Articles Online Now

Amphipathic helices (AHs) are secondary structures that can facilitate binding of proteins to the membrane by folding into a helix with hydrophobic and hydrophilic faces that interact with the same surfaces in the lipid membrane. Septins are cytoskeletal proteins that preferentially bind to domains of micron-scale curvature on the cell membrane. Studies have shown that AH domains in septin are essential for curvature sensing. We present the first computational study of septin AH interactions with lipid bilayers.

Lasso peptides are a unique class of natural products with distinctively threaded structures, conferring exceptional stability against thermal and proteolytic degradation. Despite their promising biotechnological and pharmaceutical applications, reported attempts to prepare them by chemical synthesis result in forming the nonthreaded branched-cyclic isomer, rather than the desired lassoed structure. This is likely due to the entropic challenge of folding a short, threaded motif prior to chemically mediated cyclization.

The pro-apoptotic factor BAX is a key member of the Bcl-2 family of apoptotic regulators. BAX functions by permeating the outer mitochondrial membrane, a process that begins with the targeting of soluble BAX to the membrane. Once associated, BAX refolds, inserts into the bilayer, and ultimately assembles into a multimeric pore of unknown structure. BAX targeting is initiated by an activation signal that can arise from two pathways: (a) a BH3-dependent one in which BAX is activated by one of the BH3-only effectors such as tBid, or (b) a recently discovered BH3-independent pathway, where BAX activity is modulated by changes in lipid composition.

Understanding the structure and dynamics of biological systems is often limited by the trade-off between spatial and temporal resolution. Imaging fluorescence correlation spectroscopy (ImFCS) is a powerful technique for capturing molecular dynamics with high temporal precision but remains diffraction-limited. This constraint poses challenges for quantifying dynamics of subcellular structures like membrane-proximal cortical actin fibers. Computational super-resolution microscopy (CSRM) presents an accessible strategy for enhancing spatial resolution without specialized instrumentation, enabling compatibility with ImFCS.

Chromosome organization mediated by structural maintenance of chromosome complexes is crucial in many organisms. Cohesin extrudes chromatin into loops that are thought to lengthen until it is obstructed by CTCF proteins. In complex cellular environments, the loop extrusion machinery may encounter other chromatin-binding proteins. How these proteins interfere with the cohesin-meditated extrusion process is largely unexplored, but recent experiments have shown that some proteins serve as physical barriers that block cohesin translocation.

β-Aescin is a natural additive employed for treatments of vascular insufficiency, hence its impact in red blood cell (RBC)’s adaptivity has been conjectured. Here, we report a study about the mechanical impact of the membrane stiffener aescin on the flickering motions of live RBCs maintained at the homeostatic status. An active flickering, or nonequilibrium fluctuation dynamics has been revealed by mapping flickering motions in single RBCs treated or not with aescin. Experiments show that active RBC flickers adapt mechanically to β-escin, unlike the passive thermal fluctuations observed in lipid bilayers without an active skeleton.

Electrostatically driven double stranded (ds)DNA condensation is critical in regulating many biological processes, including bacteriophage and virus replication and the packaging of chromosomal DNA in sperm heads. Here we review single-molecule (SM) measurements of dsDNA condensed by cationic proteins, polypeptides, and small multivalent cations. Optical tweezers (OT) measurements of dsDNA collapsed by cationic condensing agents reveal a critical condensing force unique to each condensing agent that is tunable with condensing agent concentration and ionic strength.

The breast tumor microenvironment is composed of heterogeneous cell populations, including normal epithelial cells, cancer-associated fibroblasts, and tumor cells that lead collective cell invasion. Both leader tumor cells and CAFs are known to play important roles in tumor invasion across the collagen-rich stromal boundary. However, their individual abilities to utilize their cell-intrinsic protrusions and perform force-based collagen remodeling to collectively invade remain unclear. To compare collective invasion phenotypes of leader-like tumor cells and CAFs, we embedded spheroids composed of 4T1 tumor cells or mouse tumor-derived CAF cell lines within 3D collagen gels and analyzed their invasion and collagen deformation.

Mutations to WNT ligands in cancer are poorly understood. WNT ligands are a family of secreted proteins that trigger the activation of the WNT pathway with essential roles in cell development and carcinogenesis, particularly of the colorectal tract. Whilst the structure of WNT ligands has been elucidated, little is known about how mutations in these proteins affect colorectal cancer. Here we show that mutations in WNT ligands found in colorectal cancer show regional specificity and selectivity for particular conserved sequences.

Single-molecule spectroscopy combined with Förster resonance energy transfer (FRET) is widely used to quantify distance dynamics and distributions in biomolecules. Most commonly, measurements are interpreted using simple analytical relations between experimental observables and the underlying distance distributions. However, these relations make simplifying assumptions, such as a separation of timescales between inter-dye distance dynamics, fluorescence lifetimes, and dye reorientation, the validity of which is notoriously difficult to assess from experimental data alone.

Statement of Significance: We describe a novel system that can read out and control tension of a membrane patch in real time. It allows measuring tension-response relationships of force-gated ion channels without the need for hands-on data analysis, thereby accelerating data collection. We envision that the system can be alternatively used to read out and control membrane curvature, thereby additionally enabling the study of how protein function is affected by membrane geometry.

Deep learning based approaches are now widely used across biophysics to help automate a variety of tasks including image segmentation, feature selection, and deconvolution. However, the presence of multiple competing deep learning architectures, each with its own advantages and disadvantages, makes it challenging to select an architecture best suited for a specific application. As such, we present a comprehensive comparison of common models. Here, we focus on the task of segmentation assuming typical (often small) training dataset sizes available from biophysics experiments and compare the following four commonly used architectures: convolutional neural networks, U-Nets, vision transformers, and vision state space models.