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MEDOC: A Fast, Scalable, and Mathematically Exact Algorithm for the Site-Specific Prediction of the Protonation Degree in Large Disordered Proteins.
J Chem Inf Model
January 2025
Max-Planck-Institut für Immunbiologie und Epigenetik (MPI-IE), Stübeweg 51, 79108 Freiburg im Breisgau, Germany.
Intrinsically disordered regions are found in most eukaryotic proteins and are enriched with positively and negatively charged residues. While it is often convenient to assume that these residues follow their model-compound p values, recent work has shown that local charge effects (charge regulation) can upshift or downshift side chain p values with major consequences for molecular function. Despite this, charge regulation is rarely considered when investigating disordered regions.
View Article and Find Full Text PDFIn Silico Structural Insights into a Glucanase from Clostridium perfringens and Prediction of Structural Stability Improvement Through Hydrophobic Interaction Network and Aromatic Interaction.
Mol Biotechnol
January 2025
Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.
Glucanases are widely applied in industrial applications such as brewing, biomass conversion, food, and animal feed. Glucanases catalyze the hydrolysis of glucan to produce the sugar hemiacetal through hydrolytic cleavage of glycosidic bonds. Current study aimed to investigate structural insights of a glucanase from Clostridium perfringens through blind molecular docking, site-specific molecular docking, molecular dynamics (MD) simulation, and binding energy calculation.
View Article and Find Full Text PDFDesign and in vitro anticancer assessment of a click chemistry-derived dinuclear copper artificial metallo-nuclease.
Nucleic Acids Res
January 2025
School of Chemical Sciences, Dublin City University, Glasnevin, Dublin 9, Ireland.
Copper compounds with artificial metallo-nuclease (AMN) activity are mechanistically unique compared to established metallodrugs. Here, we describe the development of a new dinuclear copper AMN, Cu2-BPL-C6 (BPL-C6 = bis-1,10-phenanthroline-carbon-6), prepared using click chemistry that demonstrates site-specific DNA recognition with low micromolar cleavage activity. The BPL-C6 ligand was designed to force two redox-active copper centres-central for enhancing AMN activity-to bind DNA, via two phenanthroline ligands separated by an aliphatic linker.
View Article and Find Full Text PDFUnravelling nonclassical beam damage mechanisms in metal-organic frameworks by low-dose electron microscopy.
Nat Commun
January 2025
State Key Laboratory Breeding Base of Green Chemistry Synthesis Technology and College of Chemical Engineering, Center for Electron Microscopy, Institute for Frontier and Interdisciplinary Sciences, Zhejiang University of Technology, Hangzhou, Zhejiang, China.
Recent advances in direct electron detectors and low-dose imaging techniques have opened up captivating possibilities for real-space visualization of radiation-induced structural dynamics. This has significantly contributed to our understanding of electron-beam radiation damage in materials, serving as the foundation for modern electron microscopy. In light of these developments, the exploration of more precise and specific beam damage mechanisms, along with the development of associated descriptive models, has expanded the theoretical framework of radiation damage beyond classical mechanisms.
View Article and Find Full Text PDFFrom Random Perturbation to Precise Targeting: A Comprehensive Review of Methods for Studying Gene Function in Species.
J Fungi (Basel)
December 2024
College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
, a genus of fungi known for its fermentation capability and production of bioactive compounds, such as azaphilone pigments and Monacolin K, have received considerable attention because of their potential in biotechnological applications. Understanding the genetic basis of these metabolic pathways is crucial for optimizing the fermentation and enhancing the yield and quality of these products. However, spp.
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