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Liquid-liquid phase condensation governs a wide range of protein-protein and protein-RNA interactions in vivo and drives the formation of membrane-less compartments such as the nucleolus and stress granules. We have a broad overview of the importance of multivalency and protein disorder in driving liquid-liquid phase transitions. However, the large and complex nature of key proteins and RNA components involved in forming condensates such as stress granules has inhibited a detailed understanding of how condensates form and the structural interactions that take place within them. In this work, we focused on the small human SERF2 protein. We show here that SERF2 contributes to the formation of stress granules. We also show that SERF2 specifically interacts with non-canonical tetrahelical RNA structures called G-quadruplexes, structures which have previously been linked to stress granule formation. The excellent biophysical amenability of both SERF2 and RNA G4 quadruplexes has allowed us to obtain a high-resolution visualization of the multivalent protein-RNA interactions involved in liquid-liquid phase transitions. Our visualization has enabled us to characterize the role that protein disorder plays in these transitions, identify the specific contacts involved, and describe how these interactions impact the structural dynamics of the components involved in liquid-liquid phase transitions, thus enabling a detailed understanding of the structural transitions involved in early stages of ribonucleoprotein condensate formation.
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http://dx.doi.org/10.1101/2023.10.09.561572 | DOI Listing |
J Phys Chem B
September 2025
Hefei National Research Center for Physical Sciences at the Microscale and Key Laboratory of Precision and Intelligent Chemistry, Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026, China.
Multivalent protein-protein interactions play essential roles in mediating liquid-liquid phase separation (LLPS) that drives biomolecular condensate formation. Here, we systematically investigate how the spatial distribution and relative size of protein binding domains (PBDs) would influence LLPS in a mixture of spherical proteins and RNA single strands by using a patchy-particle polymer model, wherein each protein contains a fixed number of PBDs on the surface distributed closely or sparsely. Intriguingly, we find that LLPS behavior exhibits a nontrivial dependence on the cooperative interplay between PBD distribution and protein size: while sparsely distributed PBDs are more favorable to LLPS for small proteins, closely packed PBDs facilitate LLPS for larger counterparts.
View Article and Find Full Text PDFAdv Sci (Weinh)
September 2025
Department of Physics, State Key Laboratory of Surface Physics, and Key Laboratory for Computational Physical Science (Ministry of Education), Fudan University, 2005 Songhu Road, Yangpu District, Shanghai, 200433, China.
Emerging evidence indicates that liquid-liquid phase separation of α-synuclein occurs during the nucleation step of its aggregation, a pivotal step in the onset of Parkinson's disease. Elucidating the molecular determinants governing this process is essential for understanding the pathological mechanisms of diseases and developing therapeutic strategies that target early-stage aggregation. While previous studies have identified residues critical for α-synuclein amyloid formation, the key residues and molecular drivers of its phase separation remain largely unexplored.
View Article and Find Full Text PDFBiophys Chem
September 2025
Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
A comprehensive understanding of the molecular mechanism underlying the Liquid-Liquid Phase Separation (LLPS) pathway of LCD-TDP43 remains a challenge in the context of its neuropathogenesis. The primary driving force behind the TDP-43 LLPS is the interplay of hydrophobic interactions reinforced by aromatic residues. This study presents a novel, convenient, sensitive, and probe-free approach using excitation-emission matrix (EEM) fluorescence to monitor the microenvironment of aromatic residues and π-π stacking interactions during different stages of the LLPS pathway.
View Article and Find Full Text PDFAdv Biol Regul
September 2025
Laboratory of Cancer Cell Architecture, Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, Prague, Czech Republic. Electronic address:
Biomolecular condensates (BMCs) are membrane-less organelles formed through liquid-liquid phase separation, primarily driven by multivalent interactions between scaffold and client molecules. These dynamic compartments enable cells to spatially and temporally organize biochemical reactions by locally concentrating specific biomolecules, thereby enhancing the frequency of productive molecular interactions and increasing reaction rates. BMCs are integral to normal cellular physiology, with well-characterized examples including the nucleolus and Cajal bodies.
View Article and Find Full Text PDFPlant J
September 2025
Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore.
Salicylic acid (SA), a long-characterized defense hormone, is increasingly recognized for its roles in plant growth and development. However, its involvement in mediating plant growth responses to environmental cues remains less understood. Here, we show that SA negatively affects thermomorphogenic growth in Arabidopsis thaliana.
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