Macromolecular crowding dramatically affects cellular processes such as protein folding and assembly, regulation of metabolic pathways, and condensation of DNA. Despite increased attention, we still lack a definition for how crowded a heterogeneous environment is at the molecular scale and how this manifests in basic physical phenomena like diffusion. Here, we show by means of fluorescence correlation spectroscopy and computer simulations that crowding manifests itself through the emergence of anomalous subdiffusion of cytoplasmic macromolecules. In other words, the mean square displacement of a protein will grow less than linear in time and the degree of this anomality depends on the size and conformation of the traced particle and on the total protein concentration of the solution. We therefore propose that the anomality of the diffusion can be used as a quantifiable measure for the crowdedness of the cytoplasm at the molecular scale.
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http://dx.doi.org/10.1529/biophysj.104.044263 | DOI Listing |
Proc Natl Acad Sci U S A
January 2025
Department of Chemical Engineering, Stanford University, Stanford, CA 94305.
The crowded bacterial cytoplasm is composed of biomolecules that span several orders of magnitude in size and electrical charge. This complexity has been proposed as the source of the rich spatial organization and apparent anomalous diffusion of intracellular components, although this has not been tested directly. Here, we use biplane microscopy to track the 3D motion of self-assembled bacterial genetically encoded multimeric nanoparticles (bGEMs) with tunable size (20 to 50 nm) and charge (-3,240 to +2,700 e) in live cells.
View Article and Find Full Text PDFEntropy (Basel)
January 2025
Institute of Physics, Jan Kochanowski University, Uniwersytecka 7, 25-406 Kielce, Poland.
Superdiffusion is usually defined as a random walk process of a molecule, in which the time evolution of the mean-squared displacement, σ2, of the molecule is a power function of time, σ2(t)∼t2/γ, with γ∈(1,2). An equation with a Riesz-type fractional derivative of the order γ with respect to a spatial variable (a fractional superdiffusion equation) is often used to describe superdiffusion. However, this equation leads to the formula σ2(t)=κt2/γ with κ=∞, which, in practice, makes it impossible to define the parameter γ.
View Article and Find Full Text PDFBiophys J
January 2025
Department of Physiology & Biophysics, UC Irvine, Irvine, California; Department of Biomedical Engineering, UC Irvine, Irvine, California; Center for Complex Biological Systems, UC Irvine, Irvine, California; Sue and Bill Gross Stem Cell Research Center, UC Irvine, Irvine, California. Electronic address:
The mechanically-activated ion channel PIEZO1 is critical to numerous physiological processes, and is activated by diverse mechanical cues. The channel is gated by membrane tension and has been found to be mobile in the plasma membrane. We employed single particle tracking (SPT) of endogenous, tdTomato-tagged PIEZO1 using Total Internal Reflection Fluorescence Microscopy in live cells.
View Article and Find Full Text PDFEntropy (Basel)
December 2024
Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland.
A coarse-grained model of a two-dimensional colloidal suspension was designed. The model was athermal and, in addition, a lattice approximation was introduced. It consisted of solvent (monomer) molecules, dimer molecules, and immobile impenetrable obstacles that introduced additional heterogeneity into the system.
View Article and Find Full Text PDFJ Biol Eng
December 2024
Department of Radiation Oncology, University of Iowa, Iowa City, IA, USA.
Glioblastoma tumors are the most common and aggressive adult central nervous system malignancy. Nearly all patients experience disease progression, which significantly contributes to disease mortality. Recently, it has been suggested that recurrent tumors may be characterized by a ferroptosis-prone phenotype with a significant decrease in glutathione peroxidase 4 (GPx4) expression.
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