Correction for 'Atomistic QM/MM simulations of the strength of covalent interfaces in carbon nanotube-polymer composites' by Jacek R. Gołębiowski et al., Phys. Chem. Chem. Phys., 2020, 22, 12007-12014, DOI: 10.1039/d0cp01841d.
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NAC4ED: A high-throughput computational platform for the rational design of enzyme activity and substrate selectivity.
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In silico computational methods have been widely utilized to study enzyme catalytic mechanisms and design enzyme performance, including molecular docking, molecular dynamics, quantum mechanics, and multiscale QM/MM approaches. However, the manual operation associated with these methods poses challenges for simulating enzymes and enzyme variants in a high-throughput manner. We developed the NAC4ED, a high-throughput enzyme mutagenesis computational platform based on the "near-attack conformation" design strategy for enzyme catalysis substrates.
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Pectate lyases, known for their alkaliphilic nature, are ideal for industrial applications that require specific pH conditions, particularly in industries such as textiles and pulp extraction. These enzymes, primarily from the polysaccharide lyase family 1 (PL1) of different microbial sources, play a vital role in polysaccharide degradation. Given the potent pectinolytic activity of Bacillus pectate lyases, targeting these enzymes is crucial for identifying the most effective candidates.
View Article and Find Full Text PDFFirst-principles simulations of the fluorescence modulation of a COX-2-specific fluorogenic probe upon protein dimerization for cancer discrimination.
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View Article and Find Full Text PDFHow Can One Metal Power Nucleic Acid Phosphodiester Bond Cleavage by a Nuclease? Multiscale Computational Studies Highlight a Diverse Mechanistic Landscape.
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Despite the remarkable resistance of the nucleic acid phosphodiester backbone to degradation affording genetic stability, the P-O bond must be broken during DNA repair and RNA metabolism, among many other critical cellular processes. Nucleases are powerful enzymes that can enhance the uncatalyzed rate of phosphodiester bond cleavage by up to ∼10-fold. Despite the most well accepted hydrolysis mechanism involving two metals (M to activate a water nucleophile and M to stabilize the leaving group), experimental evidence suggests that some nucleases can use a single metal to facilitate the chemical step, a controversial concept in the literature.
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Photosystem II (PSII) catalyzes light-driven water oxidation that releases dioxygen into our atmosphere and provides the electrons needed for the synthesis of biomass. The catalysis occurs in the oxygen-evolving oxo-manganese-calcium (MnOCa) cluster that drives the oxidation and deprotonation of substrate water molecules leading to the O formation. However, despite recent advances, the mechanism of these reactions remains unclear and much debated.
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