Biophysical reports最新文献

Protein condensation is the basis for formation of membrane-less organelles in the cell. Most famously, weak, polyvalent interactions, often including RNA, may lead to a liquid-liquid phase separation. This effect greatly enhances local concentrations and is thought to promote interactions that would remain rare in dilute solution. Synthetic systems provide a means to clarify the underlying biophysical mechanisms at play, both in vitro and in the cell via exogenous expression. In this regard, ferritin is a useful substrate, as its composition of 24 subunits with octahedral symmetry supports self-assembly by close packing in 3D. The conventional diagnostic tool for protein condensation is fluorescence imaging. In this work, we explore the use of refractive index mapping to detect states of condensation and decondensation. Using two related ferritin-based self-assembly systems, we find that refractive index is a sensitive indicator for reversible condensation. Surprisingly, refractive index indicates a rapid decondensation even when molecular dispersal kinetics are slow according to fluorescence. Conversely, in a photoactivated condensation where long activation results in slow decondensation kinetics, the refractive index provides reliable evidence for the physical state independent of fluorescence. The observations suggest a distinction between condensation to a sparse biomolecular network or to a material continuum that supports an optical polarizability distinct from that of the dilute phase in solution.

The presented study aimed to investigate the antibacterial activity of menthol-the main component of one of the widespread plants of the Lamiaceae family-Mentha arvensis. To investigate the mode of action of menthol, we studied its influence on kanamycin-resistant E. coli pARG-25 and wild-type E. coli BW25113 strains. For this, the effect of menthol on ATPase activity, proton and potassium fluxes, and intracellular pH was investigated under aerobic and anaerobic conditions. The results showed that menthol influences these parameters in a concentration- and condition-dependent way. It likely interacts with FoF₁-ATPase and other systems involved in energy-generating processes and ion transport, disrupting the bacterial metabolism of both antibiotic-resistant and -susceptible strains.

Skeletal muscle alpha actin (ACTA1) is important for muscle contraction and relaxation, with historical studies focused on ACTA1 mutations in muscle dysfunction. Proteomics reports have consistently observed that actin, including ACTA1, is acetylated at multiple lysine sites. However, few reports have studied the effects of actin acetylation on cellular function, and fewer have examined ACTA1 acetylation on skeletal muscle function. Here, we aimed to examine how ACTA1 acetylation affected actomyosin interactions by determining actin sliding velocity, myosin binding, and calcium sensitivity. In this study, ACTA1 was chemically acetylated via acetic anhydride (AA) to increasing levels of acetylation: low-level acetylation (using 0.1 mM AA), mid-level acetylation (0.3 mM AA), and high-level acetylation (1 mM AA). We report that ACTA1 acetylation significantly decreased actin sliding velocity and actin filament length. Further analysis showed that ACTA1 acetylation significantly increased calcium sensitivity, with a loss of tropomyosin regulation noted with high-level ACTA1 acetylation. Lastly, ACTA1 acetylation enhanced skeletal myosin half maximal binding to actin. These data highlight acetylation as an additional posttranslational modification, outside of phosphorylation, in the regulation of muscle contraction and skeletal muscle alpha actin function.

Coarse-grained (CG) models are widely used to study membrane proteins at physiologically relevant scales. However, simulating long-range bilayer deformations induced by membrane-embedded proteins at submicrometer scales remains challenging. Here, we assess a generic solvent-free CG lipid model, previously applied to membrane proteins, for large-scale molecular dynamics simulations. We find that beyond a critical membrane size, the model becomes unstable due to membrane poration and unphysical undulations. To overcome this limitation, we systematically optimize this lipid model, significantly extending its stability for larger membrane systems. Using this improved model, we simulate membrane deformation induced by the mechanosensitive ion channel PIEZO in bilayers with varying mechanical properties. This optimized CG model with tunable mechanical properties provides a timely tool for investigating bilayer-mediated membrane protein interactions and bridging the gap between continuum elasticity theory and atomistic simulations.

Controlling cancer cell fate through membrane depolarization, reactive oxygen species (ROS) dynamics, and voltage-gated ion channel (VGIC) activation represents a rapidly advancing paradigm in bioelectronic oncology. Electrically excitable cancer cells-including glioblastoma, retinoblastoma, SH-SY5Y neuroblastoma, MCF-7, and MDA-MB-231-exhibit distinct electrophysiological and redox sensitivities that govern their responsiveness to photoelectrical stimulation. Here, we develop an integrated theoretical and transcriptomic framework describing how photocapacitive and photofaradaic stimulation modulates intracellular calcium signaling, mitochondrial membrane potential (ΔΨm), and ROS homeostasis to determine apoptotic, autophagic, or proliferative outcomes. Experimental data sets from GSE59612, GSE103224 (glioblastoma), GSE97508 (retinoblastoma), and GSE45827 (breast cancer) parameterize VGIC families, antioxidant pathways, and cell death modules. New simulations using a measured 20-Hz photovoltaic waveform show that photocapacitive depolarization elevates glioblastoma ROS levels to ∼150-160 μM over 30 min, placing cells within a proliferative-to-autophagic transition region, with a small apoptotic component. Mapping these ROS trajectories to a bifurcation-based cell fate model reveals glioblastoma-specific redox thresholds that align with transcriptomic VGIC and antioxidant signatures. By unifying stimulation physics, bioelectrical modeling, and omics-based parameterization, this work provides a predictive foundation for designing photovoltaic cancer therapies tuned to cell-type-specific electrophysiological and redox landscapes. Moreover, in MDA-MB-231 cells the same stimulation induces a controlled, early-stage autophagy response, providing an intrinsic antiinflammatory benefit that can suppress early tumorigenic signaling.

Platelets are small blood cells involved in hemostasis and wound healing. After activation, platelets interact with their surrounding environment and respond to biochemical and mechanical stimuli by mechanosensitive and haptotactic mechanisms. We used microcontact printing (μCP) to mimic the physiological conditions and limited space in small blood vessels in vitro. With μCP, we created 4-μm-wide fibrinogen lines to provide a spatially confined spreading space for platelets. We then let platelets adhere and spread on these lines while imaging them with optical microscopy and scanning ion conductance microscopy (SICM). Confined platelets showed significantly altered morphology, spreading dynamics, and mechanics compared with control platelets. Altered mechanical properties of confined platelets revealed reorganization of the actin cytoskeleton and the formation of regions of increased elastic modulus at the edges of the fibrinogen lines. Our results indicate that spatial confinement affects platelet mechanics and morphology on a subcellular level.

The human brain exhibits intricate spatiotemporal dynamics, which can be described and understood through the framework of complex dynamic systems theory. In this study, we leverage functional magnetic resonance imaging (fMRI) data to investigate reaction-diffusion processes in the brain. A reaction-diffusion process refers to the interaction between two or more substances that spread through space and react with each other over time, often resulting in the formation of patterns or waves of activity. Building on this empirical foundation, we apply a reaction-diffusion framework inspired by theoretical physics to simulate the emergence of brain spacetime vortices within the brain. By exploring this framework, we investigate how reaction-diffusion processes can serve as a compelling model to govern the formation and propagation of brain spacetime vortices, which are dynamic, swirling patterns of brain activity that emerge and evolve across both time and space within the brain. Our approach integrates computational modeling with fMRI data to investigate the spatiotemporal properties of these vortices, offering new insights into the fundamental principles of brain organization. This work highlights the potential of reaction-diffusion models as an alternative framework for understanding brain spacetime dynamics.

Axial optical tweezers provide a natural geometry for performing biomechanical assays, such as rupture force measurements of protein binding. Axial traps, however, are typically weaker than their lateral counterparts and require high laser power to maintain a well-calibrated, linear restoring force. Here, we show how to extend the spatial range over which well-calibrated forces can be applied by considering aberration effects and extend the range of applied forces by accounting for the nonlinear response that appears when an optically trapped bead is moved far from the trap center. These refinements to the force calibration can be used to apply higher axial forces at reduced laser powers deeper into a sample. To illustrate the method, we reproduce both the linear extension regime and the overstretching transition observed in double-stranded DNA at significantly reduced laser powers.

Escherichia coli translocates formate/formic acid bidirectionally across the cytoplasmic membrane by the FocA/FocB formate channels during fermentation. Depending on the pH and whether formate is supplied exogenously or generated internally, the mechanisms of translocation differ. This study elucidates the role of these channels in dependence on F_OF₁ ATPase activity in stationary phase cells after cultivation by mixed-carbon fermentation at pH 7.5. In cells cultivated with glucose plus glycerol, exogenously added formate increased the N,N'-dicyclohexylcarbodiimide (DCCD)-sensitive (F_OF₁ ATPase-dependent) proton flux in single or double foc mutants. Moreover, exogenously supplied formate also increased the DCCD-sensitive potassium flux, but only in mutants where focB was absent. In the cells grown on glucose, glycerol, and formate, addition of formate in the whole-cell assays increased F_OF₁ ATPase activity by ∼60% compared with cells grown on a mixture of only glucose and glycerol. In a focA mutant cultivated to the stationary phase on glucose, glycerol, and formate, F_OF₁ ATPase activity was double that compared with cells grown on only glucose and glycerol, while in a focA-focB double-null mutant F_OF₁ ATPase activity decreased by ∼50% in formate assays. These data suggest that the cell regulates the mechanism of formate translocation depending on whether formate is generated internally or added exogenously. Thus, F_OF₁-ATPase activity and the FocA/FocB channels together with formate hydrogenlyase activity combine to balance pH and ion gradients during fermentation in stationary phase cells in response to whether formate is generated metabolically or supplied in high concentration from the environment.