BJ Articles Ahead of Print

Single-molecule and super-resolution imaging relies on successfully, sensitively, and accurately detecting the emission from fluorescent molecules. Yet, despite the widespread adoption of super-resolution microscopies, single-molecule data processing algorithms can fail to provide accurate measurements of the brightness and position of molecules in the presence of backgrounds that fluctuate significantly over time and space. Thus, samples or experiments that include obscuring backgrounds can severely—or even completely—hinder this process.

Bombolitins, a class of peptides produced by bees of the genus Bombus, target and disrupt cellular membranes, leading to lysis. Antimicrobial peptides (AMPs) exhibit various mechanisms of action resulting from the interplay between peptide structure, lipid composition, and cellular target membrane selectivity. Herein, two novel bombolitins displaying significant amino acid sequence similarity, BII and BL6, were assessed for antimicrobial activity as well as correlated dodecylphosphocholine (DPC) micelle binding and membrane-induced peptide conformational changes.

Deregulation of KRAS4b signaling pathway has been implicated in 30% of all cancers. Membrane localization of KRAS4b is an essential step for initiation of the downstream signaling cascades that guides various cellular mechanisms. KRAS4b plasma membrane (PM) binding is mediated by insertion of a prenylated moiety that is attached to the terminal carboxy-methylated cysteine, in addition to electrostatic interactions of its positively charged hypervariable region (HVR) with anionic lipids. Calmodulin has been suggested to selectively bind KRAS4b to act as a negative regulator of the RAS/MAPK signaling pathway by displacing KRAS4b from the membrane.

The architectural organization of chromatin can play an important role in genome regulation by affecting the mobility of molecules within its surroundings via binding interactions and molecular crowding. The diffusion of molecules at specific locations in the nucleus can be studied by Fluorescence Correlation Spectroscopy (FCS), a well-established technique based on the analysis of fluorescence intensity fluctuations detected in a confocal observation volume. However, detecting subtle variations of mobility between different chromatin regions remains challenging with currently available FCS methods.

The mode of interactions between palmitoyl lysophosphatidycholine (palmitoyl lyso-PC), or other lysophospholipids (lyso-PLs), and palmitoyl ceramide (PCer), or other ceramide analogs, in dioleoylphosphatidylcholine (DOPC) bilayers has been examined. PCer is known to segregate laterally into a ceramide-rich phase at concentrations that depend on the nature of the ceramides and the co-phospholipids. In DOPC bilayers, PCer forms a ceramide-rich phase at concentrations above 10 mol%. In the presence of 20 mol% palmitoyl lyso-PC in the DOPC bilayer, the lateral segregation of PCer was markedly facilitated (segregation at lower PCer concentrations).

The outer membrane (OM) of Gram-negative bacteria is an asymmetric bilayer having phospholipids in the inner leaflet and lipopolysaccharides (LPS) in the outer leaflet. This unique asymmetry and the complex carbohydrates in LPS make it a daunting task to study the asymmetrical OM structure and dynamics, its interactions with outer membrane proteins, as well as its roles in translocation of substrates including antibiotics. In this study, we combine neutron reflectometry and molecular simulation to explore physical properties of OM mimetics.

Protein dynamics in crowded environments is important for understanding protein functions in vivo and is especially relevant for membrane proteins due to the roles of protein-protein interactions in membrane protein functions and their regulation. Here, using solid-state NMR spectroscopy in combination with coarse-grained molecular dynamics simulations, we report that the rotational correlation time for the transmembrane domain of the Influenza A M2 proton channel in lipid bilayers increases dramatically at an elevated protein-to-lipid ratio.

The Influenza A virus (IAV) infects target cells through multivalent interactions of its major spike proteins hemagglutinin (HA) and neuraminidase (NA) with the cellular receptor sialic acid (SA). HA is known to mediate the attachment of the virion to the cell, while NA enables the release of newly formed virions by cleaving SA from the cell. Since both proteins target the same receptor but have antagonistic functions, virus infection depends on a properly tuned balance of the kinetics of HA and NA activities for viral entry to and release from the host cell.

The process of platelet adhesion is initiated by glycoprotein (GP)Ib and GPIIbIIIa receptors on the platelet surface binding with von Willebrand factor (VWF) on the vascular walls. This initial adhesion and detachment of a single platelet is a complex process that involves multiple bonds forming and breaking and is strongly influenced by the surrounding blood flow environment. In addition to bond-level kinetics, external factors such as shear rate, hematocrit, and GPIb and GPIIbIIIa receptor densities have also been identified to influence the platelet-level rate constants in separate studies but still leave a gap in understanding between these two length scales.

Epithelial sheet integrity is robustly maintained during morphogenesis, which is essential to shape organs and embryos. While maintaining the planar monolayer in three-dimensional space, cells dynamically flow via rearranging their connections between each other. However, little is known about how cells maintain the plane sheet integrity in three-dimensional space and provide cell flow in the in-plane sheet. In this study, using a three-dimensional vertex model, we demonstrate that apical junctional fluctuations allow stable cell rearrangements while ensuring monolayer integrity.

Flow at the molecular level induces shear-induced unfolding of single proteins and can drive their assembly, the mechanisms of which are not completely understood. To be able to analyze the role of ow on molecules we present uniform ow Molecular Dynamics (MD) simulations at atomic level. The pull module of the GROMACS package was extended to be able to force group atoms within a de_ned layer of the simulation box. Application of this external enforcement to explicit water molecules, together with the coupling to a thermostat, led to a uniform terminal velocity of the solvent water molecules.

Mechanical stresses directly regulate the function of several proteins of the integrin-mediated focal adhesion complex as they experience intra- and extra-cellular forces. Kindlin is a largely overlooked member of the focal adhesion complex whose roles in cellular mechanotransduction are only recently being identified. Recent crystallographic experiments have revealed that kindlins can form dimers that bind simultaneously to two integrins providing a mechanistic explanation of how kindlins may promote integrin activation and clustering.