Use of conformationally restricted pyridinium α-D-N-acetylneuraminides to probe specificity in bacterial and viral sialidases

2005 ◽  
Vol 83 (2) ◽  
pp. 115-122 ◽  
Author(s):  
Jacqueline N Watson ◽  
Tara L Knoll ◽  
Johnny H Chen ◽  
Doug T.H Chou ◽  
Thor J Borgford ◽  
...  
Keyword(s):  
Conformational Change ◽  
Conformationally Restricted ◽  
Rate Determining Step ◽  
Bacterial Enzyme ◽  
Catalytically Active ◽  
High Sequence Homology ◽  
Catalytic Mechanisms ◽  
Different Origins ◽  
Leaving Group Ability ◽  
Single Enzyme

Investigations into subtle changes in the catalytic activity of sialidases have been performed using enzymes from several different origins, and their results have been compared. This work highlights the potential pitfalls encountered when extending conclusions derived from mechanistic studies on a single enzyme even to those with high-sequence homology. Specifically, a panel of 5 pyridinium N-acetylneuraminides were used as substrates in a study that revealed subtle differences in the catalytic mechanisms used by 4 different sialidase enzymes. The lowest reactivity towards the artificial (pyridinium) substrates was displayed by the Newcastle disease virus hemagglutinin-neuraminidase. Moreover, in reactions involving aryl N-acetylneuraminides, the activity of the Newcastle enzyme was competitively inhibited by the 3,4-dihydro-2H-pyrano[3,2-c]pyridinium compound with a Ki = 58 µmol/L. Alternatively, the 3 bacterial enzymes tested, from Salmonella typhimurium, Clostridium perfringens, and Vibrio cholerae, were catalytically active against all members of the panel of substrates. Based on the observed effect of leaving-group ability, it is proposed that the rate-determining step for kcat (and likely for kcat/Km as well) with each bacterial enzyme is as follows: sialylation, which is concerted with conformational change for V. cholerae; and conformational change for S. typhimurium and C. perfringens.Key words: sialidases, neuraminidases, sialic acids, glycosidase, mechanism.

scholarly journals Direct Single-Enzyme Biomineralization of Catalytically Active Ceria and Ceria–Zirconia Nanocrystals

ACS Nano ◽  
2017 ◽  
Vol 11 (3) ◽  
pp. 3337-3346 ◽  
Author(s):  
Christopher D. Curran ◽  
Li Lu ◽  
Yue Jia ◽  
Christopher J. Kiely ◽  
Bryan W. Berger ◽  
...  
Keyword(s):  
Catalytically Active ◽  
Single Enzyme

Formic Acid Mediated Direct Z-Selective Reductive Coupling of Dienes and Aldehydes

2019 ◽  
Author(s):  
Christopher Cooze ◽  
Raphael Dada ◽  
Rylan Lundgren
Keyword(s):  
Formic Acid ◽  
Kinetic Analysis ◽  
Reductive Coupling ◽  
Ligand Dissociation ◽  
Rate Determining Step ◽  
Catalytically Active ◽  
Rapid Generation ◽  
Metal Catalyzed ◽  
Chain Walking

We demonstrate that formic acid mediates the Rh-catalyzed, Z-selective coupling of dienes and aldehydes. The process is distinguished by broad tolerance towards reducible or electrophilic groups. Kinetic analysis suggests that generation of the catalytically active Rh-intermediate by ligand dissociation is the rate determining step. The rapid generation and trapping of Rh-allyl intermediates is key to preventing chain-walking isomerization events that plague related protocols. Insights gained through this study may have wider implications in selective metal-catalyzed hydrofunctionalization reactions.<br>

On the water-promoted mechanism of peptide cleavage by carboxypeptidase A. A theoretical study

1994 ◽  
Vol 72 (10) ◽  
pp. 2077-2083 ◽  
Author(s):  
Silvia Alvarez-Santos ◽  
Angels González-Lafont ◽  
José M. Lluch ◽  
Baldomero Oliva ◽  
Francesc X. Avilés
Keyword(s):  
Theoretical Calculations ◽  
Peptide Bond ◽  
Proton Acceptor ◽  
Carboxypeptidase A ◽  
Peptide Cleavage ◽  
High Enthalpy ◽  
Rate Determining Step ◽  
Catalytic Mechanisms ◽  
Catalyzed Reactions ◽  
Enzyme Catalyzed Reactions

The water-promoted pathway of peptide cleavage by carboxypeptidase A has been studied by semiempirical (AM1) quantum mechanical calculations. A relatively large model for the CPA-active site elements plus substrate has been designed, using two imidazoles and one acetate as the Zn2+ ligands, acetate as the proton acceptor (simulating Glu-270), and N-ethylacetamide as the peptide-like substrate. This model, although simpler than the natural one, is one of the largest used for theoretical calculations on CPA catalytic mechanisms. To ensure that this model is able to mimic the natural system, it has been compared with the structure of the (Gly)3-L-Tyr + water + CPA complex resulting from several molecular dynamics/energy minimization simulations. Among the different steps involved in the water-promoted pathway proposed by Lipscomb's group, the attack of the oxygen atom that comes from the activated water molecule to the carbon atom of the peptide bond of the substrate has been found to be the rate-determining step, with a high enthalpy barrier of 37.9 kcal/mol. However, this enthalpy barrier is dramatically decreased when a positive charge, simulating Arg-127, is included near the scissile carbonyl. The reported results seem to favour the occurrence of the mechanism studied and indicate the limitations of using simple elements for the theoretical analysis of enzyme-catalyzed reactions.

Formic Acid Mediated Direct Z-Selective Reductive Coupling of Dienes and Aldehydes

2019 ◽  
Author(s):  
Christopher Cooze ◽  
Raphael Dada ◽  
Rylan Lundgren
Keyword(s):  
Formic Acid ◽  
Kinetic Analysis ◽  
Reductive Coupling ◽  
Ligand Dissociation ◽  
Rate Determining Step ◽  
Catalytically Active ◽  
Rapid Generation ◽  
Metal Catalyzed ◽  
Chain Walking

We demonstrate that formic acid mediates the Rh-catalyzed, Z-selective coupling of dienes and aldehydes. The process is distinguished by broad tolerance towards reducible or electrophilic groups. Kinetic analysis suggests that generation of the catalytically active Rh-intermediate by ligand dissociation is the rate determining step. The rapid generation and trapping of Rh-allyl intermediates is key to preventing chain-walking isomerization events that plague related protocols. Insights gained through this study may have wider implications in selective metal-catalyzed hydrofunctionalization reactions.<br>

scholarly journals H.p.l.c. separation and study of the charge isomers of human placental glutathione transferase

1986 ◽  
Vol 239 (1) ◽  
pp. 53-57 ◽  
Author(s):  
L L Radulovic ◽  
A P Kulkarni
Keyword(s):  
Conformational Change ◽  
Glutathione Transferase ◽  
Tissue Concentration ◽  
Polyacrylamide Gel Electrophoresis ◽  
Kinetic Studies ◽  
Anionic Form ◽  
Net Charge ◽  
Catalytically Active ◽  
Low Activity

Glutathione transferase (GST) from human placenta was purified by affinity chromatography and anion-exchange h.p.l.c. The enzyme exhibited different chromatographic and electrophoretic behaviours according to the concentration of GSH, suggesting a possible change in the net charge of the molecule and a concomitant conformational change due to ligand binding. Two interconvertible forms were quantitatively separated into distinct catalytically active states by h.p.l.c. Depending upon the GSH concentration, polyacrylamide-gel electrophoresis revealed the presence of one or two bands. A Kd of 0.42 mM for GSH was determined fluorimetrically. The loss in intrinsic fluorescence also suggested a conformational change in the enzyme. Kinetic studies using ethacrynic acid were conducted to determine whether the presumed conformational change could effect the catalytic capability of placental GST. A biphasic response in initial velocities was observed with increasing concentrations of GSH. Two apparent Km values of 0.38 and 50.27 mM were obtained for GSH, whereas Vmax. values showed a 46-fold difference. It was concluded that the enzyme assumes a highly anionic form in the presence of a low GSH concentration, whereas it is converted into relatively weaker anionic form when its immediate environment contains a high GSH concentration. Since the average tissue concentration of total GSH was estimated at 0.11 mM for term placenta, the results suggest that the high-affinity-low-activity conformer would predominate in vivo.

scholarly journals Nickel Ferrocyanide as High-Performance Next Generation Electrocatalyst for Urea Oxidation

2020 ◽  
Author(s):  
Shi-Kui Geng ◽  
Yao Zheng ◽  
Shan-Qing Li ◽  
Xu Zhao ◽  
Jun Hu ◽  
...  
Keyword(s):  
Water Oxidation ◽  
High Performance ◽  
Environmental Science ◽  
Supported Catalysts ◽  
Reaction Pathway ◽  
Next Generation ◽  
Molecular Catalyst ◽  
Rate Determining Step ◽  
Catalytically Active ◽  
Nickel Ferrocyanide

Abstract Urea oxidation, a key process in energy and environmental science, faces challenges because of the insufficient understanding of its mechanism and the lack of efficient catalysts. Here we demonstrate that nickel ferrocyanide (Ni2Fe(CN)6) molecular catalyst supported on Ni form can drive urea oxidation reaction (UOR) with the record electrochemical activity and stability among all supported catalysts reported so far. A combination of kinetics data, in-situ spectroscopic measurements and energy computations suggests a new UOR pathway that delivers such outstanding performance. Different from most studied Ni-based catalysts with NiOOH derivative as a real catalytically active site for UOR, Ni2Fe(CN)6 appears to be a next-generation catalyst able to directly facilitate a two-step reaction pathway involving a critical reaction of intermediate ammonia’s production (on Ni site) and oxidation (on Fe site). Due to the alternative rate-determining step with a more favorable thermal energetics, Ni2Fe(CN)6 broke the limiting activity of the reported so far UOR catalysts. As a result, the UOR process on Ni2Fe(CN)6 can replace conventional water oxidation process in various energy-saving systems for hydrogen and hydrogen peroxide production.

Anisotropy of damage productions in electron irradiated molybdenum

1978 ◽  
Vol 36 (1) ◽  
pp. 354-355
Author(s):  
K. Izui ◽  
S. Furuno ◽  
H. Otsu ◽  
T. Nishida ◽  
H. Maeta
Keyword(s):  
Electron Flux ◽  
Threshold Energy ◽  
High Energy ◽  
Voltage Electron ◽  
High Voltage Electron Microscope ◽  
Displacement Threshold ◽  
The Mean ◽  
Channeling Effect ◽  
Different Origins ◽  
Threshold Energies

Anisotropy of damage productions in crystals due to high energy electron bombardment are caused from two different origins. One is an anisotropic displacement threshold energy, and the other is an anisotropic distribution of electron flux near the atomic rows in crystals due to the electron channeling effect. By the n-beam dynamical calculations for germanium and molybdenum we have shown that electron flux at the atomic positions are from ∽4 to ∽7 times larger than the mean incident flux for the principal zone axis directions of incident 1 MeV electron beams, and concluded that such a locally increased electron flux results in an enhanced damage production. The present paper reports the experimental evidence for the enhanced damage production due to the locally increased electron flux and also the results of measurements of the displacement threshold energies for the <100>,<110> and <111> directions in molybdenum crystals by using a high voltage electron microscope.

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