Here we demonstrate quantitation of stimuli-induced proteome dynamics in primary cells by combining the power of bio-orthogonal noncanonical amino acid tagging (BONCAT) and stable-isotope labeling of amino acids in cell culture (SILAC). In conjunction with nanoscale liquid chromatography-tandem mass spectrometry (nanoLC-MS/MS), quantitative noncanonical amino acid tagging (QuaNCAT) allowed us to monitor the early expression changes of >600 proteins in primary resting T cells subjected to activation stimuli.
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http://dx.doi.org/10.1038/nmeth.2401 | DOI Listing |
Expert Rev Proteomics
January 2025
Biological and Environmental Science & Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Saudi Arabia.
Introduction: The DeepMind's AlphaFold (AF) has revolutionized biomedical research by providing both experts and non-experts with an invaluable tool for predicting protein structures. However, while AF is highly effective for predicting structures of rigid and globular proteins, it is not able to fully capture the dynamics, conformational variability, and interactions of proteins with ligands and other biomacromolecules.
Areas Covered: In this review, we present a comprehensive overview of the latest advancements in 3D model predictions for biomacromolecules using AF.
JBMR Plus
February 2025
Department of Osteology and Biomechanics, University Medical Center Hamburg-Eppendorf, 22529 Hamburg, Germany.
Advanced glycation end products (AGEs) accumulate in various tissues, including bone, due to aging and conditions like diabetes mellitus. To investigate the effects of AGEs on bone material quality and biomechanical properties, an study utilizing human tibial cortex, sectioned into 90 beams, and randomly assigned to three mechanical test groups was performed. Each test group included ribose ( = 0.
View Article and Find Full Text PDFNucleic Acids Res
January 2025
EGM CNRS, Université Paris-Cité,Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France.
Faced with nutritional stress, some bacteria form endospores capable of enduring extreme conditions for long periods of time; yet the function of many proteins expressed during sporulation remains a mystery. We identify one such protein, KapD, as a 3'-exoribonuclease expressed under control of the mother cell-specific transcription factors SigE and SigK in Bacillus subtilis. KapD dynamically assembles over the spore surface through a direct interaction with the major crust protein CotY.
View Article and Find Full Text PDFJ Integr Plant Biol
January 2025
Institute of Advanced Biotechnology and School of Medicine, Southern University of Science and Technology, Shenzhen, 518055, China.
In plants, proteins are fundamental to virtually all biological processes, such as photosynthesis, signal transduction, metabolic regulation, and stress responses. Studying protein distribution, function, modifications, and interactions at the cellular and tissue levels is critical for unraveling the complexities of these biological pathways. Protein abundance and localization are highly dynamic and vary widely across the proteome, presenting a challenge for global protein quantification and analysis.
View Article and Find Full Text PDFAm J Physiol Gastrointest Liver Physiol
January 2025
Metabolism and Nutrition Department. NOVA Medical School, Faculdade de Ciências Médicas, NMS, FCM, Universidade NOVA de Lisboa. Lisbon, Portugal.
Appetite, as the internal drive for food intake, is often dysregulated in a broad spectrum of conditions associated with over- and under-nutrition across the lifespan. Appetite regulation is a complex, integrative process comprising psychological and behavioral events, peripheral and metabolic inputs, and central neurotransmitter and metabolic interactions. The microbiota-gut-brain axis has emerged as a critical mediator of multiple physiological processes, including energy metabolism, brain function, and behavior.
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