scholarly journals Tailoring the framework composition of carbon nitride to improve the catalytic efficiency of the stabilised palladium atoms

2017 ◽  
Vol 5 (31) ◽  
pp. 16393-16403 ◽  
Author(s):  
E. Vorobyeva ◽  
Z. Chen ◽  
S. Mitchell ◽  
R. K. Leary ◽  
P. Midgley ◽  
...  
Keyword(s):  
Selective Hydrogenation ◽  
Carbon Nitride ◽  
Catalytic Efficiency ◽  
The Impact ◽  
Framework Composition

The C/N ratio of the carbon nitride lattice is tailored by doping with carbon to assess the impact on the stabilisation of palladium atoms and their catalytic efficiency in the selective hydrogenation of 2-methyl-3-butyn-2-ol.

P219L substitution in human D-amino acid oxidase impacts the ligand binding and catalytic efficiency

2020 ◽  
Vol 168 (5) ◽  
pp. 557-567
Author(s):  
Wanitcha Rachadech ◽  
Yusuke Kato ◽  
Rabab M Abou El-Magd ◽  
Yuji Shishido ◽  
Soo Hyeon Kim ◽  
...  
Keyword(s):  
Amino Acid ◽  
Conformational Changes ◽  
Active Site ◽  
Structural Changes ◽  
Catalytic Efficiency ◽  
Acid Oxidase ◽  
Wild Type ◽  
Amino Acid Oxidase ◽  
Adenine Ring ◽  
The Impact

Abstract Human D-amino acid oxidase (DAO) is a flavoenzyme that is implicated in neurodegenerative diseases. We investigated the impact of replacement of proline with leucine at Position 219 (P219L) in the active site lid of human DAO on the structural and enzymatic properties, because porcine DAO contains leucine at the corresponding position. The turnover numbers (kcat) of P219L were unchanged, but its Km values decreased compared with wild-type, leading to an increase in the catalytic efficiency (kcat/Km). Moreover, benzoate inhibits P219L with lower Ki value (0.7–0.9 µM) compared with wild-type (1.2–2.0 µM). Crystal structure of P219L in complex with flavin adenine dinucleotide (FAD) and benzoate at 2.25 Å resolution displayed conformational changes of the active site and lid. The distances between the H-bond-forming atoms of arginine 283 and benzoate and the relative position between the aromatic rings of tyrosine 224 and benzoate were changed in the P219L complex. Taken together, the P219L substitution leads to an increase in the catalytic efficiency and binding affinity for substrates/inhibitors due to these structural changes. Furthermore, an acetic acid was located near the adenine ring of FAD in the P219L complex. This study provides new insights into the structure–function relationship of human DAO.

Highly Selective Hydrogenation of Phenol and Derivatives over a Pd@Carbon Nitride Catalyst in Aqueous Media

2011 ◽  
Vol 133 (8) ◽  
pp. 2362-2365 ◽  
Author(s):  
Yong Wang ◽  
Jia Yao ◽  
Haoran Li ◽  
Dangsheng Su ◽  
Markus Antonietti
Keyword(s):  
Selective Hydrogenation ◽  
Carbon Nitride ◽  
Aqueous Media

scholarly journals Functional and Structural Characterization of OXA-935, a Novel OXA-10-family β-lactamase from Pseudomonas aeruginosa

2021 ◽  
Author(s):  
Nathan B Pincus ◽  
Monica Rosas-Lemus ◽  
Samuel WM Gatesy ◽  
Ludmilla A. Shuvalova ◽  
Joseph Brunzelle ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Amino Acid ◽  
Clonal Complex ◽  
Genomic Analysis ◽  
Catalytic Efficiency ◽  
Multidrug Resistant ◽  
Extended Spectrum ◽  
The Impact ◽  
Lactamase Inhibitor

Resistance to antipseudomonal penicillins and cephalosporins is often driven by the overproduction of the intrinsic β-lactamase AmpC. However, OXA-10-family β-lactamases are a rich source of resistance in Pseudomonas aeruginosa. OXA β-lactamases have a propensity for mutation leading to extended spectrum cephalosporinase and carbapenemase activity. In this study, we identified isolates from a subclade of the multidrug-resistant (MDR) high risk clonal complex CC446 with resistance to ceftazidime. Genomic analysis revealed that these isolates harbored a plasmid containing a novel allele of blaOXA-10, named blaOXA-935, which was predicted to produce an OXA-10 variant with two amino acid substitutions: an aspartic acid instead of glycine at position 157 and a serine instead of phenylalanine at position 153. The G157D mutation, present in OXA-14, is associated with resistance to ceftazidime. Deletion of blaOXA-935 restored sensitivity to ceftazidime and susceptibility profiling of P. aeruginosa laboratory strains expressing blaOXA-935 revealed that OXA-935 conferred ceftazidime resistance. To better understand the impact of the variant amino acids, we determined the crystal structures of OXA-14 and OXA-935. In contrast, both monomers of OXA-935 were decarbamylated at K70, and the F153S mutation conferred increased flexibility to the omega (Ω) loop. Compared to OXA-14, the catalytic efficiency of OXA-935 for nitrocefin was significantly reduced. Amino acid changes that confer extended spectrum cephalosporinase activity to OXA-10-family β-lactamases are concerning given rising reliance on novel β-lactam/β-lactamase inhibitor combinations such as ceftolozane-tazobactam and ceftazidime-avibactam to treat MDR P. aeruginosa infections.

scholarly journals Evaluating Group I Intron Catalytic Efficiency in Mammalian Cells

1999 ◽  
Vol 19 (10) ◽  
pp. 6479-6487 ◽  
Author(s):  
Meredith B. Long ◽  
Bruce A. Sullenger
Keyword(s):  
Rna Polymerase Ii ◽  
Mammalian Cells ◽  
Catalytic Efficiency ◽  
Human Cells ◽  
The Self ◽  
Group I Introns ◽  
Cellular Environment ◽  
Group I ◽  
Self Splicing ◽  
The Impact

ABSTRACT Recent reports have demonstrated that the group I ribozyme fromTetrahymena thermophila can performtrans-splicing reactions to repair mutant RNAs. For therapeutic use, such ribozymes must function efficiently when transcribed from genes delivered to human cells, yet it is unclear how group I splicing reactions are influenced by intracellular expression of the ribozyme. Here we evaluate the self-splicing efficiency of group I introns from transcripts expressed by RNA polymerase II in human cells to directly measure ribozyme catalysis in a therapeutically relevant setting. Intron-containing expression cassettes were transfected into a human cell line, and RNA transcripts were analyzed for intron removal. The percentage of transcripts that underwent self-splicing ranged from 0 to 50%, depending on the construct being tested. Thus, self-splicing activity is supported in the mammalian cellular environment. However, we find that the extent of self-splicing is greatly influenced by sequences flanking the intron and presumably reflects differences in the intron’s ability to fold into an active conformation inside the cell. In support of this hypothesis, we show that the ability of the intron to fold and self-splice from cellular transcripts in vitro correlates well with the catalytic efficiency observed from the same transcripts expressed inside cells. These results underscore the importance of evaluating the impact of sequence context on the activity of therapeutic group I ribozymes. The self-splicing system that we describe should facilitate these efforts as well as aid in efforts at enhancing in vivo ribozyme activity for various applications of RNA repair.

scholarly journals Local Distortions in a Prototypical Zeolite Framework Containing Double Four-Ring Cages: The Role of Framework Composition and Organic Guests

2020 ◽  
Author(s):  
Michael Fischer ◽  
Linus Freymann
Keyword(s):  
Density Functional ◽  
Zeolite Framework ◽  
Functional Theory ◽  
Organic Structure ◽  
Judicious Choice ◽  
Dynamics Simulations ◽  
The Impact ◽  
Local Distortions ◽  
Framework Composition

<p>Cube-like double four-ring (<i>d4r</i>) cages are among the most frequent building units of zeolites and zeotypes. In materials synthesised in fluoride-containing media, the fluoride anions are preferentially incorporated in these cages. In order to study the impact of framework composition and organic structure-directing agents (OSDAs) on the possible occurrence of local distortions of fluoride-containing <i>d4r</i> cages, density functional theory (DFT) calculations and DFT-based molecular dynamics simulations were performed for AST-type zeotypes, considering four different compositions (SiO<sub>2</sub>, GeO<sub>2</sub>, AlPO<sub>4</sub>, GaPO<sub>4</sub>) and two different OSDA cations (tetramethylammonium [TMA] and quinuclidinium [QNU]). All systems except SiO<sub>2</sub>-AST show significant deformations, with a pyritohedron-like distortion of the <i>d4r</i> cages occurring in GeO<sub>2</sub>- and GaPO<sub>4</sub>-AST, and a displacement of the fluoride anions towards one of the corners of the cage in AlPO<sub>4</sub>- and GaPO<sub>4</sub>-AST. While the distortions occur at random in TMA-containing zeotypes, they exhibit a preferential orientation in systems that incorporate QNU cations. </p><p>In addition to providing detailed understanding of the local structure of a complex host-guest system on the picosecond timescale, this work indicates the possibility to stabilise ordered distortions through a judicious choice of the OSDA, which might enable a tuning of the material’s properties.</p>

ChemInform Abstract: Highly Selective Hydrogenation of Phenol and Derivatives over a Pd@Carbon Nitride Catalyst in Aqueous Media.

ChemInform ◽  
2011 ◽  
Vol 42 (27) ◽  
pp. no-no ◽  
Author(s):  
Yong Wang ◽  
Jia Yao ◽  
Haoran Li ◽  
Dangsheng Su ◽  
Markus Antonietti
Keyword(s):  
Selective Hydrogenation ◽  
Carbon Nitride ◽  
Aqueous Media

scholarly journals Prediction of Deleterious Non-synonymous SNPs of Human STK11 Gene by Combining Algorithms, Molecular Docking, and Molecular Dynamics Simulation

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Md. Jahirul Islam ◽  
Akib Mahmud Khan ◽  
Md. Rimon Parves ◽  
Md Nayeem Hossain ◽  
Mohammad A. Halim
Keyword(s):  
Molecular Dynamics ◽  
Molecular Docking ◽  
Protein Structures ◽  
Catalytic Efficiency ◽  
Suppressor Gene ◽  
Kinase Domain ◽  
Dynamics Simulation ◽  
Nucleotide Polymorphisms ◽  
Stk11 Gene ◽  
The Impact

Abstract Serine-threonine kinase11 (STK11) is a tumor suppressor gene which plays a key role in regulating cell growth and apoptosis. It is widely known as a multitasking kinase and engaged in cell polarity, cell cycle arrest, chromatin remodeling, energy metabolism, and Wnt signaling. The substitutions of single amino acids in highly conserved regions of the STK11 protein are associated with Peutz–Jeghers syndrome (PJS), which is an autosomal dominant inherited disorder. The abnormal function of the STK11 protein is still not well understood. In this study, we classified disease susceptible single nucleotide polymorphisms (SNPs) in STK11 by using different computational algorithms. We identified the deleterious nsSNPs, constructed mutant protein structures, and evaluated the impact of mutation by employing molecular docking and molecular dynamics analysis. Our results show that W239R and W308C variants are likely to be highly deleterious mutations found in the catalytic kinase domain, which may destabilize structure and disrupt the activation of the STK11 protein as well as reduce its catalytic efficiency. The W239R mutant is likely to have a greater impact on destabilizing the protein structure compared to the W308C mutant. In conclusion, these mutants can help to further realize the large pool of disease susceptibilities linked with catalytic kinase domain activation of STK11 and assist to develop an effective drug for associated diseases.

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