BJ Articles Ahead of Print

Tumor cells express a unique cell-surface glycocalyx, with up-regulation of sulfated glycosaminoglycans and charged glycoproteins. Little is known about how electromagnetic fields interact with this layer, particularly with an eye to harness unique properties for therapeutic benefit. We applied a pulsed 20 mT magnetic field with rate of rise (dB/dt) in the msec range to cultured tumor cells to assess whether this affects membrane integrity, as measured using cytolytic assays. A 10 minute exposure of A549 human lung cancer cells to sequential 50 and 385 Hz oscillating magnetic fields was sufficient to induce intracellular protease release, suggesting altered membrane integrity following the field exposure.

Toroidal proteins serve as molecular machines and play crucial roles in biological processes such as DNA replication and RNA transcription. Despite progress in the structural characterization of several toroidal proteins, we still lack a mechanistic understanding of the significance of their architecture, oligomerization states and intermolecular interactions in defining their biological function. In this work, we analyze the collective dynamics of toroidal proteins with different oligomerization states, namely, dimeric and trimeric DNA sliding clamps, nucleocapsid proteins (NCPs) (4-, 5- and 6-mers) and Trp RNA-binding attenuation proteins (TRAPs) (11- and 12-mers).

Membrane proteins such as G protein-coupled receptors, channels, and transporters, as well as variations in the membrane composition itself, drive signaling across cellular membranes. These processes are key for cells to sense their environment, store energy, and respond to stimuli. There has been a significant leap in our understanding of membrane proteins in the last two decades through the deployment of novel biophysical tools at the molecular and cellular level, and an explosion of structural insights from crystallography and cryoelectron microscopy.

The ubiquitin (Ub) proteolysis pathway uses an E1, E2 and E3 enzyme cascade to label substrate proteins with ubiquitin and target them for degradation. The mechanisms of ubiquitin chain formation remain unclear and include a sequential addition model where polyubiquitin chains are built unit-by-unit on the substrate, or a preassembly model where polyubiquitin chains are pre-formed on the E2 or E3 enzyme and then transferred in one step to the substrate. The E2 conjugating enzyme UBE2K has a 150-residue catalytic core domain and a C-terminal ubiquitin-associated (UBA) domain.

Epithelial-mesenchymal transition (EMT) is a fundamental biological process that plays a central role in embryonic development, tissue regeneration, and cancer metastasis. Transforming growth factor-β (TGFβ) is a potent inducer of this cellular transition, which is comprised of transitions from an epithelial state to intermediate or partial EMT state(s), to a mesenchymal state. Using computational models to predict cell state transitions in a specific experiment is inherently difficult, for reasons including model parameter uncertainty and error associated with experimental observations.

The endothelial glycocalyx layer (EGL), consisting of long proteoglycans protruding from the endothelium, acts as a regulator of inflammation by preventing leukocyte engagement with adhesion molecules on the endothelial surface. The amount of resistance to adhesive events the EGL provides is the result of two properties: EGL thickness and stiffness. To determine these, we used an atomic force microscope to indent the surfaces of cultured endothelial cells with a glass bead and evaluated two different approaches for interpreting the resulting force-indentation curves.

Transcription factor (TF) recognition is dictated by the underlying DNA motif sequence specific for each TF. Here we reveal that DNA sequence repeat symmetry plays a central role in defining TF-DNA binding preferences. In particular, we find that different TFs bind similar symmetry patterns in the context of different developmental layers. Most TFs possess dominant preferences for similar DNA repeat symmetry types. However, in some cases preferences of specific TFs are changed during differentiation suggesting the importance of information encoded outside of known motif regions.

Spatially discordant alternans (SDA) of action potential duration (APD) has been widely observed in cardiac tissue and is linked to cardiac arrhythmogenesis. Theoretical studies have shown that conduction velocity restitution (CVR) is required for the formation of SDA. However, this theory is not completely supported by experiments, indicating that other mechanisms may exist. In this study, we carried out computer simulations using mathematical models of action potentials to investigate the mechanisms of SDA in cardiac tissue.

Cytotoxic T lymphocytes (T) and natural killer (NK) cells are the main cytotoxic killer cells of the human body to eliminate pathogen-infected or tumorigenic cells (i.e. target cells). Once a NK or T cell has identified a target cell, they form a tight contact zone, the immunological synapse (IS). One then observes a re-polarization of the cell involving the rotation of the microtubule (MT) cytoskeleton and a movement of the microtubule organizing center (MTOC) to a position that is just underneath the plasma membrane at the center of the IS.

During the preparation of single-stranded DNA catenanes, topological isomers of different linking numbers (Lk) are intrinsically produced, and they must be separated each other to construct sophisticated nanostructures accurately. In many of previous studies, however, mixtures of these isomers were directly employed to construct nanostructures without sufficient characterization. Here, we present a method which easily and clearly characterizes the isomers by polyacrylamide gel electrophoresis (PAGE).

Hydrogen-deuterium exchange combined with mass spectrometry (HDX-MS) is a widely-applied biophysical technique that probes the structure and dynamics of biomolecules without the need for site-directed modifications or bio-orthogonal labels. The mechanistic interpretation of HDX data, however, is often qualitative and subjective, owing to a lack of quantitative methods to rigorously translate observed deuteration levels into atomistic structural information. To help address this problem, we have developed a methodology to generate structural ensembles that faithfully reproduce HDX-MS measurements.

T cell receptor (TCR) phosphorylation by Lck is an essential step in T cell activation. It is known that the conformational states of Lck control enzymatic activity; however, the underlying principles of how Lck finds its substrate over the plasma membrane remain elusive. Here, single-particle tracking is paired with photoactivatable localization microscopy (sptPALM) to observe the diffusive modes of Lck in the plasma membrane. Individual Lck molecules switched between free and confined diffusion in both resting and stimulated T cells.