We report comparisons between energy-based quantum mechanics/molecular mechanics (QM/MM) and buffered force-based QM/MM simulations in silica. Local quantities-such as density of states, charges, forces, and geometries-calculated with both QM/MM approaches are compared to the results of full QM simulations. We find the length scale over which forces computed using a finite QM region converge to reference values obtained in full quantum-mechanical calculations is ∼10 Å rather than the ∼5 Å previously reported for covalent materials such as silicon. Electrostatic embedding of the QM region in the surrounding classical point charges gives only a minor contribution to the force convergence. While the energy-based approach provides accurate results in geometry optimizations of point defects, we find that the removal of large force errors at the QM/MM boundary provided by the buffered force-based scheme is necessary for accurate constrained geometry optimizations where Si-O bonds are elongated and for finite-temperature molecular dynamics simulations of crack propagation. Moreover, the buffered approach allows for more flexibility, since special-purpose QM/MM coupling terms that link QM and MM atoms are not required and the region that is treated at the QM level can be adaptively redefined during the course of a dynamical simulation.
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mLife
December 2024
Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development School of Chemistry and Molecular Engineering, East China Normal University Shanghai China.
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.
View Article and Find Full Text PDFCarbohydr Res
December 2024
Quantitative Biology Lab, Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT Deemed to Be University), Vellore, Tamil Nadu, India. Electronic address:
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 PDFProtein Sci
January 2025
Departament de Química, Universitat Autònoma de Barcelona, Barcelona, Spain.
Cyclooxygenase-2 (COX-2) plays a crucial role in inflammation and has been implicated in cancer development. Understanding the behavior of COX-2 in different cellular contexts is essential for developing targeted therapeutic strategies. In this study, we investigate the fluorescence spectrum of a fluorogenic probe, NANQ-IMC6, when bound to the active site of human COX-2 in both its monomeric and homodimeric forms.
View Article and Find Full Text PDFJ Phys Chem B
December 2024
Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, Canada T1K 3M4.
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.
View Article and Find Full Text PDFProc Natl Acad Sci U S A
December 2024
Department of Biochemistry and Biophysics, Stockholm University, Stockholm 10691, Sweden.
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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