Catalytic mechanism

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Evidence for the Formation of a Covalent Thiosulfinate Intermediate with Peroxiredoxin in the Catalytic Mechanism of Sulfiredoxin

Evidence for the Formation of a Covalent Thiosulfinate Intermediate with Peroxiredoxin in the Catalytic Mechanism of Sulfiredoxin

The typical 2-Cys peroxiredoxins are thiol-peroxidases involved in the physiology of hydrogen peroxide not only as a toxic but also as a signaling molecule. Coordination of these functions depends on the sulfinylation of the catalytic Cys, a modification reversed by ATP-dependent sulfiredoxin, which specifically reduces the sulfinic acid group of overoxidized 2-Cys peroxiredoxins into a sul- fenic acid. Sulfiredoxin was originally proposed to operate by cova- lent catalysis, with formation of a peroxiredoxin-sulfiredoxin intermediate linked by a thiosulfinate bond between the catalytic Cys of both partners, a hypothesis rejected by a study of the human enzyme. To settle the argument, we investigated the catalytic mechanism of Saccharomyces cerevisiae sulfiredoxin, by the char- acterization of the nature and kinetics of formation of the protein species formed between sulfiredoxin and its substrate in the pres- ence of ATP, using mutants of the non-essential Cys residues of both proteins. We observed the formation of a dithiothreitol-re- ducible peroxiredoxin-sulfiredoxin species using SDS-PAGE and Western blot analysis, and its mass was shown to correspond to a thiosulfinate complex by high resolution mass spectrometry cou- pled to liquid chromatography. We next measured indirectly and directly a rate constant of formation of the thiosulfinate species of ⬃2 min ⴚ1 , for both wild-type and mutant sulfiredoxins, at least equal to the steady-state rate constant of the reaction, with a stoi- chiometry of 1:1 relative to peroxiredoxin. Taken altogether, our results strongly argue in favor of the formation of a covalent thio- sulfinate peroxiredoxin-sulfiredoxin species as an intermediate on the catalytic pathway.
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Substrate binding mode and catalytic mechanism of human heparan sulfate d-glucuronyl C5 epimerase

Substrate binding mode and catalytic mechanism of human heparan sulfate d-glucuronyl C5 epimerase

Fig. 3. Proposed catalytic mechanism of Glce and comparison with lyases. (A) Structural comparison of the catalytic sites of hGlce (Left), heparinase I (Cen- ter; PDB ID code 3ILR) and chondroitin AC lyase (Right; PDB ID code 1RWG) viewed in similar orien- tation, showing the bound substrate/product and key active site residues. In all cases, the hGlce Asn510/Tyr560, heparinase I Gln149/Arg83/Lys353, and chondroitin AC lyase Asn183/His233 residues neutralize the uronic acid carboxyl group. (B) Com- parison of the hGlce and heparinase I lyase catalytic mechanisms. (Top) hGlce catalyzes C5 epimerization of GlcA into IdoA (red arrows) by abstracting the GlcA C5 proton by the general base Tyr578 on one face of GlcA and donating a proton by the general acid Glu499 through a neutral enol intermediate on the opposite face. In the reverse reaction (blue ar- rows), the IdoA C5 proton is abstracted by deproto- nated Glu499, while Tyr578 reprotonates the C5 atom on the opposite side of the uronic acid. (Bot- tom) Heparinase I catalyzes β-elimination of the glycosidic linkage between the −1 and +1 positions of the heparin substrate, with His151 and Tyr357 acting as a general base/acid through an anionic enolate intermediate (adapted with permission from ref. 33; permission conveyed through Copy- right Clearance Center, Inc.). The H-bond network that neutralizes the carboxylate anion at the epi- merization site and lowers the pK a value of the C5
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An auto-catalytic mechanism to model the fission gas release between 600°C and 800°C on UO$_2$ irradiated fuel.

An auto-catalytic mechanism to model the fission gas release between 600°C and 800°C on UO$_2$ irradiated fuel.

An auto-catalytic mechanism to model the fission gas release between 600°C and 800°C on UO_2 irradiated?. fuel.[r]

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Regulation of the type IV secretion ATPase TrwD by magnesium: implications for catalytic mechanism of the secretion ATPase superfamily.

Regulation of the type IV secretion ATPase TrwD by magnesium: implications for catalytic mechanism of the secretion ATPase superfamily.

5. Peña, A., Ripoll-Rozada, J., Zunzunegui, S., Cabezón, E., de la Cruz, F., and Arechaga, I. (2011) Autoinhibitory regulation of TrwK, an essential VirB4 ATPase in type IV secretion systems. J. Biol. Chem. 286, 17376 –17382 6. Rivas, S., Bolland, S., Cabezón, E., Goñi, F. M., and de la Cruz, F. (1997) FIGURE 8. Model of the regulatory mechanism by magnesium of VirB11 ATPases. A proposed catalytic mechanism for VirB11 proteins, adapted from Ref. 8 and extended to the secretion ATPase superfamily (27), taking into consideration the effect of Mg 2⫹ , is shown. Step 1, the nucleotide-free apo form would be flexible with the NTD (orange) and CTD (magenta/green) in equilibrium between an open and closed conformation. The papain site lim- iting the C terminus end (green) is indicated by an arrow. Step 2, high Mg 2⫹ concentrations (similar to the free Mg 2 ⫹ found in bacteria) would induce a
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Catalytic mechanism of Heparinase II investigated by site-directed mutagenesis and the crystal structure with its substrate

Catalytic mechanism of Heparinase II investigated by site-directed mutagenesis and the crystal structure with its substrate

alanine severely impaired degradation of the IdoA-containing sulfated substrate relative to the GlcA-containing sulfated sub- strate. Accordingly, the structural model is consistent with a role of His 202 as a general base for abstraction of the H5 proton FIGURE 6. Proposed mechanism of HepII-catalyzed hydrolysis of heparin and HS substrates based on structural and mutagenesis studies. In the HS hydrolysis (top), Tyr 257 is proposed to function both as a general base to abstract the H5 proton from the GlcA bound in the ⫹1 subsite, and as a general acid to protonate the living group in the ⫺1 subsite. In the heparin hydrolysis (bottom), His 202 is proposed to function as a general base to abstract the H5 proton from the IdoA bound in the ⫹1 subsite, whereas Tyr 257 would fulfill the general acid role to protonate the living group in the ⫺1 subsite. The side chains of Glu 205 , Arg 261 , and His 406 are proposed to serve to neutralize the carboxylate group of the uronic acid in both cases. Distances associated with double-headed dotted arrows are in Å units.
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A new SOS-DFPT approximation for NMR shielding calculations : the Loc.3 correction applied to the catalytic mechanism of Serine Proteases

A new SOS-DFPT approximation for NMR shielding calculations : the Loc.3 correction applied to the catalytic mechanism of Serine Proteases

6X11 Statistical analysis of the 17 absolute shieldings calculated with the SOS-DfPT Loc.3 (LDA), other DFI-based and high quality ab initio methods, reLative to experimentaL references.[r]

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An auto-catalytic mechanism to explain the fission gas release between 500°c and 800°c on UO$_2$ irradiated fuel

An auto-catalytic mechanism to explain the fission gas release between 500°c and 800°c on UO$_2$ irradiated fuel

• The High temperature burst studied a lot : it comes from the edge of the fuel pellet (HBS) [2]. • The release at 600°C cannot be explained by a diffusion mechanism. Modeling of the first burst data using a two-step mechanism: 1) a phase of nucleation of gas clusters (a sort of pre- polymerization) and 2) their growth (similar to a polymerization process).

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A specific inorganic triphosphatase from Nitrosomonas europaea: structure and catalytic mechanism

A specific inorganic triphosphatase from Nitrosomonas europaea: structure and catalytic mechanism

Shortly thereafter, Iyer and Aravind (3) observed that the catalytic domains of human 25- kDa ThTPase (1) and CyaB adenylyl cyclase (AC2) from Aeromonas hydrophila (4) define a novel superfamily of domains that, according to these authors, should bind “organic phosphates”. This superfamily was called “CYTH” (CYaB- THiamine triphosphatase), and the presence of orthologs was demonstrated in all three superkingdoms of life. This suggested that CYTH is an ancient family of proteins, and that a representative must have been present in the last universal common ancestor (LUCA) of all extant life forms. It was proposed (3) that this enzymatic domain might play a central role at
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Cyclodipeptide synthases : towards understanding their catalytic mechanism and the molecular bases of their specificity

Cyclodipeptide synthases : towards understanding their catalytic mechanism and the molecular bases of their specificity

experiments, we demonstrated that Phe1tRNA Phe is the first substrate to interact with AlbC1IMI rather than Leu1tRNA Leu substrate. Our preliminary results demonstrate that the CDPS AlbC1IMI is of great interest and studies on it should pursue. The last part of our results ( ) concerns published work on the first characterized CDPS from an animal, that is Nvec1CDPS2 identified in the sea anemone Nematostella vectensis. Nvec1CDPS2 mostly produces in vivo Trp1containing cyclodipeptides, thus exhibits a different specificity than other characterized bacterial CDPSs which synthesize Phe1, Tyr1, and Leu1containing cyclodipeptides. This difference in specificity could be attributed to residues constituting the catalytic pocket because Nvec1CDPS2 contains in the pocket a higher proportion of aromatic residues than the other characterized CDPSs. This finding also suggests that the substrate specificity of CDPSs is related to their catalytic pockets. The characterization of Nvec1CDPS2 is of great significance because we have experimentally proved the existence of CDPS in the animal. Otherwise, other four eukaryotic genomes have been found to encode CDPSs: the fungi Gibberella zeae and Fusarium oxysporum , the annelid Platynereis dumerilii and the protozoa Ichthyophthirius multifiliis (Aravind et al. 2010; Belin et al. 2012).
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Crystal structure and catalytic mechanism of the essential m¹ G37 tRNA methyltransferase TrmD from Pseudomonas aeruginosa

Crystal structure and catalytic mechanism of the essential m¹ G37 tRNA methyltransferase TrmD from Pseudomonas aeruginosa

PaTrmD competitively with respect to SAM (Fig. 8A) and uncompetitively with respect to tRNA Leu(GAG) (Fig. 8B). The K i of SFG with respect to SAM and tRNA were deter- mined as 0.41 ± 0.07 µM and 6.4 ± 0.8 µM, respectively. Based on these results, there are two models —random and ordered —that explain a ternary-complex mechanism for PaTrmD. Interestingly, the binding order of substrates appears to vary among PaTrmD, EcTrmD (Redlak et al. 1997; Brulé et al. 2004), and HiTrmD (Ito et al. 2015; Christian et al. 2016). Studies using product inhibition analysis suggested that EcTrmD uses a random-order binding mechanism, whereas structural studies of HiTrmD suggested a compulsory-order binding mecha- nism in which SAM binds first followed by tRNA (Ito et al. 2015; Christian et al. 2016). We cannot completely rule out the possibility that these variations may arise from methodological differences. Here a simple comparison of the putative cellular concentrations of SAM 180 µM (Bennett et al. 2009) with the dissociation constant of the complex (14.4 µM, Fig. 7A) indicate that most of PaTrmD molecules in vivo are preloaded with SAM, thus favoring a sequential model where tRNA binds to this preformed bi- nary complex, leading to further structural rearrange- ments, as suggested in Figure 4 and proposed by Ito et al. (2015). The results of our studies with PaTrmD reveal novel features of this tRNA-modifying enzyme that may ex- plain its unique sensitivity to SAM-competitive inhibitors (Hill et al. 2013).
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Streptomyces albus G serine β-lactamase. Probing of the catalytic mechanism via molecular modelling of mutant enzymes

Streptomyces albus G serine β-lactamase. Probing of the catalytic mechanism via molecular modelling of mutant enzymes

heterotoms) of hydrogen bonds around R73 within the active site of the K73R Streptomyces albus G Ii-lactamase mutant and the Michaelis complex formed with benzylpenicillin (' +pen').. Bo[r]

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Conservative-Bayesian Mechanism Design

Conservative-Bayesian Mechanism Design

Comment. Although player i gets no allocation, he gets a reward according to Brier’s scoring rule. The negative price indicates that the mechanism transfers money to player i. Since we insist that our players do not incur negative utilities ex post, the boundedness of Brier’s scoring rule is crucial here. Notation. Since a direct (possibly randomized) centralized-Bayesian assignment mechanism M may be conceptualized as receiving (the description of) a type-distribution D as a separate input, we use a slightly different notation to denote M’s revenue than the one used for decentralized-Bayesian mechanisms. Namely, if M always flips ` coins, then letting v be a type profile and r ∈ {0, 1} ` , M(v, D, r) denotes the unique
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Atmospheric plasma-catalytic treatment of methyl orange

Atmospheric plasma-catalytic treatment of methyl orange

Atmospheric Plasma-Catalytic Treatment of Methyl Orange B. Benstaali 1 , S. Haji 1 , N. Al-Bastaki 1 , J. L. Brisset 2 , A. Addou 3 1 Chemical Engineering Department, College of Engineering, University of Bahrain, Bahrain. 2 Laboratoire d'Electrochimie (L.E.I.C.A.); UFR Sciences, Université de Rouen; France. 3 Laboratoire des Sciences et Techniques et Valorisation, Université de Mostaganem, Algeria,

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Highly chemoselective catalytic transfer hydrosilylation of aldehydes

Highly chemoselective catalytic transfer hydrosilylation of aldehydes

To circumvent these limitations, we have developed a conceptual alternative consisting in the utilization of silyl formates (R 3 SiOC(O)H), readily prepared fram formic [r]

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The utilization of Fe-doped g-C 3 N 4 in a heterogeneous photo-Fenton-like catalytic system: the effect of different parameters and a system mechanism investigation

The utilization of Fe-doped g-C 3 N 4 in a heterogeneous photo-Fenton-like catalytic system: the effect of different parameters and a system mechanism investigation

The utilization of Fe-doped g-C 3 N 4 in a heterogeneous photo-Fenton-like catalytic system: the effect of different parameters and a system mechanism investigation Wei Luo, Wenyu Huang, Xiaoqing Feng, Ying Huang, Xiongwei Song, Hongfei Lin, Shuangfei Wang, Gilles Mailhot

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Lifeboat Release Mechanism Tests

Lifeboat Release Mechanism Tests

These tests were repeated for aft pulls at 50°, side pulls at 20° and with the release cable disconnected. 4.3 Off-Load Test Series Similar to the Inline Test Series, the off-load tests were done using the MTA to load the hook along its vertical axis. Unlike the inline series however, there were no cam angle variations. Since the off-load hook is designed to release only when the load is off, the mechanism was tested to measure the torque required to release when the load is being applied. A preset load amount was applied to the hook, at which point a torque wrench was used to open the release mechanism. Initially, the torque was applied with a torque wrench. For the latter tests, a 10-1 torque multiplier was used, and can be seen along with the torque wrench in Figure 4-1. The loads applied are listed in Table 4- 14. The top row lists the tests that used the torque wrench, and the bottom row applied the 10-1 torque multiplier.
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Compliant mechanism learning toolkit

Compliant mechanism learning toolkit

models for the constraints imposed by such a flexure have been introduced in a unique way by Douglass Blanding in Exact Constraint: Machine Design Using Kinematic Principles (1999[r]

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Degradation of paracetamol by catalytic wet air oxidation and sequential adsorption - Catalytic wet air oxidation on activated carbons

Degradation of paracetamol by catalytic wet air oxidation and sequential adsorption - Catalytic wet air oxidation on activated carbons

The concern about the fate of pharmaceutical products has raised owing to the increasing contamination of rivers, lakes and groundwater. The aim of this paper is to evaluate two different processes for paracetamol removal. The catalytic wet air oxidation (CWAO) of paracetamol on activated carbon was investigated both as a water treatment technique using an autoclave reactor and as a regenerative treatment of the carbon after adsorption in a sequential fixed bed process. Three activated carbons (ACs) from different source materials were used as catalysts: two microporous basic ACs (S23 and C1) and a meso- and micro-porous acidic one (L27). During the first CWAO experiment the adsorption capacity and catalytic performance of fresh S23 and C1 were higher than those of fresh L27 despite its higher surface area. This situation changed after AC reuse, as finally L27 gave the best results after five CWAO cycles. Respirometry tests with activated sludge revealed that in the studied conditions the use of CWAO enhanced the aerobic biodegradability of the effluent. In the ADOX process L27 also showed better oxidation performances and regeneration efficiency. This different ageing was examined through AC physico- chemical properties.
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Reconfigurable cable driven parallel mechanism

Reconfigurable cable driven parallel mechanism

29 attachment point is constrained to move along its own linear rails. In the second type, the attachment points were constrained to move along a circular base. The authors concluded that the circular base had the better wrench closure workspace where the mobile platform had the ability to reach any position and orientation within the installation workspace. Tourajizadeh et al. [85] presented an optimal regulation for an under constrained six degrees of freedom mechanism driven by six cables to maximize the dynamic load capacity of the mobile platform for a predefined path while avoiding cables interference. However, in case of a near collision between two cables, the orientation of the mobile platform is changed to avoid interference, which makes this approach not valid for some applications that require vertical movements, such as pick-and-place. Arsenault [86] studied the interference-free wrench feasible workspace of a 3 DOF translational tensegrity mechanism where this kind of parallel mechanisms consists of both cables and rigid links. The authors proposed a new design by replacing the rigid links by equivalent compression spring legs (ECSLs) to avoid interference between the mechanisms links, however, the author concluded that there is still a possibility that cables will collide with suggested ECSLs unlike the suggested approach in this research study to detect and eliminate cables interference.
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Annealing twin formation mechanism

Annealing twin formation mechanism

Fig. 2.13. In situ EBSD maps of the last three annealing steps in the grain growth regime. The black lines represent the general grain boundaries defined by a disorientation angle above 5°; the white lines denote the twin boundaries (same orientation color code as in Fig. 2.3. Note the (apparently) island grain (green) disappears as the pale blue grain grows in from the right. The decrease in annealing twin density can be attributed to disappearance mechanisms shown in Fig. 2.13. In all three examples, small grains containing several twin boundaries were consumed by large grains, which grew without producing new twins. Such a microstructural evolution is of course energetically favorable. Meanwhile, this is not the only possible annealing twin evolution mechanism observed during grain growth. The shrinkage of twin lamellae caused especially by the migration of incoherent twin boundary segments was reported previously in a Pb-based alloy [Song 2007] and in 304L stainless steel [Jin 2013 and next section]. Besides, a few annealing twins are found formed at triple junctions during grain growth in a 3D-XRD dataset of a pure nickel sample [Lin 2014]. These creation events are obviously too rare to counterbalance those leading to twin disappearance, since the net balance is negative.
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