoNT E. We also suggest that this translocation-competent conformation in BoNT E is a probable reason for its faster toxic rate compared to BoNT A. However, this needs further experimental elucidation.« less
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Push or Pull? Proton Responsive Ligand Effects in Rhenium Tricarbonyl CO 2 Reduction Catalysts
Manbeck, Gerald F.; Muckerman, James T.; Szalda, David J.; ...
2015-02-19
Proton responsive ligands offer control of catalytic reactions through modulation of pH-dependent properties, second coordination sphere stabilization of transition states, or by providing a local proton source for multi-proton, multi-electron reactions. Two fac-[ReI(α-diimine)(CO)₃Cl] complexes with α-diimine = 4,4'- (or 6,6'-) dihydroxy-2,2'-bipyridine (4DHBP and 6DHBP) have been prepared and analyzed as electrocatalysts for reduction of carbon dioxide. Consecutive electrochemical reduction of these complexes yields species identical to those obtained by chemical deprotonation. An energetically feasible mechanism for reductive deprotonation is proposed in which the bpy anion is protonated followed by loss of H₂ and 2H⁺. Cyclic voltammetry reveals a two-electron, three-wavemore » system owing to competing EEC and ECE pathways. The chemical step of the ECE pathway might be attributed to the reductive deprotonation. but cannot be distinguished from chloride dissociation. The rate obtained by digital simulation is approximately 8 s⁻¹. Under CO₂, these competing reactions generate a two-slope catalytic waveform with onset potential of –1.65 V vs Ag/AgCl. Reduction of CO₂ to CO by the [ReI (4DHBP–2H⁺)(CO)₃]⁻ suggests the interaction of CO₂ with the deprotonated species or a third reduction followed by catalysis. Conversely, the reduced form of [Re(6DHBP)(CO)₃Cl] converts CO₂ to CO with a single turnover.« less
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Li, Xiaoyu; Ouyang, Jing; Zhou, Yonghua; Yang, Huaming
2015-01-01
Nanocomposites of aluminosilicate minerals, kaolins (kaolinite and halloysite) with natural different morphologies assembling with palladium (Pd) nanoparticles have been successfully synthesized through strong electrostatic adsorption and chemical bonding after surface modification with 3-aminopropyl triethoxysilane (APTES). Meanwhile, the influence of different morphologies supports on catalytic hydrogenation properties was explored. The surface concentration of amino groups on the kaolins was related to the morphology and surface nature. Electronmicroscopy revealed that the monodisperse Pd nanoparticles were uniformly deposited onto the surface of kaolins, ranging in diameter from 0.5 nm to 5.5 nm. The functional groups could not only improve the dispersion of kaolins with different morphologies in solution, but also enhance the interaction between Pd precursors and kaolins, thus preventing small Pd nanoparticles from agglomerating and leading to high activity for the catalytic hydrogenation of styrene. Pd-FK@APTES was more active compared to other samples. Selecting the kaolin morphology with a different surface nature allows the selective surface modification of a larger fraction of the reactive facets on which the active sites can be enriched and tuned. This desirable surface coordination of catalytically active atoms could substantially improve catalytic activity. PMID:26333629
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NASA Astrophysics Data System (ADS)
Li, Xiaoyu; Ouyang, Jing; Zhou, Yonghua; Yang, Huaming
2015-09-01
Nanocomposites of aluminosilicate minerals, kaolins (kaolinite and halloysite) with natural different morphologies assembling with palladium (Pd) nanoparticles have been successfully synthesized through strong electrostatic adsorption and chemical bonding after surface modification with 3-aminopropyl triethoxysilane (APTES). Meanwhile, the influence of different morphologies supports on catalytic hydrogenation properties was explored. The surface concentration of amino groups on the kaolins was related to the morphology and surface nature. Electronmicroscopy revealed that the monodisperse Pd nanoparticles were uniformly deposited onto the surface of kaolins, ranging in diameter from 0.5 nm to 5.5 nm. The functional groups could not only improve the dispersion of kaolins with different morphologies in solution, but also enhance the interaction between Pd precursors and kaolins, thus preventing small Pd nanoparticles from agglomerating and leading to high activity for the catalytic hydrogenation of styrene. Pd-FK@APTES was more active compared to other samples. Selecting the kaolin morphology with a different surface nature allows the selective surface modification of a larger fraction of the reactive facets on which the active sites can be enriched and tuned. This desirable surface coordination of catalytically active atoms could substantially improve catalytic activity.
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Li, Xiaoyu; Ouyang, Jing; Zhou, Yonghua; Yang, Huaming
2015-09-03
Nanocomposites of aluminosilicate minerals, kaolins (kaolinite and halloysite) with natural different morphologies assembling with palladium (Pd) nanoparticles have been successfully synthesized through strong electrostatic adsorption and chemical bonding after surface modification with 3-aminopropyl triethoxysilane (APTES). Meanwhile, the influence of different morphologies supports on catalytic hydrogenation properties was explored. The surface concentration of amino groups on the kaolins was related to the morphology and surface nature. Electronmicroscopy revealed that the monodisperse Pd nanoparticles were uniformly deposited onto the surface of kaolins, ranging in diameter from 0.5 nm to 5.5 nm. The functional groups could not only improve the dispersion of kaolins with different morphologies in solution, but also enhance the interaction between Pd precursors and kaolins, thus preventing small Pd nanoparticles from agglomerating and leading to high activity for the catalytic hydrogenation of styrene. Pd-FK@APTES was more active compared to other samples. Selecting the kaolin morphology with a different surface nature allows the selective surface modification of a larger fraction of the reactive facets on which the active sites can be enriched and tuned. This desirable surface coordination of catalytically active atoms could substantially improve catalytic activity.
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NASA Astrophysics Data System (ADS)
Jeon, Byungwook; Kim, Ansoon; Lee, Young-Ahn; Seo, Hyungtak; Kim, Yu Kwon
2017-11-01
CO oxidation over Pd/WO3 films prepared on a glass substrate has been examined at the substrate temperature of 150 - 250 °C and pressures less than 1 Torr with a stoichiometric mixture of CO and O2. Under the given reaction condition, the chemical states of the Pd/WO3 film gradually change into the most catalytically active form with the highest saturation reaction rate regardless of the initial oxidation states. The measured CO oxidation rate over the Pd/WO3 is strongly dependent on the chemical states of Pd and W. Either metallic Pd or fully oxidized PdO phase is not as catalytically active as the active form with mixed metallic Pd and thin PdO layers supported on WO3 with partially reduced W5+ state which is spontaneously obtained during the catalytic reaction cycles. Our results indicate that the facile oxygen transfer between Pd and WO3 layers not only facilitate the spontaneous changes into the active form, but also act as a promotional role in CO oxidation over the Pd layer.
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Choi, Seeyoung; Love, Paul E
2018-01-05
Oxidative inactivation of cysteine-dependent Protein Tyrosine Phosphatases (PTPs) by cellular reactive oxygen species (ROS) plays a critical role in regulating signal transduction in multiple cell types. The phosphatase activity of most PTPs depends upon a 'signature' cysteine residue within the catalytic domain that is maintained in the de-protonated state at physiological pH rendering it susceptible to ROS-mediated oxidation. Direct and indirect techniques for detection of PTP oxidation have been developed (Karisch and Neel, 2013). To detect catalytically active PTPs, cell lysates are treated with iodoacetyl-polyethylene glycol-biotin (IAP-biotin), which irreversibly binds to reduced (S - ) cysteine thiols. Irreversible oxidation of SHP-1 after treatment of cells with pervanadate or H 2 O 2 is detected with antibodies specific for the sulfonic acid (SO 3 H) form of the conserved active site cysteine of PTPs. In this protocol, we describe a method for the detection of the reduced (S - ; active) or irreversibly oxidized (SO 3 H; inactive) form of the hematopoietic PTP SHP-1 in thymocytes, although this method is applicable to any cysteine-dependent PTP in any cell type.
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Zhu, Yuanqi; Hein, David W.
2007-01-01
Genetic variants of human N-acetyltransferase 1 (NAT1) are associated with cancer and birth defects. N- and O-acetyltransferase catalytic activities, Michaelis-Menten kinetic constants (Km & Vmax), and steady state expression levels of NAT1-specific mRNA and protein were determined for the reference NAT1*4 and variant human NAT1 haplotypes possessing single nucleotide polymorphisms (SNPs) in the open reading frame. Although none of the SNPs caused a significant effect on steady state levels of NAT1-specific mRNA, C97T(R33stop), C190T(R64W), C559T (R187stop) and A752T(D251V) each reduced NAT1 protein level and/or N- and O-acetyltransferase catalytic activities to levels below detection. G560A(R187Q) substantially reduced NAT1 protein level and catalytic activities and increased substrate Km. The G445A(V149I), G459A(synonymous) and T640G(S214A) haplotype present in NAT1*11 significantly (p<0.05) increased NAT1 protein level and catalytic activity. Neither T21G(synonymous), T402C(synonymous), A613G(M205V), T777C(synonymous), G781A(E261K), or A787G(I263V) significantly affected Km, catalytic activity, mRNA or protein level. These results suggest heterogeneity among slow NAT1 acetylator phenotypes. PMID:17909564
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Shah, Rachit M; Maize, Kimberly M; West, Harrison T; Strom, Alexander M; Finzel, Barry C; Wagner, Carston R
2018-05-19
Inherited peripheral neuropathies are a group of neurodegenerative disorders that clinically affect 1 in 2500 individuals. Recently, genetic mutations in human histidine nucleotide-binding protein 1 (hHint1) have been strongly and most frequently associated with patients suffering from axonal neuropathy with neuromyotonia. However, the correlation between the impact of these mutations on the hHint1 structure, enzymatic activity and in vivo function has remained ambiguous. Here, we provide detailed biochemical characterization of a set of these hHint1 mutations. Our findings indicate that half of the mutations (R37P, G93D and W123*) resulted in a destabilization of the dimeric state and a significant decrease in catalytic activity and HINT1 inhibitor binding affinity. The H112N mutant was found to be dimeric, but devoid of catalytic activity, due to the loss of the catalytically essential histidine; nevertheless, it exhibited high affinity to AMP and a HINT1 inhibitor. In contrast to the active-site mutants, the catalytic activity and dimeric structure of the surface mutants, C84R and G89V, were found to be similar to the wild-type enzyme. Taken together, our results suggest that the pathophysiology of inherited axonal neuropathy with neuromyotonia can be induced by conversion of HINT1 from a homodimer to monomer, by modification of select surface residues or by a significant reduction of the enzyme's catalytic efficiency. Copyright © 2018. Published by Elsevier Ltd.
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Filippakopoulos, Panagis; Kofler, Michael; Hantschel, Oliver; Gish, Gerald D; Grebien, Florian; Salah, Eidarus; Neudecker, Philipp; Kay, Lewis E; Turk, Benjamin E; Superti-Furga, Giulio; Pawson, Tony; Knapp, Stefan
2008-09-05
The SH2 domain of cytoplasmic tyrosine kinases can enhance catalytic activity and substrate recognition, but the molecular mechanisms by which this is achieved are poorly understood. We have solved the structure of the prototypic SH2-kinase unit of the human Fes tyrosine kinase, which appears specialized for positive signaling. In its active conformation, the SH2 domain tightly interacts with the kinase N-terminal lobe and positions the kinase alphaC helix in an active configuration through essential packing and electrostatic interactions. This interaction is stabilized by ligand binding to the SH2 domain. Our data indicate that Fes kinase activation is closely coupled to substrate recognition through cooperative SH2-kinase-substrate interactions. Similarly, we find that the SH2 domain of the active Abl kinase stimulates catalytic activity and substrate phosphorylation through a distinct SH2-kinase interface. Thus, the SH2 and catalytic domains of active Fes and Abl pro-oncogenic kinases form integrated structures essential for effective tyrosine kinase signaling.
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NASA Astrophysics Data System (ADS)
Ni, Yuyang; Li, Jun; Huang, Zhenzhen; He, Ke; Zhuang, Jiaqi; Yang, Wensheng
2013-11-01
The using of macromolecular additives is known to be a simple and effective way to improve the activity of immobilized enzymes on solid support, yet the mechanism has not been well understood. Taking horseradish peroxidase (HRP) as an example, only 30 % of its catalytic activity was kept after being immobilized on the surface of 25-nm Au nanoparticles, mainly attributed to the conformational change of the heme-containing active site. The catalytic activity of HRP was significantly improved to 80 % when a certain amount of bovine serum albumin (BSA) was added at the initial stage of the immobilization. Systematic spectral investigation indicated that the addition of BSA inhibited the tertiary structure change around the active site, which was a prerequisite for improved activity of the immobilized HRP. Steady-state kinetic analyses revealed that the introduction of BSA could effectively improve the turnover rate of substrate to product in spite of slight reduced affinity to substrates, which also contributed to the improved catalytic activity.
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Kumar, Rajinder; Musiyenko, Alla; Oldenburg, Anja; Adams, Brian; Barik, Sailen
2004-01-01
Background Although the complete genome sequences of a large number of organisms have been determined, the exact proteomes need to be characterized. More specifically, the extent to which post-translational processes such as proteolysis affect the synthesized proteins has remained unappreciated. We examined this issue in selected protein phosphatases of the protease-rich malaria parasite, Plasmodium falciparum. Results P. falciparum encodes a number of Ser/Thr protein phosphatases (PP) whose catalytic subunits are composed of a catalytic core and accessory domains essential for regulation of the catalytic activity. Two examples of such regulatory domains are found in the Ca+2-regulated phosphatases, PP7 and PP2B (calcineurin). The EF-hand domains of PP7 and the calmodulin-binding domain of PP2B are essential for stimulation of the phosphatase activity by Ca+2. We present biochemical evidence that P. falciparum generates these full-length phosphatases as well as their catalytic cores, most likely as intermediates of a proteolytic degradation pathway. While the full-length phosphatases are activated by Ca+2, the processed cores are constitutively active and either less responsive or unresponsive to Ca+2. The processing is extremely rapid, specific, and occurs in vivo. Conclusions Post-translational cleavage efficiently degrades complex full-length phosphatases in P. falciparum. In the course of such degradation, enzymatically active catalytic cores are produced as relatively stable intermediates. The universality of such proteolysis in other phosphatases or other multi-domain proteins and its potential impact on the overall proteome of a cell merits further investigation. PMID:15230980
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Zhu, Yuanqi; States, J. Christopher; Wang, Yang; Hein, David W.
2011-01-01
BACKGROUND The functional effects of N-acetyltransferase 1 (NAT1) polymorphisms and haplotypes are poorly understood, compromising the validity of associations reported with diseases including birth defects and numerous cancers. METHODS We investigated the effects of genetic polymorphisms within the NAT1 coding region and the 3′-untranslated region (3′-UTR) and their associated haplotypes on N- and O-acetyltransferase catalytic activities, and NAT1 mRNA and protein levels following recombinant expression in COS-1 cells. RESULTS 1088T>A (rs1057126; 3′-UTR) and 1095C>A (rs15561; 3′-UTR) each slightly reduced NAT1 catalytic activity and NAT1 mRNA and protein levels. A 9-base pair (TAATAATAA) deletion between nucleotides 1065-1090 (3′-UTR) reduced NAT1 catalytic activity and NAT1 mRNA and protein levels. In contrast, a 445G>A (rs4987076; V149I), 459G>A (rs4986990; T153T), 640T>G (rs4986783; S214A) coding region haplotype present in NAT1*11 increased NAT1 catalytic activity and NAT1 protein, but not NAT1 mRNA levels. A combination of the 9-base pair (TAATAATAA) deletion and the 445G>A, 459G>A, 640T>G coding region haplotypes, both present in NAT1*11, appeared to neutralize the opposing effects on NAT1 protein and catalytic activity, resulting in levels of NAT1 protein and catalytic activity that did not differ significantly from the NAT1*4 reference. CONCLUSIONS Since 1095C>A (3′-UTR) is the sole polymorphism present in NAT1*3, our data suggests that NAT1*3 is not functionally equivalent to the NAT1*4 reference. Furthermore, our findings provide biological support for reported associations of 1088T>A and 1095C>A polymorphisms with birth defects. PMID:21290563
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Coello, Patricia; Martínez-Barajas, Eleazar
2014-07-01
SnRK1 activity is developmentally regulated in bean seeds and exhibits a transient increase with the highest value at 20 days after anthesis (DAA), which coincides with the beginning of protein and starch accumulation. The catalytic subunit of SnRK1 shows a consistent decrease throughout the seed development period. However, by 15 DAA a significant proportion of the catalytic subunit appears phosphorylated. The increase in activity and phosphorylation of the catalytic subunit coincides with a decrease in hexoses. However, SnRK1 activity is differentially regulated in the cotyledon and embryo axe, where a larger proportion of the catalytic subunit is phosphorylated. SnRK1 obtained from endosperm extract is inhibited by T6P and to a lesser extent by ADPG and UDPG, whereas the enzyme isolated from embryo is virtually insensitive to T6P but exhibits some inhibition by ADPG and UDPG. In cotyledon extracts, the effects of T6P and ADPG on SnRK1 activity are additive, whereas in embryo extract, T6P inhibits the enzyme only when ADPG is present. After fractionation on Sephacryl-S300, SnRK1 activity obtained from cotyledon extracts is detected as a single peak associated with a molecular weight of 250 kDa whereas that obtained form embryo axe extracts detected as 2 peaks associated with molecular weight of 250 and 180 kDa. In both cases, the catalytic subunit exhibits a wide distribution but is concentrated in the fractions with the highest activity. To analyse the composition of the complex, cotyledon and embryo extracts were treated with a reversible crosslinker (DSP). DSP induced the formation of complexes with molecular weights of 97 and 180 kDa in the cotyledon and embryo extracts, respectively. Since all the phosphorylated catalytic subunit is present in the complexes induced by DSP, it appears that the phosphorylation favors its interaction with other proteins. Copyright © 2014 Elsevier Masson SAS. All rights reserved.
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Novel Attrition-Resistant Fischer Tropsch Catalyst
DOE Office of Scientific and Technical Information (OSTI.GOV)
Weast, Logan, E.; Staats, William, R.
2009-05-01
There is a strong national interest in the Fischer-Tropsch synthesis process because it offers the possibility of making liquid hydrocarbon fuels from reformed natural gas or coal and biomass gasification products. This project explored a new approach that had been developed to produce active, attrition-resistant Fischer-Tropsch catalysts that are based on glass-ceramic materials and technology. This novel approach represented a promising solution to the problem of reducing or eliminating catalyst attrition and maximizing catalytic activity, thus reducing costs. The technical objective of the Phase I work was to demonstrate that glass-ceramic based catalytic materials for Fischer-Tropsch synthesis have resistance tomore » catalytic deactivation and reduction of particle size superior to traditional supported Fischer-Tropsch catalyst materials. Additionally, these novel glass-ceramic-based materials were expected to exhibit catalytic activity similar to the traditional materials. If successfully developed, the attrition-resistant Fischer-Tropsch catalyst materials would be expected to result in significant technical, economic, and social benefits for both producers and public consumers of Fischer-Tropsch products such as liquid fuels from coal or biomass gasification. This program demonstrated the anticipated high attrition resistance of the glass-ceramic materials. However, the observed catalytic activity of the materials was not sufficient to justify further development at this time. Additional testing documented that a lack of pore volume in the glass-ceramic materials limited the amount of surface area available for catalysis and consequently limited catalytic activity. However, previous work on glass-ceramic catalysts to promote other reactions demonstrated that commercial levels of activity can be achieved, at least for those reactions. Therefore, we recommend that glass-ceramic materials be considered again as potential Fischer-Tropsch catalysts if it can be demonstrated that materials with adequate pore volume can be produced. During the attrition resistance tests, it was learned that the glass-ceramic materials are very abrasive. Attention should be paid in any further developmental efforts to the potential for these hard, abrasive materials to damage reactors.« less
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USDA-ARS?s Scientific Manuscript database
Catalytic fast pyrolysis of eucalyptus wood was performed on a continuous laboratory scale fluidized bed fast pyrolysis system. Catalytic activity was monitored from use of fresh catalyst up to a cumulative biomass to catalyst ratio (B/C) of 4/1 over extruded pellets of three different ZSM-5 catalys...
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Vohra, M Ismail; Li, De-Jing; Gu, Zhi-Gang; Zhang, Jian
2017-06-14
A palladium catalyst (Pd-Cs) encapsulated metalloporphyrin network PIZA-1 thin film with bifunctional properties has been developed through a modified epitaxial layer-by-layer encapsulation approach. Combining the oxidation activity of Pd-Cs and the acetalization activity of the Lewis acidic sites in the PIZA-1 thin film, this bifunctional catalyst of the Pd-Cs@PIZA-1 thin film exhibits a good catalytic activity in a one-pot tandem oxidation-acetalization reaction. Furthermore, the surface components can be controlled by ending the top layer with different precursors in the thin film preparation procedures. The catalytic performances of these thin films with different surface composites were studied under the same conditions, which showed different reaction conversions. The result revealed that the surface component can influence the catalytic performance of the thin films. This epitaxial encapsulation offers a good understanding of the tandem catalysis for thin film materials and provides useful guidance to develop new thin film materials with catalytic properties.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Chan-Thaw, Carine E.; Villa, Alberto; Wang, Di
The confinement of a Pd nanoparticle within a nitrogen-containing covalent triazine framework (CTF) material was investigated to understand if the highly tunable CTF chemistry mediates the Pd catalytic properties through an ensemble effect with the CTF nitrogen atoms or a confinement effect within the CTF pores. The results surprisingly demonstrate that the CTF stabilizes the formation of 2.6 nm PdHx particles within the pores. These PdHx particles are very active for the liquid phase oxidation of glycerol due to the in situ formation of H2O2 which catalytically promotes the initial C-C cleavage. In addition the confined particles are stable overmore » many catalytic cycles whereas nanoparticles trapped outside of the pores loose activity rapidly. These results indicate that there is the potential to tune the CTF chemistry to significantly modify the chemistry of the catalytic metals.« less
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Goswami, Abir; Pramanik, Susnata; Schmittel, Michael
2018-04-17
A catalytically active three-component nanorotor is reversibly self-assembled and disassembled by remote control. When zinc(ii) ions (2 equiv.) are added as an external chemical trigger to the mixture of transmitter [Cu(1)]+ and pre-rotor assembly [(S)·(R)], two equiv. of copper(i) ions translocate from [Cu(1)]+ to the two phenanthroline sites of [(S)·(R)]. As a result, [Zn(1)]2+ forms along with the three-component assembly [Cu2(S)(R)]2+, which is both a nanorotor (k298 = 46 kHz, ΔH‡ = 49.1 ± 0.4 kJ mol-1, ΔS‡ = 9.5 ± 1.7 J mol-1 K-1) and a catalyst for click reactions (catalysis ON: A + B→AB). Removal of zinc from the mixture reverts the translocation sequence and thus commands disassembly of the catalytically active rotor (catalysis OFF). The ON/OFF catalytic cycle was run twice in situ in the full network.
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Chan-Thaw, Carine E.; Villa, Alberto; Wang, Di; ...
2015-06-25
The confinement of a Pd nanoparticle within a nitrogen-containing covalent triazine framework (CTF) material was investigated to understand if the highly tunable CTF chemistry mediates the Pd catalytic properties through an ensemble effect with the CTF nitrogen atoms or a confinement effect within the CTF pores. The results surprisingly demonstrate that the CTF stabilizes the formation of 2.6 nm PdHx particles within the pores. These PdHx particles are very active for the liquid phase oxidation of glycerol due to the in situ formation of H2O2 which catalytically promotes the initial C-C cleavage. In addition the confined particles are stable overmore » many catalytic cycles whereas nanoparticles trapped outside of the pores loose activity rapidly. These results indicate that there is the potential to tune the CTF chemistry to significantly modify the chemistry of the catalytic metals.« less
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Betaine protects urea-induced denaturation of myosin subfragment-1.
Ortiz-Costa, Susana; Sorenson, Martha M; Sola-Penna, Mauro
2008-07-01
We have demonstrated previously that urea inhibits the activity and alters the tertiary structure of skeletal muscle myosin in a biphasic manner. This was attributed to differential effects on its globular and filamentous portion. The inhibition of catalytic activity was counteracted by methylamines. With the aim of comprehending the effects of urea on the catalytic (globular) portion of myosin, this study examines the effects of urea and the countereffects of betaine on the catalytic activity and structure of myosin subfragment-1. It is shown that urea inactivates subfragment-1 in parallel with its ability to induce exposure of the enzyme hydrophobic domains, as assessed using intrinsic and extrinsic fluorescence. Both effects are counteracted by betaine, which alone does not significantly affect subfragment-1. Urea also enhances the accessibility of thiol groups, promotes aggregation and decreases the alpha-helix content of S1, effects that are also counteracted by betaine. We conclude that urea-induced inactivation of the enzyme is caused by partial unfolding of the myosin catalytic domain.
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Bickert, Andreas; Kern, Paul; van Uelft, Martina; Herresthal, Stefanie; Ulas, Thomas; Gutbrod, Katharina; Breiden, Bernadette; Degen, Joachim; Sandhoff, Konrad; Schultze, Joachim L; Dörmann, Peter; Hartmann, Dieter; Bauer, Reinhard; Willecke, Klaus
2018-07-01
The replacement of two consecutive histidine residues by alanine residues in the catalytic center of ceramide synthase 2 in a new transgenic mouse mutant (CerS2 H/A) leads to inactivation of catalytic activity and reduces protein level to 60% of the WT level. We show here by qRT-PCR and transcriptome analyses that several transcripts of genes involved in lipid metabolism and cell division are differentially regulated in livers of CerS2 H/A mice. Thus, very long chain ceramides produced by CerS2 are required for transcriptional regulation of target genes. The hepatocellular carcinomata previously described in old CerS2 KO mice were already present in 8-week-old CerS2 H/A animals and thus are caused by the loss of CerS2 catalytic activity already during early life. Copyright © 2018 Elsevier B.V. All rights reserved.
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Nanoparticle mediated micromotor motion.
Liu, Mei; Liu, Limei; Gao, Wenlong; Su, Miaoda; Ge, Ya; Shi, Lili; Zhang, Hui; Dong, Bin; Li, Christopher Y
2015-03-21
In this paper, we report the utilization of nanoparticles to mediate the motion of a polymer single crystal catalytic micromotor. Micromotors have been fabricated by directly self-assembling functional nanoparticles (platinum and iron oxide nanoparticles) onto one or both sides of two-dimensional polymer single crystals. We show that the moving velocity of these micromotors in fluids can be readily tuned by controlling the nanoparticles' surface wettability and catalytic activity. A 3 times velocity increase has been achieved for a hydrophobic micromotor as opposed to the hydrophilic ones. Furthermore, we demonstrate that the catalytic activity of platinum nanoparticles inside the micromotor can be enhanced by their synergetic interactions with iron oxide nanoparticles and an electric field. Both strategies lead to dramatically increased moving velocities, with the highest value reaching ∼200 μm s(-1). By decreasing the nanoparticles' surface wettability and increasing their catalytic activity, a maximum of a ∼10-fold increase in the moving speed of the nanoparticle based micromotor can be achieved. Our results demonstrate the advantages of using nanoparticles in micromotor systems.
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Quantum mechanical design of enzyme active sites.
Zhang, Xiyun; DeChancie, Jason; Gunaydin, Hakan; Chowdry, Arnab B; Clemente, Fernando R; Smith, Adam J T; Handel, T M; Houk, K N
2008-02-01
The design of active sites has been carried out using quantum mechanical calculations to predict the rate-determining transition state of a desired reaction in presence of the optimal arrangement of catalytic functional groups (theozyme). Eleven versatile reaction targets were chosen, including hydrolysis, dehydration, isomerization, aldol, and Diels-Alder reactions. For each of the targets, the predicted mechanism and the rate-determining transition state (TS) of the uncatalyzed reaction in water is presented. For the rate-determining TS, a catalytic site was designed using naturalistic catalytic units followed by an estimation of the rate acceleration provided by a reoptimization of the catalytic site. Finally, the geometries of the sites were compared to the X-ray structures of related natural enzymes. Recent advances in computational algorithms and power, coupled with successes in computational protein design, have provided a powerful context for undertaking such an endeavor. We propose that theozymes are excellent candidates to serve as the active site models for design processes.
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A Phosphoenzyme Mimic, Overlapping Catalytic Sites and Reaction Coordinate Motion for Human NAMPT
DOE Office of Scientific and Technical Information (OSTI.GOV)
Burgos, E.; Ho, M; Almo, S
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 reactionmore » 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.« less
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Haesuwannakij, Setsiri; Kimura, Tetsunari; Furutani, Yuji; Okumura, Kazu; Kokubo, Ken; Sakata, Takao; Yasuda, Hidehiro; Yakiyama, Yumi; Sakurai, Hidehiro
2017-08-29
Poly(N-vinyl-2-pyrrolidone) (PVP) of varying molecular weight (M w = 40-360 kDa) were employed to stabilize gold nanoclusters of varying size. The resulting Au:PVP clusters were subsequently used as catalysts for a kinetic study on the sized-dependent aerobic oxidation of 1-indanol, which was monitored by time-resolved in situ infrared spectroscopy. The obtained results suggest that the catalytic behaviour is intimately correlated to the size of the clusters, which in turn depends on the molecular weight of the PVPs. The highest catalytic activity was observed for clusters with a core size of ~7 nm, and the size of the cluster should increase with the molecular weight of the polymer in order to maintain optimal catalytic activity. Studies on the electronic and colloid structure of these clusters revealed that the negative charge density on the cluster surface also strongly depends on the molecular weight of the stabilizing polymers.
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2011-01-01
In this article, PtAg alloy nanoislands/graphene hybrid composites were prepared based on the self-organization of Au@PtAg nanorods on graphene sheets. Graphite oxides (GO) were prepared and separated to individual sheets using Hummer's method. Graphene nano-sheets were prepared by chemical reduction with hydrazine. The prepared PtAg alloy nanomaterial and the hybrid composites with graphene were characterized by SEM, TEM, and zeta potential measurements. It is confirmed that the prepared Au@PtAg alloy nanorods/graphene hybrid composites own good catalytic function for methanol electro-oxidation by cyclic voltammograms measurements, and exhibited higher catalytic activity and more stability than pure Au@Pt nanorods and Au@AgPt alloy nanorods. In conclusion, the prepared PtAg alloy nanoislands/graphene hybrid composites own high stability and catalytic activity in methanol electro-oxidation, so that it is one kind of high-performance catalyst, and has great potential in applications such as methanol fuel cells in near future. PMID:21982417
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Gu, Jing; Aguiar, Jeffery A.; Ferrere, Suzanne
Achieving solar-to-hydrogen efficiencies above 15% is key for the commercial success of photoelectrochemical water splitting devices. While tandem cells can reach those efficiencies, increasing the catalytic activity and long-term stability remains a significant challenge. We show that annealing a bilayer of amorphous titanium dioxide (TiO x) and molybdenum sulfide (MoS x) deposited onto GaInP 2 results in a photocathode with high catalytic activity (current density of 11 mA/cm -2 at 0 V vs. the reversible hydrogen electrode under 1 sun illumination) and stability (retention of 80% of initial photocurrent density over a 20 h durability test) for the hydrogen evolutionmore » reaction. Microscopy and spectroscopy reveal that annealing results in a graded MoS x/MoO x/TiO 2 layer that retains much of the high catalytic activity of amorphous MoS x but with stability similar to crystalline MoS 2. These findings demonstrate the potential of utilizing a hybridized, heterogeneous surface layer as a cost-effective catalytic and protective interface for solar hydrogen production.« less
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Zhang, Li; Liu, Jiewei; Fan, Yan-Zhong; Li, Xin; Xu, Yao-Wei; Su, Cheng-Yong
2018-05-22
Porous porphyrin metal-organic frameworks (PMOFs) provide a promising platform to study CO2 capture and conversion (C3) owing to their versatility in photoelectric, catalytic and redox activities and porphyrin coordination chemistry. Herein, we report the C3 application of two PMOFs by engineering the coordination space through introduction of two catalytic metalloporphyrins, Rh-PMOF-1 and Ir-PMOF-1, both of which can serve as heterogeneous catalysts for the chemical fixation of CO2 into cyclic carbonates with up to 99% yields. Remarkably, the catalytic reactions can effectively proceed under low concentration of CO2, and the high yields of 83% and 73% can be obtained under 5% concentration of CO2 in the presence of Rh-PMOF-1 and Ir-PMOF-1, respectively. The synergistic effect of the metalloporphyrin ligand and the Zr6O8 cluster, in combination with the CO2 concentrating effect from the pore space, might account for the excellent catalytic performance of Rh-PMOF-1 under low CO2 concentration. Recycling tests of Rh-PMOF-1 show negligible loss of catalytic activity after 10 runs. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Fedarovich, Alena; Nicholas, Robert A.; Davies, Christopher
Penicillin-binding protein A (PBPA) is a class B penicillin-binding protein that is important for cell division in Mycobacterium tuberculosis. We have determined a second crystal structure of PBPA in apo form and compared it with an earlier structure of apoenzyme. Significant structural differences in the active site region are apparent, including increased ordering of a β-hairpin loop and a shift of the SxN active site motif such that it now occupies a position that appears catalytically competent. Using two assays, including one that uses the intrinsic fluorescence of a tryptophan residue, we have also measured the second-order acylation rate constantsmore » for the antibiotics imipenem, penicillin G, and ceftriaxone. Of these, imipenem, which has demonstrable anti-tubercular activity, shows the highest acylation efficiency. Crystal structures of PBPA in complex with the same antibiotics were also determined, and all show conformational differences in the β5–α11 loop near the active site, but these differ for each β-lactam and also for each of the two molecules in the crystallographic asymmetric unit. Overall, these data reveal the β5–α11 loop of PBPA as a flexible region that appears important for acylation and provide further evidence that penicillin-binding proteins in apo form can occupy different conformational states.« less
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Current advances in precious metal core-shell catalyst design.
Wang, Xiaohong; He, Beibei; Hu, Zhiyu; Zeng, Zhigang; Han, Sheng
2014-08-01
Precious metal nanoparticles are commonly used as the main active components of various catalysts. Given their high cost, limited quantity, and easy loss of catalytic activity under severe conditions, precious metals should be used in catalysts at low volumes and be protected from damaging environments. Accordingly, reducing the amount of precious metals without compromising their catalytic performance is difficult, particularly under challenging conditions. As multifunctional materials, core-shell nanoparticles are highly important owing to their wide range of applications in chemistry, physics, biology, and environmental areas. Compared with their single-component counterparts and other composites, core-shell nanoparticles offer a new active interface and a potential synergistic effect between the core and shell, making these materials highly attractive in catalytic application. On one hand, when a precious metal is used as the shell material, the catalytic activity can be greatly improved because of the increased surface area and the closed interfacial interaction between the core and the shell. On the other hand, when a precious metal is applied as the core material, the catalytic stability can be remarkably improved because of the protection conferred by the shell material. Therefore, a reasonable design of the core-shell catalyst for target applications must be developed. We summarize the latest advances in the fabrications, properties, and applications of core-shell nanoparticles in this paper. The current research trends of these core-shell catalysts are also highlighted.
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Li, Hongwei; Yang, Fan; Kang, Xue; Xia, Bin; Jin, Changwen
2008-04-15
Rhodanese catalyzes the sulfur-transfer reaction that transfers sulfur from thiosulfate to cyanide by a double-displacement mechanism, in which an active cysteine residue plays a central role. Previous studies indicated that the phage-shock protein E (PspE) from Escherichia coli is a rhodanese composed of a single active domain and is the only accessible rhodanese among the three single-domain rhodaneses in E. coli. To understand the catalytic mechanism of rhodanese at the molecular level, we determined the solution structures of the sulfur-free and persulfide-intermediate forms of PspE by nuclear magnetic resonance (NMR) spectroscopy and identified the active site by NMR titration experiments. To obtain further insights into the catalytic mechanism, we studied backbone dynamics by NMR relaxation experiments. Our results demonstrated that the overall structures in both sulfur-free and persulfide-intermediate forms are highly similar, suggesting that no significant conformational changes occurred during the catalytic reaction. However, the backbone dynamics revealed that the motional properties of PspE in its sulfur-free form are different from the persulfide-intermediate state. The conformational exchanges are largely enhanced in the persulfide-intermediate form of PspE, especially around the active site. The present structural and biochemical studies in combination with backbone dynamics provide further insights in understanding the catalytic mechanism of rhodanese.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Shi, Fan; Wang, Ping; Duan, Yuhua
2012-08-02
Due to continuing high demand, depletion of non-renewable resources and increasing concerns about climate change, the use of fossil fuel-derived transportation fuels faces relentless challenges both from a world markets and an environmental perspective. The production of renewable transportation fuel from microalgae continues to attract much attention because of its potential for fast growth rates, high oil content, ability to grow in unconventional scenarios, and inherent carbon neutrality. Moreover, the use of microalgae would minimize “food versus fuel” concerns associated with several biomass strategies, as microalgae do not compete with food crops in the food chain. This paper reviews themore » progress of recent research on the production of transportation fuels via homogeneous and heterogeneous catalytic conversions of microalgae. This review also describes the development of tools that may allow for a more fundamental understanding of catalyst selection and conversion processes using computational modelling. The catalytic conversion reaction pathways that have been investigated are fully discussed based on both experimental and theoretical approaches. Finally, this work makes several projections for the potential of various thermocatalytic pathways to produce alternative transportation fuels from algae, and identifies key areas where the authors feel that computational modelling should be directed to elucidate key information to optimize the process.« less
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Zheng, Hong; Yu, Wen-Mei; Waclaw, Ronald R; Kontaridis, Maria I; Neel, Benjamin G; Qu, Cheng-Kui
2018-03-20
Catalytically activating mutations in Ptpn11 , which encodes the protein tyrosine phosphatase SHP2, cause 50% of Noonan syndrome (NS) cases, whereas inactivating mutations in Ptpn11 are responsible for nearly all cases of the similar, but distinct, developmental disorder Noonan syndrome with multiple lentigines (NSML; formerly called LEOPARD syndrome). However, both types of disease mutations are gain-of-function mutations because they cause SHP2 to constitutively adopt an open conformation. We found that the catalytic activity of SHP2 was required for the pathogenic effects of gain-of-function, disease-associated mutations on the development of hydrocephalus in the mouse. Targeted pan-neuronal knockin of a Ptpn11 allele encoding the active SHP2 E76K mutant resulted in hydrocephalus due to aberrant development of ependymal cells and their cilia. These pathogenic effects of the E76K mutation were suppressed by the additional mutation C459S, which abolished the catalytic activity of SHP2. Moreover, ependymal cells in NSML mice bearing the inactive SHP2 mutant Y279C were also unaffected. Mechanistically, the SHP2 E76K mutant induced developmental defects in ependymal cells by enhancing dephosphorylation and inhibition of the transcription activator STAT3. Whereas STAT3 activity was reduced in Ptpn11 E76K/+ cells, the activities of the kinases ERK and AKT were enhanced, and neural cell-specific Stat3 knockout mice also manifested developmental defects in ependymal cells and cilia. These genetic and biochemical data demonstrate a catalytic-dependent role of SHP2 gain-of-function disease mutants in the pathogenesis of hydrocephalus. Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.
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SABER: a computational method for identifying active sites for new reactions.
Nosrati, Geoffrey R; Houk, K N
2012-05-01
A software suite, SABER (Selection of Active/Binding sites for Enzyme Redesign), has been developed for the analysis of atomic geometries in protein structures, using a geometric hashing algorithm (Barker and Thornton, Bioinformatics 2003;19:1644-1649). SABER is used to explore the Protein Data Bank (PDB) to locate proteins with a specific 3D arrangement of catalytic groups to identify active sites that might be redesigned to catalyze new reactions. As a proof-of-principle test, SABER was used to identify enzymes that have the same catalytic group arrangement present in o-succinyl benzoate synthase (OSBS). Among the highest-scoring scaffolds identified by the SABER search for enzymes with the same catalytic group arrangement as OSBS were L-Ala D/L-Glu epimerase (AEE) and muconate lactonizing enzyme II (MLE), both of which have been redesigned to become effective OSBS catalysts, demonstrated by experiments. Next, we used SABER to search for naturally existing active sites in the PDB with catalytic groups similar to those present in the designed Kemp elimination enzyme KE07. From over 2000 geometric matches to the KE07 active site, SABER identified 23 matches that corresponded to residues from known active sites. The best of these matches, with a 0.28 Å catalytic atom RMSD to KE07, was then redesigned to be compatible with the Kemp elimination using RosettaDesign. We also used SABER to search for potential Kemp eliminases using a theozyme predicted to provide a greater rate acceleration than the active site of KE07, and used Rosetta to create a design based on the proteins identified. Copyright © 2012 The Protein Society.
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Neubauer, Nicole; Seipenbusch, Martin; Kasper, Gerhard
2013-08-01
A new type of detector which we call the Catalytic Activity Aerosol Monitor (CAAM) was investigated towards its capability to detect traces of commonly used industrial catalysts in ambient air in quasi real time. Its metric is defined as the catalytic activity concentration (CAC) expressed per volume of sampled workplace air. We thus propose a new metric which expresses the presence of nanoparticles in terms of their functionality - in this case a functionality of potential relevance for damaging effects - rather than their number, surface, or mass concentration in workplace air. The CAAM samples a few micrograms of known or anticipated airborne catalyst material onto a filter first and then initiates a chemical reaction which is specific to that catalyst. The concentration of specific gases is recorded using an IR sensor, thereby giving the desired catalytic activity. Due to a miniaturization effort, the laboratory prototype is compact and portable. Sensitivity and linearity of the CAAM response were investigated with catalytically active palladium and nickel nano-aerosols of known mass concentration and precisely adjustable primary particle size in the range of 3-30 nm. With the miniature IR sensor, the smallest detectable particle mass was found to be in the range of a few micrograms, giving estimated sampling times on the order of minutes for workplace aerosol concentrations typically reported in the literature. Tests were also performed in the presence of inert background aerosols of SiO2, TiO2, and Al2O3. It was found that the active material is detectable via its catalytic activity even when the particles are attached to a non-active background aerosol.
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Wulff, Günter; Liu, Junqiu
2012-02-21
The impressive efficiency and selectivity of biological catalysts has engendered a long-standing effort to understand the details of enzyme action. It is widely accepted that enzymes accelerate reactions through their steric and electronic complementarity to the reactants in the rate-determining transition states. Thus, tight binding to the transition state of a reactant (rather than to the corresponding substrate) lowers the activation energy of the reaction, providing strong catalytic activity. Debates concerning the fundamentals of enzyme catalysis continue, however, and non-natural enzyme mimics offer important additional insight in this area. Molecular structures that mimic enzymes through the design of a predetermined binding site that stabilizes the transition state of a desired reaction are invaluable in this regard. Catalytic antibodies, which can be quite active when raised against stable transition state analogues of the corresponding reaction, represent particularly successful examples. Recently, synthetic chemistry has begun to match nature's ability to produce antibody-like binding sites with high affinities for the transition state. Thus, synthetic, molecularly imprinted polymers have been engineered to provide enzyme-like specificity and activity, and they now represent a powerful tool for creating highly efficient catalysts. In this Account, we review recent efforts to develop enzyme models through the concept of transition state stabilization. In particular, models for carboxypeptidase A were prepared through the molecular imprinting of synthetic polymers. On the basis of successful experiments with phosphonic esters as templates to arrange amidinium groups in the active site, the method was further improved by combining the concept of transition state stabilization with the introduction of special catalytic moieties, such as metal ions in a defined orientation in the active site. In this way, the imprinted polymers were able to provide both an electrostatic stabilization for the transition state through the amidinium group as well as a synergism of transition state recognition and metal ion catalysis. The result was an excellent catalyst for carbonate hydrolysis. These enzyme mimics represent the most active catalysts ever prepared through the molecular imprinting strategy. Their catalytic activity, catalytic efficiency, and catalytic proficiency clearly surpass those of the corresponding catalytic antibodies. The active structures in natural enzymes evolve within soluble proteins, typically by the refining of the folding of one polypeptide chain. To incorporate these characteristics into synthetic polymers, we used the concept of transition state stabilization to develop soluble, nanosized carboxypeptidase A models using a new polymerization method we term the "post-dilution polymerization method". With this methodology, we were able to prepare soluble, highly cross-linked, single-molecule nanoparticles. These particles have controlled molecular weights (39 kDa, for example) and, on average, one catalytically active site per particle. Our strategies have made it possible to obtain efficient new enzyme models and further advance the structural and functional analogy with natural enzymes. Moreover, this bioinspired design based on molecular imprinting in synthetic polymers offers further support for the concept of transition state stabilization in catalysis.
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OBSERVATIONS UPON THE ACTION OF SALTS ON THE CATALASE OF THE BLOOD IN RABBITS.
Winternitz, M C; Rogers, W B
1910-11-01
Bicarbonate of soda fed in varying quantities over a period of months has no direct effect upon the catalytic activity of the blood. When fed to rabbits, it invariably causes a slight albuminuria and occasional casts. The kidneys of pregnant animals, especially in the later stages of pregnancy, seem to be more susceptible to this salt, and in some instances there may be complete suppression of urine followed by death. In these cases there is a decline in the catalytic activity of the blood similar to that observed in cases of acute nephritis, following the administration of uranium nitrate. The subcutaneous injection of salts is impracticable on account of the slow absorption. In intravenous injections it is important to make observations during the injection and at short intervals after the injection has been discontinued, since there is a rapid compensation on the part of the organism with a return of the normal catalytic activity of the blood. The simple diluting effect brought about by the injection of distilled water into the circulation manifests itself as a slight transitory decrease in the catalytic activity of the blood. This must be taken into consideration when estimating the effect of the injection of solutions of salt upon the catalase of the blood. Salts, such as sodium chloride, sodium bicarbonate, sodium sulphate and potassium iodide, acids, such as sulphuric, and alkalies, such as sodium hydrate, cause a definite decrease in the catalytic activity of the blood. This decrease varies directly with the concentration of the salt. The organism compensates rapidly and brings about a return to the normal activity. This compensation becomes less and less complete as larger quantities or repeated infusions are made. For example, twenty cubic centimeters of a five per cent. bicarbonate of soda solution causes a marked fall in the catalytic action of the blood. This is rapidly recovered from in from one to five minutes, and then a much more marked fall in the activity, requiring a longer time for compensation, occurs after the injection of six cubic centimeters of the same solution. It is of interest to note that sodium sulphate and potassium iodide, which have been shown to accelerate the catalytic activity of liver extract in the test-tube, have an inhibiting effect on the action of the blood when injected intravenously. This is only another instance of the dangers to be encountered from the immediate application of test-tube experiments to the living organism. The inhalation of carbon dioxide gas, even until convulsions are manifested, is without effect on the catalytic activity of the blood. On the other hand, there is a definite decline in this activity following the administration of illuminating gas. In this respect our results are directly at variance with those of Jolles.
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Anti-EGFR monoclonal antibody in cancer treatment: in vitro and in vivo evidence
Quatrale, Anna Elisa; Petriella, Daniela; Porcelli, Letizia; Tommasi, Stefania; Silvestris, Nicola; Colucci, Giuseppe; Angelo, Angelo; Azzariti, Amalia
2011-01-01
The complexity of EGFR signaling network suggests that the receptor could be promising targets for new personalised therapy. In clinical practice two strategies targeting the receptor are available; they utilise monoclonal antibodies, directed towards the extracellular domain of EGFR, and small molecule tyrosine kinase inhibitors, which bind the catalytic kinase domain of the receptor. In this review, we summarise currently known pre-clinical data on the antitumor effects of monoclonal antibodies, which bind to EGFR in its inactive configuration, competing for ligand binding and thereby blocking ligand-induced EGFR tyrosine kinase activation. As a consequence of treatment, key EGFR-dependent intracellular signals in cancer cells are affected. Data explaining the mechanisms of action of anti-EGFR monoclonal antibodies, currently used in clinical setting and under development for the treatment of solid tumors, are revised with the aim to provide an overview of the most important preclinical studies showing the impact of this class of EGFR targeted agents on tumor biology.
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Denmark, Scott E; Heemstra, John R
2007-07-20
The generality of Lewis base catalyzed, Lewis acid mediated, enantioselective vinylogous aldol addition reactions has been investigated. The combination of silicon tetrachloride and chiral phosphoramides is a competent catalyst for highly selective additions of a variety of alpha,beta-unsaturated ketone-, 1,3-diketone-, and alpha,beta-unsaturated amide-derived dienolates to aldehydes. These reactions provided high levels of gamma-site selectivity for a variety of substitution patterns on the dienyl unit. Both ketone- and morpholine amide-derived dienol ethers afforded high enantio- and diastereoselectivity in the addition to conjugated aldehydes. Although alpha,beta-unsaturated ketone-derived dienolate did not react with aliphatic aldehydes, alpha,beta-unsaturated amide-derived dienolates underwent addition at reasonable rates affording high yields of vinylogous aldol product. The enantioselectivities achieved with the morpholine derived-dienolate in the addition to aliphatic aldehydes was the highest afforded to date with the silicon tetrachloride-chiral phosphoramide system. Furthermore, the ability to cleanly convert the morpholine amide to a methyl ketone was demonstrated.
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Wei, Zelan; Satram-Maharaj, Tamara; Chaharyn, Bradley; Kuski, Kelly; Pennington, Paul R; Cao, Xia; Chlan, Jennifer; Mousseau, Darrell D
2012-11-01
Post-translational influences could underlie the ambiguous roles of monoamine oxidase-A (MAO-A) in pathologies such as depression, cancer and Alzheimer disease. In support of this, we recently demonstrated that the Ca²⁺-sensitive component of MAO-A catalytic activity is inhibited by a pro-survival p38 (MAPK)-dependent mechanism. We substituted three aspartic acid (D) residues in human MAO-A that reside in putative Ca²⁺-binding motifs and overexpressed the individual proteins in the human HEK293 cell line. We assayed the overexpressed proteins for catalytic activity and for their influence on cell viability (using MTT conversion and trypan blue exclusion) and proliferation/DNA synthesis [using bromodeoxyuridine (BrdU) incorporation]. Innate MAO-A catalytic activity (and the capacity for generating hydrogen peroxide) was unaffected by the D61A substitution, but inhibited moderately or completely by the D248A and D328G substitutions, respectively. The Ca²⁺-sensitive activities of wild-type and D248A MAO-A proteins were enhanced by treatment with the selective p38(MAPK) inhibitor, SB203580, but was completely abrogated by the D61A substitution. Monoamine oxidase-A(D61A) was toxic to cells and exerted no effect on cell proliferation, while MAO-A(D248A) was generally comparable to wild-type MAO-A. As expected, the catalytic-dead MAO-A(D328G) was not cytotoxic, but unexpectedly enhanced both MTT conversion and BrdU staining. Variant-dependent changes in Bax and Bcl-2/Bcl-XL protein expression were observed. A different pattern of effects in N2-a cells suggests cell line-dependent roles for MAO-A. A catalytic-dependent mechanism influences MAO-A-mediated cytotoxicity, whereas a catalytic-independent mechanism contributes to proliferation. Context-dependent inputs by either mechanism could underlie the ambiguous pathological contributions of MAO-A.
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Zhang, Peng; Shen, Yu; Guo, Jin-Song; Li, Chun; Wang, Han; Chen, You-Peng; Yan, Peng; Yang, Ji-Xiang; Fang, Fang
2015-07-10
In this work, proteins in extracellular polymeric substances extracted from anaerobic, anoxic and aerobic sludges of wastewater treatment plant (WWTP) were analyzed to probe their origins and functions. Extracellular proteins in WWTP sludges were identified using shotgun proteomics, and 130, 108 and 114 proteins in anaerobic, anoxic and aerobic samples were classified, respectively. Most proteins originated from cell and cell part, and their most major molecular functions were catalytic activity and binding activity. The results exhibited that the main roles of extracellular proteins in activated sludges were multivalence cations and organic molecules binding, as well as in catalysis and degradation. The catalytic activity proteins were more widespread in anaerobic sludge compared with those in anoxic and aerobic sludges. The structure difference between anaerobic and aerobic sludges could be associated with their catalytic activities proteins. The results also put forward a relation between the macro characteristics of activated sludges and micro functions of extracellular proteins in biological wastewater treatment process.
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Milgrom, Y M; Ehler, L L; Boyer, P D
1990-11-05
The F1-ATPase from chloroplasts (CF1) lacks catalytic capacity for ATP hydrolysis if ATP is not bound at noncatalytic sites. CF1 heat activated in the presence of ADP, with less than one ADP and no ATP at non-catalytic sites, shows a pronounced lag in the onset of ATP hydrolysis after exposure to 5-20 microM ATP. The onset of activity correlates well with the binding of ATP at the last two of the three noncatalytic sites. The dependence of activity on the presence of ATP at non-catalytic sites is shown at relatively low or high free Mg2+ concentrations, with or without bicarbonate as an activating anion, and when the binding of ATP at noncatalytic sites is slowed 3-4-fold by sulfate. The latent CF1 activated by dithiothreitol also requires ATP at noncatalytic sites for ATPase activity. A similar requirement by other F1-ATPases and by ATP synthases seems plausible.
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ERIC Educational Resources Information Center
Pappenfus, Ted M.; Hermanson, David L.; Ekerholm, Daniel P.; Lilliquist, Stacie L.; Mekoli, Megan L.
2007-01-01
A series of experiments for undergraduate laboratory courses (e.g., inorganic, organometallic or advanced organic) have been developed. These experiments focus on understanding the design and catalytic activity of ruthenium-indenylidene complexes for olefin metathesis. Included in the experiments are the syntheses of two ruthenium-indenylidene…
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This study reports improved catalytic activities and stabilities for the oxidation of dimethyl sulfide (DMS), a major pollutant of pulp and paper mills. Ozone was used as an oxidant and activities of Cu, Mo, Cr and Mn oxides, and mixed metal oxides supported on -alumina, were tes...
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COMPARISON OF HOPCALITE AND A SUPPORTED HOPCALITE FOR APPLICABILITY TO SUBMARINE USE.
have been investigated with regard to suitable physical properties and catalytic activity. In this report the presently used Hopcalite catalyst is...compared with a supported Hopcalite catalyst with an alumina base. It was found that the present Hopcalite was clearly superior in almost all aspects of catalytic activity to the supported Hopcalite . (Author)
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Enhancement of Catalytic Activity of Reduced Graphene Oxide Via Transition Metal Doping Strategy
NASA Astrophysics Data System (ADS)
Lee, Hangil; Hong, Jung A.
2017-06-01
To compare the catalytic oxidation activities of reduced graphene oxide (rGO) and rGO samples doped with five different transition metals (TM-rGO), we determine their effects on the oxidation of L-cysteine (Cys) in aqueous solution by performing electrochemistry (EC) measurements and on the photocatalytic oxidation of Cys by using high-resolution photoemission spectroscopy (HRPES) under UV illumination. Our results show that Cr-, Fe-, and Co-doped rGO with 3+ charge states (stable oxide forms: Cr3+, Fe3+, and Co3+) exhibit enhanced catalytic activities that are due to the charge states of the doped metal ions as we compare them with Cr-, Fe-, and Co-doped rGO with 2+ charge states.
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Recent Developments of Electrochemical Promotion of Catalysis in the Techniques of DeNOx
Tang, Xiaolong; Yi, Honghong; Chen, Chen; Wang, Chuan
2013-01-01
Electrochemical promotion of catalysis reactions (EPOC) is one of the most significant discoveries in the field of catalytic and environmental protection. The work presented in this paper focuses on the aspects of reaction mechanism, influencing factors, and recent positive results. It has been shown with more than 80 different catalytic systems that the catalytic activity and selectivity of conductive catalysts deposited on solid electrolytes can be altered in the last 30 years. The active ingredient of catalyst can be activated by applying constant voltage or constant current to the catalysts/electrolyte interface. The effect of EPOC can improve greatly the conversion rate of NOx. And it can also improve the lifetime of catalyst by inhibiting its poisoning. PMID:23970835
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Berry, David A; Shekhawat, Dushyant; Smith, Mark; Haynes, Daniel
2013-07-16
The disclosure relates to a method of utilizing a catalyst system for an oxidation process on a gaseous hydrocarbon stream with a mitigation of carbon accumulation. The system is comprised of a catalytically active phase deposited onto an oxygen conducting phase, with or without supplemental support. The catalytically active phase has a specified crystal structure where at least one catalytically active metal is a cation within the crystal structure and coordinated with oxygen atoms within the crystal structure. The catalyst system employs an optimum coverage ratio for a given set of oxidation conditions, based on a specified hydrocarbon conversion and a carbon deposition limit. Specific embodiments of the catalyst system are disclosed.
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Renny, Andrew; Santhosh, Viswanathan; Somkuwar, Nitin; Gokak, D T; Sharma, Pankaj; Bhargava, Sanjay
2016-11-01
The aim of this work was to study the pyrolysis of de-oiled seed cake of Jatropha Curcas and catalytic steam reforming of pyrolytic bio-oil to hydrogen. As per literature, presence of heavy nitrogenous and oxygenated compounds leads to catalyst deactivation. Here, an attempt has been made to tune pyrolytic reactions to optimize the N and O content of the pyrolytic bio-oil. Bio-oil conversion and hydrogen yield decreased as reaction progressed, which attributes to temporary loss of catalytic activity by blockage of catalyst pores by carbon deposition. Further, retention of steam reforming activity after repetitive steam activation suggests long-term catalyst usage. Copyright © 2016 Elsevier Ltd. All rights reserved.
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Tajwar, Razia; Shahid, Saher; Zafar, Rehan; Akhtar, Muhammad Waheed
2017-11-01
Xylanase XynB of the hyperthermophile Thermotoga maritima, which belongs to glycoside hydrolase family 10 (GH10), does not have an associated carbohydrate binding module (CBM) in the native state. CBM6 and CBM22 from a thermophile Clostridium thermocellum were fused to the catalytic domain of XynB (XynB-C) to determine the effects on activity and other properties. XynB-B22C and XynB-CB22, produced by fusing CBM22 to the N- and C-terminal of XynB-C, showed 1.7- and 3.24-fold increase in activity against the insoluble birchwood xylan, respectively. Similarly, CBM6 when attached to the C-terminal of XynB-C resulted in 2.0-fold increase in activity, whereas its attachment to the N-terminal did not show any increase of activity. XynB-B22C and XynB-CB22 retained all the activity, whereas XynB-B6C and XynB-CB6 lost 17 and 11% of activity, respectively, at 60°C for 4h. Thermostability data and the secondary structure contents obtained by molecular modelling are in agreement with the data from circular dichroism analysis. Molecular modelling analysis showed that the active site residues of the catalytic domain and the binding residues of CBM6 and CBM22 were located on the surface of molecule, except XynB-B6C, where the binding residues were found somewhat buried. In the case of XynB-CB22, the catalytic and the binding residues seem to be located favorably adjacent to each other, thus showing higher increase in activity. This study shows that the active site residues of the catalytic domain and the binding residues of the CBM are arranged in a unique fashion, not reported before. Copyright © 2017 Elsevier Inc. All rights reserved.
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An Extended Structure of the APOBEC3G Catalytic Domain Suggests a Unique Holoenzyme Model
Harjes, Elena; Gross, Phillip J.; Chen, Kuan-Ming; Lu, Yongjian; Shindo, Keisuke; Nowarski, Roni; Gross, John D.; Kotler, Moshe; Harris, Reuben S.; Matsuo, Hiroshi
2009-01-01
Summary Human APOBEC3G (A3G) belongs to a family of polynucleotide cytidine deaminases. This family includes APOBEC1 and AID, which edit APOB mRNA and antibody gene DNA, respectively. A3G deaminates cytidines to uridines in single-strand DNA and inhibits the replication of HIV-1, other retroviruses and retrotransposons. Although the mechanism of A3G-catalyzed DNA deamination has been investigated genetically and biochemically, atomic details are just starting to emerge. Here, we compare the DNA cytidine deaminase activities and NMR structures of two A3G catalytic domain constructs. The longer A3G191-384 protein is considerably more active than the shorter A3G198-384 variant. The longer structure has an α1 helix (residues 201–206) that was not apparent in the shorter protein and it contributes to catalytic activity through interactions with hydrophobic core structures (β1, β3, α5 and α6). Both A3G catalytic domain solution structures have a discontinuous β2 region that is clearly different than the continuous β2 strand of another family member APOBEC2. In addition, the longer A3G191-384 structure revealed part of the N-terminal pseudo-catalytic domain including the inter-domain linker and some of the last α-helix. These structured residues (191–196) enabled a novel full-length A3G model by providing physical overlap between the N-terminal pseudo-catalytic domain and the new C-terminal catalytic domain structure. Contrary to predictions, this structurally constrained model suggested that the two domains are tethered by structured residues and that the N- and C-terminal β2 regions are too distant from one another to participate in this interaction. PMID:19389408
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Chakraborty, Sandeep; Rao, Basuthkar J.
2012-01-01
Promiscuity, the basis for the evolution of new functions through ‘tinkering’ of residues in the vicinity of the catalytic site, is yet to be quantitatively defined. We present a computational method Promiscuity Indices Estimator (PROMISE) - based on signatures derived from the spatial and electrostatic properties of the catalytic residues, to estimate the promiscuity (PromIndex) of proteins with known active site residues and 3D structure. PromIndex reflects the number of different active site signatures that have congruent matches in close proximity of its native catalytic site, the quality of the matches and difference in the enzymatic activity. Promiscuity in proteins is observed to follow a lognormal distribution (μ = 0.28, σ = 1.1 reduced chi-square = 3.0E-5). The PROMISE predicted promiscuous functions in any protein can serve as the starting point for directed evolution experiments. PROMISE ranks carboxypeptidase A and ribonuclease A amongst the more promiscuous proteins. We have also investigated the properties of the residues in the vicinity of the catalytic site that regulates its promiscuity. Linear regression establishes a weak correlation (R2∼0.1) between certain properties of the residues (charge, polar, etc) in the neighborhood of the catalytic residues and PromIndex. A stronger relationship states that most proteins with high promiscuity have high percentages of charged and polar residues within a radius of 3 Å of the catalytic site, which is validated using one-tailed hypothesis tests (P-values∼0.05). Since it is known that these characteristics are key factors in catalysis, their relationship with the promiscuity index cross validates the methodology of PROMISE. PMID:22359655
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Exploration of alternate catalytic mechanisms and optimization strategies for retroaldolase design.
Bjelic, Sinisa; Kipnis, Yakov; Wang, Ling; Pianowski, Zbigniew; Vorobiev, Sergey; Su, Min; Seetharaman, Jayaraman; Xiao, Rong; Kornhaber, Gregory; Hunt, John F; Tong, Liang; Hilvert, Donald; Baker, David
2014-01-09
Designed retroaldolases have utilized a nucleophilic lysine to promote carbon-carbon bond cleavage of β-hydroxy-ketones via a covalent Schiff base intermediate. Previous computational designs have incorporated a water molecule to facilitate formation and breakdown of the carbinolamine intermediate to give the Schiff base and to function as a general acid/base. Here we investigate an alternative active-site design in which the catalytic water molecule was replaced by the side chain of a glutamic acid. Five out of seven designs expressed solubly and exhibited catalytic efficiencies similar to previously designed retroaldolases for the conversion of 4-hydroxy-4-(6-methoxy-2-naphthyl)-2-butanone to 6-methoxy-2-naphthaldehyde and acetone. After one round of site-directed saturation mutagenesis, improved variants of the two best designs, RA114 and RA117, exhibited among the highest kcat (>10(-3)s(-1)) and kcat/KM (11-25M(-1)s(-1)) values observed for retroaldolase designs prior to comprehensive directed evolution. In both cases, the >10(5)-fold rate accelerations that were achieved are within 1-3 orders of magnitude of the rate enhancements reported for the best catalysts for related reactions, including catalytic antibodies (kcat/kuncat=10(6) to 10(8)) and an extensively evolved computational design (kcat/kuncat>10(7)). The catalytic sites, revealed by X-ray structures of optimized versions of the two active designs, are in close agreement with the design models except for the catalytic lysine in RA114. We further improved the variants by computational remodeling of the loops and yeast display selection for reactivity of the catalytic lysine with a diketone probe, obtaining an additional order of magnitude enhancement in activity with both approaches. © 2013.
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Zhao, Guangshan; Ali, Ehsan; Araki, Rie; Sakka, Makiko; Kimura, Tetsuya; Sakka, Kazuo
2005-08-01
Clostridium stercorarium Xyn10B having hydrolytic activities on xylan and beta-1,3-1,4-glucan is a modular enzyme composed of two family-22 carbohydrate-binding modules (CBMs), a family-10 catalytic module of the glycoside hydrolases, a family-9 CBM, and two S-layer homologous modules, consecutively from the N-terminus. We investigated the function of family-9 and family-22 CBMs in a modular enzyme by comparing the enzymatic properties of a truncated enzyme composed of two family-22 CBMs and the catalytic module (rCBM22-CM), an enzyme composed of the catalytic module and family-9 CBM (rCM-CBM9), an enzyme composed of two family-22 CBMs, the catalytic module, and family-9 CBM (rCBM22-CM-CBM9), and the catalytic module polypeptide (rCM). Although the addition of family-9 CBM to rCM and rCBM22-CM did not significantly change catalytic activity toward xylan and beta-1,3-1,4-glucan, the addition of family-22 CBM to rCM and rCM-CBM9 drastically enhanced catalytic activity toward xylan and especially beta-1,3-1,4-glucan. Furthermore, the addition of family-22 CBM to rCM and rCM-CBM9 shifted the optimum temperature from 65 degrees C to 75 degrees C, but that of family-9 CBM to rCM and rCBM22-CM did not affect the optimum temperature. These facts suggest that the enzyme properties of Xyn10B were mainly dependent on the presence of the family-22 CBMs but not family-9 CBM.
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Jordán-Pla, Antonio; Yu, Simei; Waldholm, Johan; Källman, Thomas; Östlund Farrants, Ann-Kristin; Visa, Neus
2018-05-18
Brahma (BRM) is the only catalytic subunit of the SWI/SNF chromatin-remodeling complex of Drosophila melanogaster. The function of SWI/SNF in transcription has long been attributed to its ability to remodel nucleosomes, which requires the ATPase activity of BRM. However, recent studies have provided evidence for a non-catalytic function of BRM in the transcriptional regulation of a few specific genes. Here we have used RNA-seq and ChIP-seq to identify the BRM target genes in S2 cells, and we have used a catalytically inactive BRM mutant (K804R) that is unable to hydrolyze ATP to investigate the magnitude of the non-catalytic function of BRM in transcription regulation. We show that 49% of the BRM target genes in S2 cells are regulated through mechanisms that do not require BRM to have an ATPase activity. We also show that the catalytic and non-catalytic mechanisms of SWI/SNF regulation operate on two subsets of genes that differ in promoter architecture and are linked to different biological processes. This study shows that the non-catalytic role of SWI/SNF in transcription regulation is far more prevalent than previously anticipated and that the genes that are regulated by SWI/SNF through ATPase-dependent and ATPase-independent mechanisms have specialized roles in different cellular and developmental processes.
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Yu, Qin; Hu, Liyan; Yao, Qing; Zhu, Yongqun; Dong, Na; Wang, Da-Cheng; Shao, Feng
2013-06-01
Rab GTPases are emerging targets of diverse bacterial pathogens. Here, we perform biochemical and structural analyses of LepB, a Rab GTPase-activating protein (GAP) effector from Legionella pneumophila. We map LepB GAP domain to residues 313-618 and show that the GAP domain is Rab1 specific with a catalytic activity higher than the canonical eukaryotic TBC GAP and the newly identified VirA/EspG family of bacterial RabGAP effectors. Exhaustive mutation analyses identify Arg444 as the arginine finger, but no catalytically essential glutamine residues. Crystal structures of LepB313-618 alone and the GAP domain of Legionella drancourtii LepB in complex with Rab1-GDP-AlF3 support the catalytic role of Arg444, and also further reveal a 3D architecture and a GTPase-binding mode distinct from all known GAPs. Glu449, structurally equivalent to TBC RabGAP glutamine finger in apo-LepB, undergoes a drastic movement upon Rab1 binding, which induces Rab1 Gln70 side-chain flipping towards GDP-AlF3 through a strong ionic interaction. This conformationally rearranged Gln70 acts as the catalytic cis-glutamine, therefore uncovering an unexpected RasGAP-like catalytic mechanism for LepB. Our studies highlight an extraordinary structural and catalytic diversity of RabGAPs, particularly those from bacterial pathogens.
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Lu, Ping; Campbell, Charles T; Xia, Younan
2013-10-09
A triphasic catalytic system (Pt/TiO2-SiO2) with an "islands in the sea" configuration was fabricated by controlling the selectivity of SiO2 deposition onto the surface of TiO2 versus the surface of Pt nanoparticles. The Pt surface was exposed, while the nanoparticles were supported on TiO2 and isolated from each other by SiO2 to achieve both significantly improved sinter resistance up to 700 °C and outstanding activity after high-temperature calcination. This work not only demonstrates the feasibility of using a new triphasic system with uncovered catalyst to maximize the thermal stability and catalytic activity but also offers a general approach to the synthesis of high-performance catalytic systems with tunable compositions.
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[Catalytic stability in wet air oxidation of carboxylic acids over ZnFe0.25Al1.75 O4 catalyst].
Xu, Ai-hua; Yang, Min; Du, Hong-zhang; Peng, Fu-yong; Sun, Cheng-lin
2007-07-01
Oxalic, formic and acetic acid are main intermediate products in catalytic wet air oxidation process (CWAO). The catalytic activity and stability in CWAO of the three short-chain organic acids over ZnFe0.25Al1.75O4 catalyst were studied. Oxalic acid is the only oxidizable intermediate and the largest amount of Fe leaching is 9.5 mg L(-1) at 160 degrees C during CWAO process. Formic and acetic acid have little influence on Fe leaching. Due to the strong reducible ability of oxalic acid, the amount of Fe leaching is larger in nitrogen atmosphere than that in oxygen atmosphere. Salicylic acid can be also degraded by ZnFe0.25Al1.75O4 catalyst with a high catalytic activity and stability.
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Crystal structure of metagenomic β-xylosidase/ α-l-arabinofuranosidase activated by calcium.
Matsuzawa, Tomohiko; Kaneko, Satoshi; Kishine, Naomi; Fujimoto, Zui; Yaoi, Katsuro
2017-09-01
The crystal structure of metagenomic β-xylosidase/α-l-arabinofuranosidase CoXyl43, activated by calcium ions, was determined in its apo and complexed forms with xylotriose or l-arabinose in the presence and absence of calcium. The presence of calcium ions dramatically increases the kcat of CoXyl43 for p-nitrophenyl β-d-xylopyranoside and reduces the Michaelis constant for p-nitrophenyl α-l-arabinofuranoside. CoXyl43 consists of a single catalytic domain comprised of a five-bladed β-propeller. In the presence of calcium, a single calcium ion was observed at the centre of this catalytic domain, behind the catalytic pocket. In the absence of calcium, the calcium ion was replaced with one sodium ion and one water molecule, and the positions of these cations were shifted by 1.3 Å. The histidine-319 side chain, which coordinates to the 2-hydroxyl oxygen atom of the bound xylose molecule in the catalytic pocket, also coordinates to the calcium ion, but not to the sodium ion. The calcium-dependent increase in activity appears to be caused by the structural change in the catalytic pocket induced by the tightly bound calcium ion and coordinating water molecules, and by the protonation state of glutamic acid-268, the catalytic acid of the enzyme. Our findings further elucidate the complex relationship between metal ions and glycosidases. © The Authors 2017. Published by Oxford University Press on behalf of the Japanese Biochemical Society. All rights reserved.
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Ren, Xiaohua; Guo, Huanhuan; Feng, Jinkui; Si, Pengchao; Zhang, Lin; Ci, Lijie
2018-01-01
3D porous N-doped reduced graphene oxide (N-rGO) aerogels were synthesized by a hydrothermal reduction of graphene oxide (GO) with urea and following freeze-drying process. N-rGO aerogels have a high BET surface of 499.70 m 2 /g and a high N doping content (5.93-7.46 at%) including three kinds of N (graphitic, pyridinic and pyrrolic). Their high catalytic performance for phenol oxidation in aqueous solution was investigated by catalytic activation of persulfate (PS). We have demonstrated that N-rGO aerogels are promising metal-free catalysts for phenol removal. Kinetics studies indicate that phenol degradation follows first-order reaction kinetics with the reaction rate constant of 0.16799 min -1 for N-rGO-A(1:30). Interestingly, the comparison of direct catalytic oxidation with adsorption-catalytic oxidation experiments indicates that adsorption plays an important role in the catalytic oxidation of phenol by decreasing the phenol degradation time. Spin density and adsorption modeling demonstrates that graphitic N in N-rGO plays the most important role for the catalytic performance by inducing high positive charge densities to adjacent carbon atoms and facilitating phenol adsorption on these carbon sites. Furthermore, the activation mechanism of persulfate (PS) on N-rGO was first investigated by DFT method and PS can be activated to generate strongly oxidative radical (SO 4 · - ) by transferring electrons to N-rGO. Copyright © 2017 Elsevier Ltd. All rights reserved.
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Purification and characterization of the glycogen-bound protein phosphatase from rat liver.
Wera, S; Bollen, M; Stalmans, W
1991-01-05
Glycogen-bound protein phosphatase G from rat liver was transferred from glycogen to beta-cyclodextrin (cycloheptaamylose) linked to Sepharose 6B. After removal of the catalytic subunit and of contaminating proteins with 2 M NaCl, elution with beta-cyclodextrin yielded a single protein on native polyacrylamide gel electrophoresis and two polypeptides (161 and 54 kDa) on sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Several lines of evidence indicate that the latter polypeptides are subunits of the protein phosphatase G holoenzyme. First, these polypeptides were also present, together with the catalytic subunit, in the extensively purified holoenzyme. Also, polyclonal antibodies against these polypeptides were able to bind the holoenzyme. Further, while bound to cyclodextrin-Sepharose, the polypeptides were able to recombine with separately purified type-1 (AMD) catalytic subunit, but not with type-2A (PCS) catalytic subunit. The characteristics of the reconstituted enzyme resembled those of the nonpurified protein phosphatase G. At low dilutions, the spontaneous phosphorylase phosphatase activity of the reconstituted enzyme was about 10 times lower than that of the catalytic subunit, but it was about 1000-fold more resistant to inhibition by the modulator protein (inhibitor-2). In contrast with the free catalytic subunit, the reconstituted enzyme co-sedimented with glycogen, and it was able to activate purified liver glycogen synthase b. Also, the synthase phosphatase activity was synergistically increased by a cytosolic phosphatase and inhibited by physiological concentrations of phosphorylase alpha and of Ca2+.
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Bi, Xiaoyi; Wang, Peng; Jiang, Hong
2008-06-15
In order to develop a catalyst with high activity and stability for microwave assisted ClO2 catalytic oxidation, we prepared CuOn-La2O3/gamma-Al2O3 by impregnation-deposition method, and determined its properties using BET, XRF, XPS and chemical analysis techniques. The test results show that, better thermal ability of gamma-Al2O3 and high loading of Cu in the catalyst can be achieved by adding La2O3. The microwave assisted ClO2 catalytic oxidation process with CuOn-La2O3/gamma-Al2O3 used as catalyst was also investigated, and the results show that the catalyst has an excellent catalytic activity in treating synthetic wastewater containing 100 mg/L phenol, and 91.66% of phenol and 50.35% of total organic carbon (TOC) can be removed under the optimum process conditions. Compared with no catalyst process, CuOn-La2O3/gamma-Al2O3 can effectively degrade contaminants in short reaction time and with low oxidant dosage, extensive pH range. The comparison of phenol removal efficiency in the different process indicates that microwave irradiation and catalyst work together to oxidize phenol effectively. It can therefore be concluded from results and discussion that CuOn-La2O3/gamma-Al2O3 is a suitable catalyst in microwave assisted ClO2 catalytic oxidation process.
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Siletsky, Sergey A; Belevich, Ilya; Belevich, Nikolai P; Soulimane, Tewfik; Verkhovsky, Michael I
2011-09-01
The oxidative part of the catalytic cycle of the caa(3)-type cytochrome c oxidase from Thermus thermophilus was followed by time-resolved optical spectroscopy. Rate constants, chemical nature and the spectral properties of the catalytic cycle intermediates (Compounds A, P, F) reproduce generally the features typical for the aa(3)-type oxidases with some distinctive peculiarities caused by the presence of an additional 5-th redox-center-a heme center of the covalently bound cytochrome c. Compound A was formed with significantly smaller yield compared to aa(3) oxidases in general and to ba(3) oxidase from the same organism. Two electrons, equilibrated between three input redox-centers: heme a, Cu(A) and heme c are transferred in a single transition to the binuclear center during reduction of the compound F, converting the binuclear center through the highly reactive O(H) state into the final product of the reaction-E(H) (one-electron reduced) state of the catalytic site. In contrast to previous works on the caa(3)-type enzymes, we concluded that the finally produced E(H) state of caa(3) oxidase is characterized by the localization of the fifth electron in the binuclear center, similar to the O(H)→E(H) transition of the aa(3)-type oxidases. So, the fully-reduced caa(3) oxidase is competent in rapid electron transfer from the input redox-centers into the catalytic heme-copper site. 2011 Elsevier B.V. All rights reserved.
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Le, Dung Tien; Nguyen, Kim-Lien; Chu, Ha Duc; Vu, Nam Tuan; Pham, Thu Thi Ly; Tran, Lam-Son Phan
2018-05-28
In plants, two types of methionine sulfoxide reductase (MSR) exist, namely methionine-S-sulfoxide reductase (MSRA) and methionine-R-sulfoxide reductase (MSRB). These enzymes catalyze the reduction of methionine sulfoxides (MetO) back to methionine (Met) by a catalytic cysteine (Cys) and one or two resolving Cys residues. Interestingly, a group of MSRA encoded by plant genomes does not have a catalytic residue. We asked that if this group of MSRA did not have any function (as fitness), why it was not lost during the evolutionary process. To challenge this question, we analyzed the gene family encoding MSRA in soybean (GmMSRAs). We found seven genes encoding GmMSRAs, which included three segmental duplicated pairs. Among them, a pair of duplicated genes, namely GmMSRA1 and GmMSRA6, was without a catalytic Cys residue. Pseudogenes were ruled out as their transcripts were detected in various tissues and their Ka/Ks ratio indicated a negative selection pressure. In vivo analysis in Δ3MSR yeast strain indicated that the GmMSRA6 did not have activity toward MetO, contrasting to GmMSRA3 which had catalytic Cys and had activity. When exposed to H 2 O 2 -induced oxidative stress, GmMSRA6 did not confer any protection to the Δ3MSR yeast strain. Overexpression of GmMSRA6 in Arabidopsis thaliana did not alter the plant's phenotype under physiological conditions. However, the transgenic plants exhibited slightly higher sensitivity toward salinity-induced stress. Taken together, this data suggested that the plant MSRAs without the catalytic Cys are not enzymatically active and their existence may be explained by a role in regulating plant MSR activity via dominant-negative substrate competition mechanism.
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Abay, Angaw Kelemework; Kuo, Dong-Hau; Chen, Xiaoyun; Saragih, Albert Daniel
2017-12-01
A new type of convenient, and environmentally friendly, Vanadium (V)-doped Bi 2 (O,S) 3 oxysulfide catalyst with different V contents was successfully synthesized via a simple and facile method. The obtained V-doped Bi 2 (O,S) 3 solid solution catalysts were fully characterized by conventional methods. The catalytic performance of the samples was tested by using the reduction of 2-nitroaniline (2-NA) in aqueous solution. The reduction/decolorization of methylene blue (MB) and rhodamine B (RhB) was also chosen to evaluate the universality of catalysts. It was observed that the introduction of V can improve the catalytic performance, and 20%V-Bi 2 (O,S) 3 was found to be the optimal V doping concentration for the reduction of 2-NA, MB, and RhB dyes. For comparative purposes, a related V-free Bi 2 (O, S) 3 oxysulfide material was synthesized and tested as the catalyst. The superior activity of V-doped Bi 2 (O,S) 3 over pure Bi 2 (O,S) 3 was ascribed mainly to an increase in active sites of the material and also due to the presence of synergistic effects. The presence of V 5+ as found from XPS analysis may interact with Bi atoms and enhancing the catalytic activity of the sample. In the catalytic reduction of 2-NA, MB and RhB, the obtained V-doped Bi 2 (O,S) 3 oxysulfide catalyst exhibited excellent catalytic activity as compared with other reported catalysts. Furthermore this highly efficient, low-cost and easily reusable V-doped Bi 2 (O,S) 3 catalyst is anticipated to be of great potential in catalysis in the future. Copyright © 2017 Elsevier Ltd. All rights reserved.
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NASA Astrophysics Data System (ADS)
Hosseini, Farshad; Rasuli, Reza; Jafarian, Vahab
2018-04-01
We present the antibacterial and photo-catalytic activity of immobilized WO3 nanoparticles on graphene oxide sheets. WO3 nanoparticles were immobilized on graphene oxide using the arc discharge method in arc currents of 5, 20, 40 and 60 A. Tauc plots of the UV-visible spectra show that the band gap of the prepared samples decreases (to ~2.7 eV) with respect to the WO3 nanoparticles. Photo-catalytic activity was examined by the degradation of rhodamine B under ultra-violet irradiation and the results show that the photo-catalytic activity of WO3 nanoparticles is increased by immobilizing them on graphene oxide sheets. In addition, the photo-degradation yield of the samples prepared by the 5 A arc current is 84% in 120 min, which is more than that of the other samples. The antibacterial activity of the prepared samples was studied against Bacillus pumilus (B. pumilus) bacteria, showing high resistance to ultra-violet exposure. Our results show that the bare and immobilized WO3 nanoparticles become more active under UV irradiation and their antibacterial properties are comparable with Ag nanoparticles. Besides this, the results show that although the photo-catalytic activity of the post-annealed samples at 500 °C is less than the as-prepared samples, it is, however, more active against B. pumilus bacteria under UV irradiation.
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Samudrala, Shanthi Priya; Kandasamy, Shalini; Bhattacharya, Sankar
2018-05-10
Direct C-O hydrogenolysis of bioglycerine to produce 1,3-propanediol selectively is a vital technology that can expand the scope of biodiesel industry and green chemical production from biomass. Herein we report sulphuric acid-activated montmorillonite clay supported platinum nanoparticles as highly effective solid acid catalysts for the selective production of 1,3-propanediol from glycerol. The catalytic performances of the catalysts were investigated in the hydrogenolysis of glycerol with a fixed bed reactor under ambient pressure. The results were found promising and showed that the activation of montmorillonite by sulphuric acid incorporated Brønsted acidity in the catalyst and significantly improved the selectivity to 1,3-propanediol. The catalytic performance of different platinum loaded catalysts was examined and 2 wt% Pt/S-MMT catalyst presented superior activity among others validating 62% 1,3-propanediol selectivity at 94% glycerol conversion. The catalytic activity of 2Pt/S-MMT was systematically investigated under varying reaction parameters including reaction temperature, hydrogen flow rate, glycerol concentration, weight hourly space velocity, and contact time to derive the optimum conditions for the reaction. The catalyst stability, reusability and structure-activity correlation were also elucidated. The high performance of the catalyst could be ascribed to well disperse Pt nanoparticles immobilized on acid-activated montmorillonite, wider pore-structure and appropriate acid sites of the catalyst.
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CRISPR-Cas9 conformational activation as elucidated from enhanced molecular simulations
Miao, Yinglong; Walker, Ross C.; Jinek, Martin; McCammon, J. Andrew
2017-01-01
CRISPR-Cas9 has become a facile genome editing technology, yet the structural and mechanistic features underlying its function are unclear. Here, we perform extensive molecular simulations in an enhanced sampling regime, using a Gaussian-accelerated molecular dynamics (GaMD) methodology, which probes displacements over hundreds of microseconds to milliseconds, to reveal the conformational dynamics of the endonuclease Cas9 during its activation toward catalysis. We disclose the conformational transition of Cas9 from its apo form to the RNA-bound form, suggesting a mechanism for RNA recruitment in which the domain relocations cause the formation of a positively charged cavity for nucleic acid binding. GaMD also reveals the conformation of a catalytically competent Cas9, which is prone for catalysis and whose experimental characterization is still limited. We show that, upon DNA binding, the conformational dynamics of the HNH domain triggers the formation of the active state, explaining how the HNH domain exerts a conformational control domain over DNA cleavage [Sternberg SH et al. (2015) Nature, 527, 110–113]. These results provide atomic-level information on the molecular mechanism of CRISPR-Cas9 that will inspire future experimental investigations aimed at fully clarifying the biophysics of this unique genome editing machinery and at developing new tools for nucleic acid manipulation based on CRISPR-Cas9. PMID:28652374
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CRISPR-Cas9 conformational activation as elucidated from enhanced molecular simulations.
Palermo, Giulia; Miao, Yinglong; Walker, Ross C; Jinek, Martin; McCammon, J Andrew
2017-07-11
CRISPR-Cas9 has become a facile genome editing technology, yet the structural and mechanistic features underlying its function are unclear. Here, we perform extensive molecular simulations in an enhanced sampling regime, using a Gaussian-accelerated molecular dynamics (GaMD) methodology, which probes displacements over hundreds of microseconds to milliseconds, to reveal the conformational dynamics of the endonuclease Cas9 during its activation toward catalysis. We disclose the conformational transition of Cas9 from its apo form to the RNA-bound form, suggesting a mechanism for RNA recruitment in which the domain relocations cause the formation of a positively charged cavity for nucleic acid binding. GaMD also reveals the conformation of a catalytically competent Cas9, which is prone for catalysis and whose experimental characterization is still limited. We show that, upon DNA binding, the conformational dynamics of the HNH domain triggers the formation of the active state, explaining how the HNH domain exerts a conformational control domain over DNA cleavage [Sternberg SH et al. (2015) Nature , 527 , 110-113]. These results provide atomic-level information on the molecular mechanism of CRISPR-Cas9 that will inspire future experimental investigations aimed at fully clarifying the biophysics of this unique genome editing machinery and at developing new tools for nucleic acid manipulation based on CRISPR-Cas9.
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Tan, Hao; Wu, Xiang; Xie, Liyuan; Huang, Zhongqian; Peng, Weihong; Gan, Bingcheng
2016-01-01
Four novel phytases of the histidine acid phosphatase family were identified in two publicly available metagenomic datasets of an acidic peat-soil microbiome in northeastern Bavaria, Germany. These enzymes have low similarity to all the reported phytases. They were overexpressed in Escherichia coli and purified. Catalytic efficacy in simulated gastric fluid was measured and compared among the four candidates. The phytase named rPhyPt4 was selected for its high activity. It is the first phytase identified from unculturable Acidobacteria. The phytase showed a longer half-life than all the gastric-stable phytases that have been reported to date, suggesting a strong resistance to low pH and pepsin. A wide pH profile was observed between pH 1.5 and 5.0. At the optimum pH (2.5) the activity was 2,790 μmol/min/mg at the physiological temperature of 37°C and 3,989 μmol/min/mg at the optimum temperature of 60°C. Due to the competent activity level as well as the high gastric stability, the phytase could be a potential candidate for practical use in livestock and poultry feeding. © 2016 S. Karger AG, Basel.
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Khodaverdi, Zeinab; Bahram, Abbas; Stodden, David; Kazemnejad, Anoshirvan
2016-08-01
The purpose of this study was to investigate whether perceived motor competence and components of health-related physical fitness mediated the relationship between actual motor competence and physical activity in 8- to 9-year-old Iranian girls. A convenience sample of 352 girls (mean age = 8.7, SD = 0.3 years) participated in the study. Actual motor competence, perceived motor competence and children's physical activity were assessed using the Test of Gross Motor Development-2, the physical ability sub-scale of Marsh's Self-Description Questionnaire and Physical Activity Questionnaire for Older Children, respectively. Body mass index, the 600 yard run/walk, curl-ups, push-ups, and back-saver sit and reach tests assessed health-related physical fitness. Preacher & Hayes (2004) bootstrap method was used to assess the potential mediating effects of fitness and perceived competence on the direct relationship between actual motor competence and physical activity. Regression analyses revealed that aerobic fitness (b = .28, 95% CI = [.21, .39]), as the only fitness measure, and perceived competence (b = .16, 95% CI = [.12, .32]) were measures that mediated the relationship between actual motor competence and physical activity with the models. Development of strategies targeting motor skill acquisition, children's self-perceptions of competence and cardiorespiratory fitness should be targeted to promote girls' moderate-to-vigorous physical activity.
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Guo, Xiao-Hui; Mao, Chao-Chao; Zhang, Ji; Huang, Jun; Wang, Wa-Nv; Deng, Yong-Hui; Wang, Yao-Yu; Cao, Yong; Huang, Wei-Xin; Yu, Shu-Hong
2012-05-21
High-quality cobalt-doped ceria nanostructures with triangular column, triangular slab, and disklike shapes are synthesized by tuning the doping amount of cobalt nitrate in a facile hydrothermal reaction. The cobalt-doped ceria nanodisks display significantly enhanced catalytic activity in CO oxidation due to exposed highly active crystal planes and the presence of numerous surface defects. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
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Barnett, Lisa M; Ridgers, Nicola D; Salmon, Jo
2015-03-01
The relationship between actual and perceived object control competence (ball skills) and the contribution to young children's physical activity is not known. Cross sectional study. The Test Gross Motor Development-2 assessed actual object control competence and a modified version of the Pictorial Scale of Perceived Competence and Social Acceptance for Young Children assessed perceived object control competence. Moderate- to vigorous-intensity physical activity was measured via accelerometry. Three mixed regression models were performed: (i) object control competence as the predictor and the outcome as perceived object control, (ii) perceived object control competence as the predictor and the outcome moderate to vigorous physical activity and (iii) actual object control as the predictor and the outcome moderate to vigorous physical activity. Models adjusted for school clustering, monitor wear time, sex and age. Interactions between respective predictor variables and sex were performed if warranted. A total of 102 children (56% boys, 44% girls) aged 4-8 years (M 6.3, SD 0.92) completed assessments. Girls had lower perceived and actual object control competence and were less active than boys. Actual object control competence was positively associated with perceived object control competence (B=0.11, t(96)=2.25, p<0.001, p=0.027) and this relationship did not differ by sex (p=0.449); however, neither actual (p=0.092) nor perceived object control competence (p=0.827) were associated with moderate to vigorous physical activity. Young children's perceived ball skill abilities appear to relate to actual competence; however, these measures were not associated with physical activity. In older children, object control skill is associated with physical activity so targeting young children's object control skills is an intervention priority. Crown Copyright © 2014. Published by Elsevier Ltd. All rights reserved.
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NASA Astrophysics Data System (ADS)
Lan, Yuan-Pei; Sohn, Hong Yong
2018-03-01
Nanoceria powder was treated by hydrogen or air at different temperatures and atmospheres, and the phases, oxygen vacancies, catalytic properties of the treated samples were investigated. After treating, the crystallites on the ceria surface were fused, and the SEM and TEM images indicated that the particle size increased with treatment temperature. Both Raman and XPS spectra showed the oxygen vacancies in nanoceria increased with treatment temperature in hydrogen, and at the same temperature CeO2 treated in hydrogen had a higher Ce3+ fraction than that treated in air. The nanoceria after being treated in hydrogen at 900 °C contained the Ce2O3 phase together with CeO2 which was revealed by XRD and TEM results. Oxygen vacancies were found to enhance CO conversion, but the high temperature needed to generate the oxygen vacancies caused the fusion of the crystallites on the ceria surface and thus its area decreased, which resulted in lower catalytic activity. The catalytic activity of nanoceria treated in hydrogen at 900 °C measured higher than that of the ceria powders treated at 700 °C in hydrogen or 900 °C in air, which indicated that the Ce2O3 phase present in the treated nanoceria particles enhanced the catalytic activity.
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Antony, R; Suja Pon Mini, P S; Theodore David Manickam, S; Sanjeev, Ganesh; Mitu, Liviu; Balakumar, S
2015-01-01
Chitosan (a biopolymer) anchored Cu(II) and Ni(II) Schiff base complexes, [M(OIAC)Cl2] (M: Cu/Ni and OIAC: ([2-oxo-1H-indol-3-ylidene]amino)chitosan) were electron beam irradiated by different doses (100 Gy, 1 kGy and 10 kGy). The electron beam has shown potential impact on biopolymer's support, in detail chain linking and chain scissoring, as evidenced by viscosity studies, FT-IR and X-ray diffraction spectroscopic techniques. Due to these structural changes, thermal properties of the complexes were found to be changed. The surface of these heterogeneous complexes was also effectually altered by electron beam. As a consequence, pores and holes were created as probed by SEM technique. The catalytic activity of both non-irradiated and irradiated complexes was investigated in the aerobic oxidation of cyclohexane using hydrogen peroxide oxidant. The catalytic ability of the complexes was enhanced significantly after irradiation as the result of surface changes. The reusability of the complexes was also greatly affected because of the structural variations in polymeric support. In terms of both better catalytic activity along with the reusability, 1 kGy is suggested as the best dose to attain adequate increase in catalytic activity and good reusability. Copyright © 2015 Elsevier B.V. All rights reserved.
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Isomerization of Cyclooctadiene to Cyclooctyne with a Zinc/Zirconium Heterobimetallic Complex.
Butler, Michael J; White, Andrew J P; Crimmin, Mark R
2016-06-06
Reaction of a zinc/zirconium heterobimetallic complex with 1,5-cyclooctadiene (1,5-COD) results in slow isomerization to 1,3-cyclooctadiene (1,3-COD), along with the formation of a new complex that includes a cyclooctyne ligand bridging two metal centers. While analogous magnesium/zirconium and aluminum/zirconium heterobimetallic complexes are competent for the catalytic isomerization of 1,5-COD to 1,3-COD, only in the case of the zinc species is the cyclooctyne adduct observed. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
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2008-10-07
in a competent orientation for attack by the catalytic water in the protease, resulting in the cleavage of the peptide bond. A cocrystal structure of...in future struc- ture-based discovery and design investigations. Implications for BoNT/A LC Inhibitor Development Our cocrystal provides a new...the Met residues in I1 and SNAP-25 are shown as sticks, with the sulfur atom colored yellow. The Zn2+ is shown as a light blue sphere.The cocrystal
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Isomerization of Cyclooctadiene to Cyclooctyne with a Zinc/Zirconium Heterobimetallic Complex
Butler, Michael J.; White, Andrew J. P.
2016-01-01
Abstract Reaction of a zinc/zirconium heterobimetallic complex with 1,5‐cyclooctadiene (1,5‐COD) results in slow isomerization to 1,3‐cyclooctadiene (1,3‐COD), along with the formation of a new complex that includes a cyclooctyne ligand bridging two metal centers. While analogous magnesium/zirconium and aluminum/zirconium heterobimetallic complexes are competent for the catalytic isomerization of 1,5‐COD to 1,3‐COD, only in the case of the zinc species is the cyclooctyne adduct observed. PMID:27071992
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Kalp, Ericka L; Marx, James F; Davis, James
2017-06-01
The Association for Professionals in Infection Control and Epidemiology (APIC) MegaSurvey, administered in 2015, was completed by approximately 4,079 APIC members. The survey sought to gain a better understanding the current state of 4 components of infection prevention practice: demographic characteristics, compensation, organizational structure, and practice and competency. The data for this analysis come from the APIC MegaSurvey Practice and Competency domain. Descriptive statistics and χ 2 analyses were conducted to examine differences in infection preventionist (IP) competency, roles, and activity self-assessments. The majority of IPs self-assessed their competency as Proficient compared with Novice or Expert for each of the 8 IP core competency activities. Forty percent of IPs self-rated their competency as Expert in the Preventing/Controlling the Transmission of Infectious Agents/HAIs component. IPs reported Novice competency in Employee/Occupational Health (29%); Cleaning, Sterilization, Disinfection, and Asepsis (23%); and Education and Research categories (22%). Differences in self-rated competency among IPs by discipline type (public health, nurse, and laboratory) were identified. Differences in self-rated competency were identified for each of the 8 IP core competency activities. IPs report using various resource types to gain competency. Future research is needed to identify opportunities to increase competency levels in the weakest-rated competency activities. Copyright © 2017 Association for Professionals in Infection Control and Epidemiology, Inc. Published by Elsevier Inc. All rights reserved.
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Using steric hindrance to design new inhibitors of class C beta-lactamases
DOE Office of Scientific and Technical Information (OSTI.GOV)
Trehan, Indi; Morandi, F.; Blaszczak, L.C.
{beta}-lactamases confer resistance to {beta}-lactam antibiotics such as penicillins and cephalosporins. However, {beta}-lactams that form an acyl-intermediate with the enzyme but subsequently are hindered from forming a catalytically competent conformation seem to be inhibitors of {beta}-lactamases. This inhibition may be imparted by specific groups on the ubiquitous R1 side chain of {beta}-lactams, such as the 2-amino-4-thiazolyl methoxyimino (ATMO) group common among third-generation cephalosporins. Using steric hindrance of deacylation as a design guide, penicillin and carbacephem substrates were converted into effective {beta}-lactamase inhibitors and antiresistance antibiotics. To investigate the structural bases of inhibition, the crystal structures of the acyl-adducts of themore » penicillin substrate amoxicillin and the new analogous inhibitor ATMO-penicillin were determined. ATMO-penicillin binds in a catalytically incompetent conformation resembling that adopted by third-generation cephalosporins, demonstrating the transferability of such sterically hindered groups in inhibitor design.« less
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Detection of Damaged DNA Bases by DNA Glycosylase Enzymes†
Friedman, Joshua I.; Stivers, James T.
2010-01-01
A fundamental and shared process in all forms of life is the use of DNA glycosylase enzymes to excise rare damaged bases from genomic DNA. Without such enzymes, the highly-ordered primary sequences of genes would rapidly deteriorate. Recent structural and biophysical studies are beginning to reveal a fascinating multistep mechanism for damaged base detection that begins with short-range sliding of the glycosylase along the DNA chain in a distinct conformation we refer to as the search complex (SC). Sliding is frequently punctuated by the formation of a transient “interrogation” complex (IC) where the enzyme extrahelically inspects both normal and damaged bases in an exosite pocket that is distant from the active site. When normal bases are presented in the exosite, the IC rapidly collapses back to the SC, while a damaged base will efficiently partition forward into the active site to form the catalytically competent excision complex (EC). Here we review the unique problems associated with enzymatic detection of rare damaged DNA bases in the genome, and emphasize how each complex must have specific dynamic properties that are tuned to optimize the rate and efficiency of damage site location. PMID:20469926
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Tools to investigate how interprofessional education activities link to competencies.
West, Courtney; Veronin, Michael; Landry, Karen; Kurz, Terri; Watzak, Bree; Quiram, Barbara; Graham, Lori
2015-01-01
Integrating interprofessional education (IPE) activities and curricular components in health professions education has been emphasized recently by the inclusion of accreditation standards across disciplines. The Interprofessional Education Collaborative (IPEC) established IPE competencies in 2009, but evaluating how activities link to competencies has not been investigated in depth. The purpose of this project is to investigate how well two IPE activities align with IPEC competencies. To evaluate how our IPE activities met IPEC competencies, we developed a checklist and an observation instrument. A brief description of each is included as well as the outcomes. We analyzed Disaster Day, a simulation exercise that includes participants from Nursing, Medicine, and Pharmacy, and Interprofessional Healthcare Ethics (IPHCE), a course that introduced medical, nursing, and pharmacy students to ethical issues using didactic sessions and case discussions. While both activities appeared to facilitate the development of IPE competencies, Disaster Day aligned more with IPEC competencies than the IPHCE course and appears to be a more comprehensive way of addressing IPEC competencies. However, offering one IPE activity or curricular element is not sufficient. Having several IPE options available, utilizing the tools we developed to map the IPE curriculum and evaluating competency coverage is recommended.
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Yu, Xuehua; Zhao, Zhen; Wei, Yuechang; Liu, Jian
2017-01-01
A series of novel oxide catalysts, which contain three-dimensionally ordered macroporous (3DOM) and microporous structure, were firstly designed and successfully synthesized by simple method. In the as-prepared catalysts, 3DOM SiO2 is used as support and microporous K-OMS-2 oxide nanoparticles are supported on the wall of SiO2. 3DOM K-OMS-2/SiO2 oxide catalysts were firstly used in soot particle oxidation reaction and they show very high catalytic activities. The high activities of K-OMS-2/SiO2 oxide catalysts can be assigned to three possible reasons: macroporous effect of 3DOM structure for improving contact between soot and catalyst, microporous effect of K-OMS-2 for adsorption of small gas molecules and interaction of K and Mn for activation of gas molecules. The catalytic activities of catalysts are comparable to or even higher than noble metal catalyst in the medium and high temperature range. For example, the T50 of K-OMS-2/SiO2-50, 328 °C, is much lower than those of Pt/Al2O3 and 3DOM Au/LaFeO3, 464 and 356 °C,respectively. Moreover, catalysts exhibited high catalytic stability. It is attributed to that the K+ ions are introduced into the microporous structure of OMS-2 and stabilized in the catalytic reaction. Meanwhile, the K+ ions play an important role in templating and stabilizing the tunneled framework of OMS-2. PMID:28443610
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Drosophila immunity: analysis of PGRP-SB1 expression, enzymatic activity and function.
Zaidman-Rémy, Anna; Poidevin, Mickael; Hervé, Mireille; Welchman, David P; Paredes, Juan C; Fahlander, Carina; Steiner, Hakan; Mengin-Lecreulx, Dominique; Lemaitre, Bruno
2011-02-18
Peptidoglycan is an essential and specific component of the bacterial cell wall and therefore is an ideal recognition signature for the immune system. Peptidoglycan recognition proteins (PGRPs) are conserved from insects to mammals and able to bind PGN (non-catalytic PGRPs) and, in some cases, to efficiently degrade it (catalytic PGRPs). In Drosophila, several non-catalytic PGRPs function as selective peptidoglycan receptors upstream of the Toll and Imd pathways, the two major signalling cascades regulating the systemic production of antimicrobial peptides. Recognition PGRPs specifically activate the Toll pathway in response to Lys-type peptidoglycan found in most Gram-positive bacteria and the Imd pathway in response to DAP-type peptidoglycan encountered in Gram-positive bacilli-type bacteria and in Gram-negative bacteria. Catalytic PGRPs on the other hand can potentially reduce the level of immune activation by scavenging peptidoglycan. In accordance with this, PGRP-LB and PGRP-SC1A/B/2 have been shown to act as negative regulators of the Imd pathway. In this study, we report a biochemical and genetic analysis of PGRP-SB1, a catalytic PGRP. Our data show that PGRP-SB1 is abundantly secreted into the hemolymph following Imd pathway activation in the fat body, and exhibits an enzymatic activity towards DAP-type polymeric peptidoglycan. We have generated a PGRP-SB1/2 null mutant by homologous recombination, but its thorough phenotypic analysis did not reveal any immune function, suggesting a subtle role or redundancy of PGRP-SB1/2 with other molecules. Possible immune functions of PGRP-SB1 are discussed.
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Wang, Junjie; Nemeria, Natalia S.; Chandrasekhar, Krishnamoorthy; Kumaran, Sowmini; Arjunan, Palaniappa; Reynolds, Shelley; Calero, Guillermo; Brukh, Roman; Kakalis, Lazaros; Furey, William; Jordan, Frank
2014-01-01
The Escherichia coli pyruvate dehydrogenase complex (PDHc) catalyzing conversion of pyruvate to acetyl-CoA comprises three components: E1p, E2p, and E3. The E2p is the five-domain core component, consisting of three tandem lipoyl domains (LDs), a peripheral subunit binding domain (PSBD), and a catalytic domain (E2pCD). Herein are reported the following. 1) The x-ray structure of E2pCD revealed both intra- and intertrimer interactions, similar to those reported for other E2pCDs. 2) Reconstitution of recombinant LD and E2pCD with E1p and E3p into PDHc could maintain at least 6.4% activity (NADH production), confirming the functional competence of the E2pCD and active center coupling among E1p, LD, E2pCD, and E3 even in the absence of PSBD and of a covalent link between domains within E2p. 3) Direct acetyl transfer between LD and coenzyme A catalyzed by E2pCD was observed with a rate constant of 199 s−1, comparable with the rate of NADH production in the PDHc reaction. Hence, neither reductive acetylation of E2p nor acetyl transfer within E2p is rate-limiting. 4) An unprecedented finding is that although no interaction could be detected between E1p and E2pCD by itself, a domain-induced interaction was identified on E1p active centers upon assembly with E2p and C-terminally truncated E2p proteins by hydrogen/deuterium exchange mass spectrometry. The inclusion of each additional domain of E2p strengthened the interaction with E1p, and the interaction was strongest with intact E2p. E2p domain-induced changes at the E1p active site were also manifested by the appearance of a circular dichroism band characteristic of the canonical 4′-aminopyrimidine tautomer of bound thiamin diphosphate (AP). PMID:24742683
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Wang, Junjie; Nemeria, Natalia S; Chandrasekhar, Krishnamoorthy; Kumaran, Sowmini; Arjunan, Palaniappa; Reynolds, Shelley; Calero, Guillermo; Brukh, Roman; Kakalis, Lazaros; Furey, William; Jordan, Frank
2014-05-30
The Escherichia coli pyruvate dehydrogenase complex (PDHc) catalyzing conversion of pyruvate to acetyl-CoA comprises three components: E1p, E2p, and E3. The E2p is the five-domain core component, consisting of three tandem lipoyl domains (LDs), a peripheral subunit binding domain (PSBD), and a catalytic domain (E2pCD). Herein are reported the following. 1) The x-ray structure of E2pCD revealed both intra- and intertrimer interactions, similar to those reported for other E2pCDs. 2) Reconstitution of recombinant LD and E2pCD with E1p and E3p into PDHc could maintain at least 6.4% activity (NADH production), confirming the functional competence of the E2pCD and active center coupling among E1p, LD, E2pCD, and E3 even in the absence of PSBD and of a covalent link between domains within E2p. 3) Direct acetyl transfer between LD and coenzyme A catalyzed by E2pCD was observed with a rate constant of 199 s(-1), comparable with the rate of NADH production in the PDHc reaction. Hence, neither reductive acetylation of E2p nor acetyl transfer within E2p is rate-limiting. 4) An unprecedented finding is that although no interaction could be detected between E1p and E2pCD by itself, a domain-induced interaction was identified on E1p active centers upon assembly with E2p and C-terminally truncated E2p proteins by hydrogen/deuterium exchange mass spectrometry. The inclusion of each additional domain of E2p strengthened the interaction with E1p, and the interaction was strongest with intact E2p. E2p domain-induced changes at the E1p active site were also manifested by the appearance of a circular dichroism band characteristic of the canonical 4'-aminopyrimidine tautomer of bound thiamin diphosphate (AP). © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.
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Rodríguez-Escudero, Isabel; Oliver, María D; Andrés-Pons, Amparo; Molina, María; Cid, Víctor J; Pulido, Rafael
2011-11-01
The PTEN (phosphatase and tensin homolog) phosphatase is unique in mammals in terms of its tumor suppressor activity, exerted by dephosphorylation of the lipid second messenger PIP(3) (phosphatidylinositol 3,4,5-trisphosphate), which activates the phosphoinositide 3-kinase/Akt/mTOR (mammalian target of rapamycin) oncogenic pathway. Loss-of-function mutations in the PTEN gene are frequent in human cancer and in the germline of patients with PTEN hamartoma tumor-related syndromes (PHTSs). In addition, PTEN is mutated in patients with autism spectrum disorders (ASDs), although no functional information on these mutations is available. Here, we report a comprehensive in vivo functional analysis of human PTEN using a heterologous yeast reconstitution system. Ala-scanning mutagenesis at the catalytic loops of PTEN outlined the critical role of residues within the P-catalytic loop for PIP(3) phosphatase activity in vivo. PTEN mutations that mimic the P-catalytic loop of mammalian PTEN-like proteins (TPTE, TPIP, tensins and auxilins) affected PTEN function variably, whereas tumor- or PHTS-associated mutations targeting the PTEN P-loop produced complete loss of function. Conversely, Ala-substitutions, as well as tumor-related mutations at the WPD- and TI-catalytic loops, displayed partial activity in many cases. Interestingly, a tumor-related D92N mutation was partially active, supporting the notion that the PTEN Asp92 residue might not function as the catalytic general acid. The analysis of a panel of ASD-associated hereditary PTEN mutations revealed that most of them did not substantially abrogate PTEN activity in vivo, whereas most of PHTS-associated mutations did. Our findings reveal distinctive functional patterns among PTEN mutations found in tumors and in the germline of PHTS and ASD patients, which could be relevant for therapy.
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Density Functional Theory Study of Oxygen Reduction Activity on Ultrathin Platinum Nanotubes
DOE Office of Scientific and Technical Information (OSTI.GOV)
Matanovic, Ivana; Kent, Paul; Garzon, Fernando
2012-07-13
The structure, stability, and catalytic activity of a number of single- and double-wall platinum (n,m) nanotubes ranging in diameter from 0.3 to 2.0 nm were studied using plane-wave based density functional theory in the gas phase and water environment. The change in the catalytic activity toward the oxygen reduction reaction (ORR) with the size and chirality of the nanotube was studied by calculating equilibrium adsorption potentials for ORR intermediates and by constructing free energy diagrams in the ORR dissociative mechanism network. In addition, the stability of the platinum nanotubes is investigated in terms of electrochemical dissolution potentials and by determiningmore » the most stable state of the material as a function of pH and potential, as represented in Pourbaix diagrams. Our results show that the catalytic activity and the stability toward electrochemical dissolution depend greatly on the diameter and chirality of the nanotube. On the basis of the estimated overpotentials for ORR, we conclude that smaller, approximately 0.5 nm in diameter single-wall platinum nanotubes consistently show a huge, up to 400 mV larger overpotential than platinum, indicating very poor catalytic activity toward ORR. This is the result of substantial structural changes induced by the adsorption of any chemical species on these tubes. Single-wall n = m platinum nanotubes with a diameter larger than 1 nm have smaller ORR overpotentials than bulk platinum for up to 180 mV and thus show improved catalytic activity relative to bulk. We also predict that these nanotubes can endure the highest cell potentials but dissolution potentials are still for 110 mV lower than for the bulk, indicating a possible corrosion problem.« less
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Tom, Moshe; Shmul, Merav; Shefer, Edna; Chen, Nir; Slor, Hanoch; Rinkevich, Baruch; Herut, Barak
2003-09-01
Hepatic cytochrome P4501A (CYP1A) expression was partially characterized in the striped sea bream (Lithognathus mormyrus) from the Mediterranean coast of Israel as part of the process of establishing the CYP1A gene as an environmental biomarker. Reverse transcription-competitive polymerase chain reaction, competitive enzyme-linked immunosorbent assay, and ethoxyresorufin O-deethylase (EROD) assay were used for evaluating transcript, protein, and catalytic activity levels, respectively, in absolute units. Highest elucidated transcript, protein, and catalytic activity levels were 0.264 +/- SD 0.084 fmol/microg total RNA, 0.88 +/- 0.52 pmol/microg total protein, and 1.11 +/- 0.52 pmol resorufin/min/microg total protein, respectively, and the lower levels were 0.009 +/- 0.007 fmol/microg total RNA, 0.17 +/- 0.08 pmol/microg total protein, and 0.11 +/- 0.06 pmol resorufin/min/microg total protein, respectively, demonstrating substantial induction potential. All alternate pairs of seven examined field samples, revealing a transcript-level ratio higher than 1.7, also demonstrated a significant difference between their transcript levels, indicating a potential to detect relatively small biomarker changes (1.7-fold) caused by environmental effects. Simultaneous triple measurements of transcript, protein, and catalytic activity were carried out in individuals from two field samples and during a 318-d decay experiment. Fish from the field samples revealed significant alternate bivariate correlation between transcript, protein, and enzymatic activity. Conflicting results were found when analyzing the decay experiment, in which both protein and catalytic activity levels decreased significantly to basal levels, in contrast to no significant change in transcript levels throughout the experiment. No significant difference was observed between males and females regarding the levels of CYP1A transcript, protein, and EROD.
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Wear, Maggie P.; Cordero, Radames J. B.; Oscarson, Stefan
2017-01-01
Studies in the 1980s first showed that some natural antibodies were “catalytic” and able to hydrolyze peptide or phosphodiester bonds in antigens. Many naturally occurring catalytic antibodies have since been isolated from human sera and associated with positive and negative outcomes in autoimmune disease and infection. The function and prevalence of these antibodies, however, remain unclear. A previous study suggested that the 18B7 monoclonal antibody against glucuronoxylomannan (GXM), the major component of the Cryptococcus neoformans polysaccharide capsule, hydrolyzed a peptide antigen mimetic. Using mass spectrometry and Förster resonance energy transfer techniques, we confirm and characterize the hydrolytic activity of 18B7 against peptide mimetics and show that 18B7 is able to hydrolyze an oligosaccharide substrate, providing the first example of a naturally occurring catalytic antibody for polysaccharides. Additionally, we show that the catalytic 18B7 antibody increases release of capsular polysaccharide from fungal cells. A serine protease inhibitor blocked peptide and oligosaccharide hydrolysis by 18B7, and a putative serine protease-like active site was identified in the light chain variable region of the antibody. An algorithm was developed to detect similar sites present in unique antibody structures in the Protein Data Bank. The putative site was found in 14 of 63 (22.2%) catalytic antibody structures and 119 of 1602 (7.4%) antibodies with no annotation of catalytic activity. The ability of many antibodies to cleave antigen, albeit slowly, supports the notion that this activity is an important immunoglobulin function in host defense. The discovery of GXM hydrolytic activity suggests new therapeutic possibilities for polysaccharide-binding antibodies. PMID:27872188
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Tu, Tao; Bai, Yingguo; Luo, Huiying; Ma, Rui; Wang, Yaru; Shi, Pengjun; Yang, Peilong; Meng, Kun; Yao, Bin
2014-06-01
A multimodular pectinase of glycoside hydrolase family 28, S6A, was identified in Penicillium oxalicum SX6 that consists of an N-terminal catalytic domain of pectin methylesterase, a Thr/Ser-rich linker region, and a C-terminal catalytic domain of polygalacturonase. Recombinant S6A and its two derivatives, S6PE (the catalytic domain of pectin methylesterase) and S6PG (the catalytic domain of polygalacturonase), were produced in Pichia pastoris. S6A was a bifunctional protein and had both pectin methylesterase and polygalacturonase activities. Three enzymes showed similar biochemical properties, such as optimal pH and temperature (pH 5.0 and 50 °C) and excellent stability at pH 3.5-6.0 and 40 °C. Most metal ions tested (Na(+), K(+), Ca(2+), Li(+), Co(2+), Cr(3+), Ni(2+), Cu(2+), Mn(2+),Mg(2+), Fe(3+), Zn(2+), and Pb(2+)) enhanced the pectin methylesterase activities of S6PE and S6A, but had little or inhibitory effects on the polygalacturonase activities of S6A and S6PG. In comparison with most fungal pectin methylesterases, S6A had higher specific activity (271.1 U/mg) towards 70 % DM citrus pectin. When S6PE and S6PG were combined at the activity ratio of 1:4, the most significant synergistic effect was observed in citrus pectin degradation and degumming of sisal fiber, which is comparable with the performance of S6A (95 v.s. 100 % and 16.9 v.s. 17.2 %, respectively). To the best of our knowledge, this work represents the first report of gene cloning, heterologous expression, and biochemical characterization of a bifunctional pectinase with separate catalytic domains.
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Design of catalysts by different substituent groups to the ;cut g-C3N4; single layer
NASA Astrophysics Data System (ADS)
Xu, Weiwei; Tang, Chao; Chen, Chongyang; Li, Youyong; Xu, Lai
2017-09-01
Graphitic carbon nitride has been wildly studied as a kind of promising photocatalysts for hydrogen evolution. However, it has a low intrinsic activity. Herein, we designed new periodic structures "cut g-C3N4", and adding the new substituent groups. We employed density functional theory to calculate the charge distribution and catalytic properties of hydrogen evolution on the structures. We got a theoretical view that introducing conjugate substituents can enhance the catalytic performance for hydrogen evolution. Furthermore, it provided a theoretical guidance for the reasonable design of two dimensional non-metallic photocatalysts, with lower activation barrier of the catalytic reaction.
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NASA Astrophysics Data System (ADS)
El Majdoub, Lotfia; Shi, Yasai; Yuan, Yuan; Zhou, Annan; Abutartour, Abubaker; Xu, Qinghong
2015-10-01
Zirconocene catalyst supported on silica gel was prepared for olefin polymerization by surface modification of calcined silica with SiCl4, and the reaction between the modified silica and cyclopentadienyl sodium and ZrCl4. The catalyst was characterized by using Fourier-transform infrared (FT-IR) spectrometer, thermogravimetric (TG), and differential scanning calorimetric (DSC) analytic spectrometer. It was found that the metallocene structure could be formed and connected on silica surface by chemical bond. Initial catalytic tests showed that the supported metallocene was catalytically active (methylaluminoxane as a cocatalyst), producing polymer with higher molecular weight than the metallocene just immobilized on the surface of silica gel.
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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.
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Self-propulsion and interactions of catalytic particles in a chemically active medium.
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.
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H2O-Polyaluminium chloride-TBAB as synergistic catalysts for the synthesis of cyclic carbonate
NASA Astrophysics Data System (ADS)
Liu, X. J.; Yan, P.; Han, Y.
2018-01-01
An efficient catalytic system consisting of H2O, Polyaluminium chloride (PAC) and Tetrabutylammonium bromide (TBAB) was applied to the cycloaddition of carbon dioxide (CO2) to epoxides under mild conditions. Their catalytic cycloaddition activities were found to be well correlated with H2O and polyaluminium chloride, which had a synergetic effect with the halide anion of TBAB. The presence of H2O and PAC could remarkably improve the yield of propylene carbonate (PC) by which the reaction yield is about 4-5 times higher than TBAB. alone.The catalytic system also exhibited excellent cycloaddition activities for various epoxide substrates.
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Fukuta, Yuhei; Ohshima, Takashi; Gnanadesikan, Vijay; Shibuguchi, Tomoyuki; Nemoto, Tetsuhiro; Kisugi, Takaya; Okino, Tatsufumi; Shibasaki, Masakatsu
2004-01-01
Aeruginosin 298-A was isolated from the freshwater cyanobacterium Microcystis aeruginosa (NIES-298) and is an equipotent thrombin and trypsin inhibitor. A variety of analogs were synthesized to gain insight into the structure–activity relations. We developed a versatile synthetic process for aeruginosin 298-A as well as several attractive analogs, in which all stereocenters were controlled by catalytic asymmetric phase-transfer reaction promoted by two-center asymmetric catalysts and catalytic asymmetric epoxidation promoted by a lanthanide–BINOL complex. Furthermore, serine protease inhibitory activities of aeruginosin 298-A and its analogs were examined. PMID:15004282
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Fukuta, Yuhei; Ohshima, Takashi; Gnanadesikan, Vijay; Shibuguchi, Tomoyuki; Nemoto, Tetsuhiro; Kisugi, Takaya; Okino, Tatsufumi; Shibasaki, Masakatsu
2004-04-13
Aeruginosin 298-A was isolated from the freshwater cyanobacterium Microcystis aeruginosa (NIES-298) and is an equipotent thrombin and trypsin inhibitor. A variety of analogs were synthesized to gain insight into the structure-activity relations. We developed a versatile synthetic process for aeruginosin 298-A as well as several attractive analogs, in which all stereocenters were controlled by catalytic asymmetric phase-transfer reaction promoted by two-center asymmetric catalysts and catalytic asymmetric epoxidation promoted by a lanthanide-BINOL complex. Furthermore, serine protease inhibitory activities of aeruginosin 298-A and its analogs were examined.