Protein condensates resulting from liquid-liquid phase separation have long been studied as bio-adhesives and coating materials for various applications. More recently, they are also being scrutinized as models for membraneless organelles in cells. Quantifying their interfacial mechanics and rheology at micrometer scales is vital for better understanding the physics underlying membraneless organelles in cells and for developing and improving technological applications of protein condensates. This study demonstrates how colloidal probe atomic force microscopy with an oscillating tip can be used to simultaneously investigate the interfacial mechanics and dynamic rheological properties of micro-scale protein condensates, formed via carefully controlled capillary condensation. This new approach can access oscillation frequencies ranging from 1 to 10 rad/s. By analyzing the data using an equivalent mechanical model, three characteristic frequency domains for the mechanics of micro-scale protein condensates are found: an interfacial tension-dominated domain at low frequencies, a transition domain (viscous-to-elastic crossover) at intermediate frequencies, and an elasticity-dominated domain at high frequencies, covering a broad range of time scales relevant in biology and technological applications of protein condensates.
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http://dx.doi.org/10.1016/j.jcis.2022.11.071 | DOI Listing |
Mol Biol Cell
January 2025
Department of Biology, Institute of Biochemistry, ETH (Eidgenössische Technische Hochschule) Zürich, 8093 Zürich, Switzerland.
Biomolecular condensation has emerged as an important mechanism to control various cellular processes through the formation of membraneless organelles. Fluorescent protein tags have been extensively used to study the formation and the properties of condensates and , but there is evidence that tags may perturb the condensation properties of proteins. In this study, we carefully assess the effects of protein tags on the yeast DEAD-box ATPase Dhh1, a central regulator of processing bodies (P-bodies), which are biomolecular condensates involved in mRNA metabolism.
View Article and Find Full Text PDFAnal Chem
January 2025
Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States.
The nuclear pore complex (NPC) is the proteinous nanopore that solely regulates molecular transport between the nucleus and cytoplasm of a eukaryotic cell. Hypothetically, the NPC utilizes the hydrophobic barriers based on the repeats of phenylalanine-glycine (FG) units to selectively and efficiently transport macromolecules. Herein, we quantitatively assess the hydrophobicity of transport barriers confined in the nanopore by applying scanning electrochemical microscopy (SECM).
View Article and Find Full Text PDFNucleic Acids Res
January 2025
Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Biomedicinbyggnaden 6K och 6L, Umeå universitetssjukhus, 901 87, Umeå, Sweden.
Single-cell RNA-seq methods can be used to delineate cell types and states at unprecedented resolution but do little to explain why certain genes are expressed. Single-cell ATAC-seq and multiome (ATAC + RNA) have emerged to give a complementary view of the cell state. It is however unclear what additional information can be extracted from ATAC-seq data besides transcription factor binding sites.
View Article and Find Full Text PDFProtein Sci
February 2025
Graduate School of Engineering, Osaka University, Osaka, Japan.
Amyloid fibril formation of α-synuclein (αSN) is a hallmark of synucleinopathies. Although the previous studies have provided numerous insights into the molecular basis of αSN amyloid formation, it remains unclear how αSN self-assembles into amyloid fibrils in vivo. Here, we show that αSN amyloid formation is accelerated in the presence of two macromolecular crowders, polyethylene glycol (PEG) (MW: ~10,000) and dextran (DEX) (MW: ~500,000), with a maximum at approximately 7% (w/v) PEG and 7% (w/v) DEX.
View Article and Find Full Text PDFNat Rev Immunol
January 2025
Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA.
Fate decisions during immune cell development require temporally precise changes in gene expression. Evidence suggests that the dynamic modulation of these changes is associated with the formation of diverse, membrane-less nucleoprotein assemblies that are termed biomolecular condensates. These condensates are thought to orchestrate fate-determining transcriptional and post-transcriptional processes by locally and transiently concentrating DNA or RNA molecules alongside their regulatory proteins.
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