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Cellular membranes are dynamic, heterogeneous structures where lipid nanodomains (e.g., lipid rafts) play key roles in signalling, membrane trafficking, and protein function. Single-Molecule Localisation Microscopy (SMLM) reveals the spatial organisation of these nanoscale features; however, traditional analyses focus only on spatial patterns and neglect biochemical and biophysical properties critical for membrane function. By combining SMLM with environmentally sensitive fluorescent probes, such as di-4-ANEPPDHQ, we can produce marked point patterns which couple spatial coordinates with environmental information, such as membrane lipid order quantified by generalised polarisation (GP) values.

—In this work we developed a coarse-grained model for RNA that is compatible with the Martini 3 force field. The model is parameterized following the Martini philosophy combining the top-down and bottom-up approaches. The nonbonded interactions in the model are derived from the partitioning of nucleobases between polar and nonpolar solvents, along with calculations of the potential of mean force between bases. For bonded interactions, parameters were refined based on atomistic simulations of double-stranded RNA.

(Biophysical Journal 124, 2362–2379; July 15, 2025)

Number & Brightness, and Photon Counting Histogram analyses are powerful techniques for measuring stoichiometry in living cells. However, the accuracy of the results can be compromised by data temporal correlation, which increases with shorter acquisition times and slower molecular dynamics. Through simulations, we demonstrate that failing to account for data temporal correlation systematically underestimates the true molecular brightness. To overcome this limitation, we introduce the Mixed Assays To Evaluate Brightness Analysis (MATE-BA) method, which decorrelates the data, allowing for accurate calculation of molecular brightness and achieving better precision with fewer data points.

In sinoatrial node cells (SANC), stochastic Ca2+ release from the sarcoplasmic reticulum (SR) interacts with membrane channels, inducing their stochastic opening and closing, leading to inter-beat interval (IBI) variability (BIV). Additionally, stochastic neurotransmitter release activates cAMP/PKA signaling, influencing membrane channels and SR proteins, further contributing to BIV. Most computational models produce deterministic IBIs, lacking physiological BIV.We tested three hypotheses: (i) incorporating stochastic behavior into intrinsic mechanisms mimics experimental BIV, (ii) increased neurotransmitter stimulation via β-adrenergic receptor (β-AR) activation, phosphodiesterase (PDE) inhibition, or enhanced SERCA activity shortens IBI and reduces BIV, and (iii) these interventions affect BIV parameters differently at short- and long-time scales.

Three-color single-molecule Förster resonance energy transfer (FRET) is a valuable tool to study conformational dynamics of macromolecules. In this work, we present a maximum likelihood method for analyzing three-color fluorescence bursts collected from freely diffusing molecules in confocal microscopy. In three-color single-molecule FRET measurements, the third dye with the longest wavelength typically has a much lower quantum yield than the other two dyes, which leads to significantly reduced brightness, particularly for molecular states with high energy transfer to the third dye.

The activation of integrins by Mn2+ is a crucial area of research, yet the underlying mechanisms remain poorly understood. Previous studies have shown that substituting Mg2+ with Mn2+ at the Metal Ion-Dependent Adhesion Site (MIDAS) enhances the affinities of high-affinity open and low-affinity closed integrins. However, the molecular effect of Mn2+ and how it compares to physiological activation mediated by Mg2+/Ca2+ remain unclear. This is partly due to the lack of experimental techniques capable of detecting these processes dynamically.

We developed a simple reverse evolution method to explore the protein folding transition and knotting process in globular proteins throughout evolution using as a proxy for evolutionary time the length of the amino acid alphabet. Three small proteins were considered. An unknotted one featuring a beta-sandwich fold (FN3), a protein embedding a shallow trefoil knot (MJ0366), and a deeply knotted trefoil protein (YibK). Results from Monte Carlo simulations of a native-centric Cα model show that thermal stability increases throughout evolution for all considered proteins suggesting it provided a selective pressure for the introduction of biosynthetic amino acids in the alphabet repertoire.

Dynamic changes in sarcomere spacing in a live, micropatterned neonatal mouse cardiac myocyte during axial stretch, illustrating the cellular basis of the length–tension relationship at the single-cell level.

Poly [ADP-ribose] polymerase 2 (PARP2) plays a crucial role in DNA repair. A common single-nucleotide polymorphism (SNP) in the PARP2 gene, rs3093921, has been associated with pancreatic cancer and marginal zone lymphoma (MZL). This SNP results in a missense mutation, D235G, in the PARP2 protein. PARP2 is also reported to undergo post-translational modifications (PTMs), particularly phosphorylation at serine residues 226, 232, and 353. The C–terminal region of PARP2 includes the Trp-Gly-Arg (WGR) domain, ADP-ribosyl transferase (ART) domain, and the helical subdomain (HD).

Emerging studies suggest that a wide range of chronic diseases can be linked to prior physical trauma and, in some cases, to the supraphysiological deformation rates experienced by cells during injury. However, the mechanical behavior of cells during these deformations is poorly understood. Here, we studied the strain rate dependent mechanics of vascular smooth muscle cells over rates spanning five orders of magnitude, from physiological to supraphysiological. We find that cells deformed at increasing rates undergo substantial rate-softening in tension but have no rate-dependence when returned to zero strain.

Cardiomyocyte ultrastructure and pathological disruptions, such as myofibrillar disarray and mitochondrial disorganization, are important determinants of contractile function and dysfunction. Our previous model simulation assumed idealized periodicity and symmetry of cardiomyocyte structures limiting their ability to replicate pathological abnormalities. Utilizing image-based modeling, here we extend previous simulations by incorporating realistic 3-D structures based on mouse cardiomyocyte images from serial block-face scanning electron microscopy (SBEM).