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Scoring Conformational Metastability of Macrocyclic Peptides with Binding Pose Metadynamics.
J Chem Inf Model
January 2025
Department of Modeling and Informatics, Merck & Co., Inc., Rahway, New Jersey 07065, United States.
Potency optimization of macrocyclic peptides can include both modifying intermolecular interactions and modifying the conformational stability of the bioactive conformation. However, the number of possible modifications is vast. To identify modifications that enhance the stability of the binding conformations in a cost-effective manner, there is a need for a high-throughput in-silico method that scores the conformational stability of these modified molecules.
View Article and Find Full Text PDFChronic Cr(VI) exposure-induced biotoxicity involved in liver microbiota-gut axis disruption in Phoxinus lagowskii Dybowski based on multi-omics technologies.
Environ Pollut
January 2025
Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin 150070, China. Electronic address:
Cr(VI) is widely used in industry and has high toxicity, making it one of the most common environmental pollutants. Long-term exposure to Cr(VI) can cause metabolic disorders and tissue damage. However, the effects of Cr(VI) on liver and gut microbes in fish have rarely been reported.
View Article and Find Full Text PDFTrehalose enhances macrophage autophagy to promote myelin debris clearance after spinal cord injury.
Cell Biosci
January 2025
Department of Orthopaedics, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, China.
Background: Myelin-laden foamy macrophages accumulate extensively in the lesion epicenter, exhibiting characteristics of autophagolysosomal dysfunction, which leads to prolonged inflammatory responses after spinal cord injury (SCI). Trehalose, known for its neuroprotective properties as an autophagy inducer, has yet to be fully explored for its potential to mitigate foamy macrophage formation and exert therapeutic effects in the context of SCI.
Results: We observed that trehalose significantly enhances macrophage phagocytosis and clearance of myelin in a dose-dependent manner in vitro.
Circadian clockwork controls the balance between mitochondrial turnover and dynamics: What is life … without time marking?
Biochim Biophys Acta Bioenerg
January 2025
Department of Clinical and Experimental Medicine, University of Foggia, Foggia, Italy. Electronic address:
Circadian rhythms driven by biological clocks regulate physiological processes in all living organisms by anticipating daily geophysical changes, thus enhancing environmental adaptation. Time-resolved serial multi-omic analyses in vivo, ex vivo, and in synchronized cell cultures have revealed rhythmic changes in the transcriptome, proteome, and metabolome, involving up to 50 % of the mammalian genome. Mitochondrial oxidative metabolism is central to cellular bioenergetics, and many nuclear genes encoding mitochondrial proteins exhibit both circadian and ultradian oscillatory expression.
View Article and Find Full Text PDFLocalized K63 ubiquitin signaling is regulated by VCP/p97 during oxidative stress.
Mol Cell Proteomics
January 2025
Department of Biology, Duke University, Durham, NC, 27708, USA. Electronic address:
Under stress conditions, cells reprogram their molecular machineries to mitigate damage and promote survival. Ubiquitin signaling is globally increased during oxidative stress, controlling protein fate and supporting stress defenses at several subcellular compartments. However, the rules driving subcellular ubiquitin localization to promote concerted response mechanisms remain understudied.
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