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The two action mechanisms of plant cryptochromes.
Trends Plant Sci
January 2025
Basic Forestry and Plant Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China. Electronic address:
Plant cryptochromes (CRYs) are photolyase-like blue-light receptors that contain a flavin adenine dinucleotide (FAD) chromophore. In plants grown in darkness, CRYs are present as monomers. Photoexcited CRYs oligomerize to form homo-tetramers.
View Article and Find Full Text PDFGenomic clustering tendency of transcription factors reflects phase-separated transcriptional condensates at super-enhancers.
Nucleic Acids Res
January 2025
Department of Genome Sciences, University of Virginia, PO Box 800717, Charlottesville, VA 22908, USA.
Many transcription factors (TFs) have been shown to bind to super-enhancers, forming transcriptional condensates to activate transcription in various cellular systems. However, the genomic and epigenomic determinants of phase-separated transcriptional condensate formation remain poorly understood. Questions regarding which TFs tend to associate with transcriptional condensates and what factors influence their association are largely unanswered.
View Article and Find Full Text PDFA variational graph-partitioning approach to modeling protein liquid-liquid phase separation.
Cell Rep Phys Sci
November 2024
Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA.
Graph neural networks (GNNs) have emerged as powerful tools for representation learning. Their efficacy depends on their having an optimal underlying graph. In many cases, the most relevant information comes from specific subgraphs.
View Article and Find Full Text PDFEnzyme-induced liquid-to-solid phase transition of a mitochondria-targeted AIEgen in cancer theranostics.
Mater Horiz
January 2025
Bioorganic Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur P.O., Bengaluru 560064, Karnataka, India.
Enzyme-instructed self-assembly (EISA) is a promising approach to anti-cancer therapeutics due to its precise targeting and unique cell death mechanism. In this study, we introduce a small molecule, DN6, which undergoes nitroreductase (NTR)-responsive liquid-liquid phase separation (LLPS) followed by a liquid-to-solid phase transition (LST) through a gel-like intermediate state, resulting in the formation of nanoaggregates with spatiotemporal control. The reduced form of DN6 (DN6R), owing to its aggregation-induced emission (AIE) and mitochondria-targeting capabilities, has been employed for organelle-specific imaging of tumor hypoxia.
View Article and Find Full Text PDFA Single Amino Acid Model for Hydrophobically Driven Liquid-Liquid Phase Separation.
Biomacromolecules
January 2025
Department of Applied Chemistry, Kyung Hee University, Yongin, Gyeonggi 17104, South Korea.
This study proposes fluorenylmethoxycarbonyl (Fmoc)-protected single amino acids (Fmoc-AAs) as a minimalistic model system to investigate liquid-liquid phase separation (LLPS) and the elusive liquid-to-solid transition of condensates. We demonstrated that Fmoc-AAs exhibit LLPS depending on the pH and ionic strength, primarily driven by hydrophobic interactions. Systematic examination of the conditions under which each Fmoc-AA undergoes LLPS revealed distinct residue-dependent trends in the critical concentrations and phase behavior.
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