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Lipases/acyltransferases, such as CpLIP2 from Candida parapsilosis and CduLAc from Candida dubliniensis, catalyze acyl transfer preferentially over hydrolysis if a suitable nucleophile is present, even in a medium with a high thermodynamic activity of water (a ). These enzymes are related to CAL-A from Moesziomyces antarcticus, which, in comparison, displays a lower acyl transfer ability. The 3D structures of wild types and mutants of CAL-A, CpLIP2, and CduLAc revealed differences in size and hydrophobicity of a large pocket located under the catalytic triad. The kinetic behavior of site-directed mutants confirmed the role of this pocket in competition between methanol and water as the nucleophile acceptor for the deacylation step. The mutations provided a better understanding of key structural determinants for variable levels of acyltransferase ability observed and supported the existence of a complex network of nucleophile interactions within the enzymes. The shape and size of the possible nucleophile pocket identified also suggested that multiple binding sites could exist, which supported the hypothesis of non-overlapping leaving and accepting nucleophile binding sites.
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http://dx.doi.org/10.1002/cbic.201800279 | DOI Listing |
J Chem Inf Model
December 2024
School of Data Science and Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia 22904, United States.
In designing covalent kinase inhibitors (CKIs), the inclusion of electrophiles as attacking warheads demands careful choreography, ensuring not only their presence on the scaffold moiety but also their precise interaction with nucleophiles in the binding sites. Given the limited number of known electrophiles, exploring adjacent chemical space to broaden the palette of available electrophiles capable of covalent inhibition is desirable. Here, we systematically analyze the characteristics of warheads and the corresponding adjacent fragments for use in CKI design.
View Article and Find Full Text PDFNat Commun
December 2024
Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
Reverse transcription of the retroviral RNA genome into DNA is an integral step during HIV-1 replication. Despite a wealth of structural information on reverse transcriptase (RT), we lack insight into the intermediate states of DNA synthesis. Using catalytically active substrates, and a blot/diffusion cryo-electron microscopy approach, we capture 11 structures encompassing reactant, intermediate and product states of dATP addition by RT at 2.
View Article and Find Full Text PDFChemosphere
December 2024
Key Laboratory of Crop Genomics and Molecular Breeding of Jiangsu Province, State Key Laboratory of Hybrid Rice, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225009, China; Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China. Electronic address:
Latest observations indicated that exposure of organic environmental neurotoxins may increase the potential risk of Alzheimer's diseases (AD). As a suspected food-derived risk factor, permethrin, composed of cis-isomer and trans-isomer, is widely used as a broad-spectrum pyrethroid insecticide in agricultural crops for the arthropod pests controlling. Thus, evaluating the impact of permethrin exposure is of great importance to human health.
View Article and Find Full Text PDFJ Agric Food Chem
December 2024
Engineering Research Center of Industrial Microbiology of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian 350117, China.
l-Tryptophan decarboxylase (TDC) and l-3,4-dihydroxyphenylalanine decarboxylase (DDC) catalyze the decarboxylation of l-tryptophan, 5-hydroxytryptophan, and l-3,4-dihydroxyphenylalanine. In this study, we analyzed the amino acid compositions of the substrate-binding pockets of TDC from (TDC) and DDC from (DDC), explored the specificity of key amino acids within these pockets, and elucidated mechanisms influencing substrate selectivity and catalytic activity in both enzymes, using whole-cell catalysis to screen mutants and determine enzymatic kinetic parameters. The results demonstrated that residues Ala-103 and Val-122 in TDC, along with their corresponding sites Thr-82 and Ile-101 in DDC, significantly influence substrate selectivity and catalytic efficiency.
View Article and Find Full Text PDFPolymers (Basel)
October 2024
Department of Chemistry and Biology, University of Salerno, Via Giovanni Piano II, 84084 Fisciano, Salerno, Italy.
A new aluminum complex (NSO)AlMe featuring a hydrogen bond donor on the ligand backbone has been synthesized via the reaction of AlMe with 1-((2-(isopropylamino)phenyl)thio)propan-2-ol (NSO-H) and spectroscopically characterized. In the complex, the aluminum atom is in a distorted tetrahedral coordination sphere determined by the anionic oxygen and neutral nitrogen atoms of the ligand and by the two carbon atoms of the alkyl groups. After proper activation, the complex (NSO)AlMe was able to promote the ring-opening polymerization of -, -lactide, -caprolactone and --butyrolactone.
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