In order to translate messenger RNA into proteins, the ribosome must coordinate a wide range of conformational rearrangements. Some steps involve individual molecules, whereas others require synchronization of multiple collective motions. For example, the ribosomal "small" subunit (∼1 MDa) is known to undergo rotational motion (∼10°) that is correlated with large-scale displacements of tRNA molecules

The attachment of bacteria to solid surfaces has been studied primarily through the modes of pili or flagella tethering. We report on a common feature of tethering in pililess strains of three species of monotrichous bacteria-(Vibrio alginolyticus, Pseudomonas aeruginosa, and Caulobacter crescentus)-namely, that they may become tethered to the surface by their cell body rather than by their flagellum

Symmetric homo-oligomeric proteins comprising multiple copies of identical subunits are abundant in all domains of life. To fulfill their biological function, these complexes undergo conformational changes, binding events, or post-translational modifications leading to loss of symmetry. Processivity clamp proteins that encircle DNA and play multiple roles in DNA replication and repair are archetypical

Autosomal dominant retinitis pigmentosa (ADRP) is a visual disorder which can result from many different mutations of the rhodopsin gene. In most cases the mutation results in a misfolded rhodopsin protein or a protein that does not bind with the retinal chromophore. Some mutations, however, yield rhodopsins which fold properly and bind the retinal chromophore, yet still result in ADRP. Here we investigate

When a blood clot occludes cerebral arteries, causing a stroke, a common cause of global death, thrombolytic therapy steps in as a highly effective treatment to restore the blood flow by dissolving the clot. Thrombolytic therapy is the use of plasminogen activators, including tissue plasminogen activator (tPA) and urokinase plasminogen activator (uPA), either separately or in combination. In this study

Förster resonance energy transfer (FRET) is a short-range distance-dependent photophysical phenomenon that allows the measurement of intra- and inter-molecular distances through fluorescence detection. FRET measurements are sensitive to the movements of fluorescently labeled molecules as they produce fluorescence fluctuations. Fluorescence correlation spectroscopy (FCS) analyzes these fluctuations

The assembly of integrin adhesion complexes at the inner leaflet of the plasma membrane regulates cell adhesion to the extracellular matrix. The multivalent protein interactions within the complexes and with the cell membrane display characteristics of membrane-associated biomolecular condensates driven by liquid-liquid phase separation. The composition of lipids and the distribution of the cell membrane

A SNAP25-based FRET construct named SCORE (SNARE complex reporter) has revealed a transient FRET increase that specifically occurred at fusion sites preceding fusion events by tens of milliseconds and presumably reflects vesicle priming. The FRET increase lasts for a few seconds until it is reversed. In those experiments, the FRET increase was found to be localized to areas <0.5 μm2 at sites of transmitter

Surfactant protein D (SP-D) plays an important role in the innate immune system by recognizing and binding to glycans on the surface of pathogens, facilitating their clearance. Despite its importance, the detailed binding mechanisms between SP-D and various pathogenic surface glycans remain elusive due to the limited experimentally solved protein-glycan crystal structures. To address this, we developed

Through experimental studies, many details of the pathway of integrin αIIbβ3 activation by ADP during the platelet aggregation process have been mapped out. ADP binds to two separate G protein-coupled receptors on platelet surfaces, leading to alterations in the regulation of the small GTPase RAP1. We seek to 1) gain insights into the relative contributions of both pathways to RAP1-mediated integrin

To provide insight into the basic properties of emerging structures when bacteria or other microorganisms conquer surfaces, it is crucial to analyze their growth behavior during the formation of thin films. In this regard, many theoretical studies focus on the behavior of elongating straight objects. They repel each other through volume exclusion and divide into two halves when reaching a certain threshold

Biomolecular condensates formed via liquid-liquid phase separation are ubiquitous in cells, especially in the nucleus. While condensates containing one or two kinds of biomolecules have been relatively well characterized, those with more heterogeneous biomolecular components and interactions between biomolecules inside are largely unknown. This study used residue-resolution molecular dynamics simulations

The mitochondrion-endoplasmic reticulum (ER) contact sites (MERCs, also known as mitochondrial-associated membranes [MAMs]) are specialized regions of the ER that are in close proximity to the mitochondrion. These organelle structures play essential roles in a variety of processes, such as calcium signaling, lipid metabolism, renin-angiotensin-aldosterone system control, the unfolded protein response

Transposons, DNA sequences capable of relocating within the genome, make up a significant portion of eukaryotic genomes and are often found in clusters. Within the cell nucleus, the genome is organized into chromatin, a structure with varying degrees of compaction due to three-dimensional folding. Transposon insertion or activation can lead to chromatin decompaction, increasing accessibility and potentially

Bacteriorhodopsin (bR) is perhaps the best-studied proton pump. Over about four decades, research on this fascinating photocyclic light-driven protein inspired the development of key experimental and computational methodologies that are now widely used in membrane protein studies. We review here failures and successes in computational approaches that have been applied to study the bR proton-transfer

Glycolysis is a conserved metabolic pathway that produces ATP and biosynthetic precursors. It is not well understood how the control of mammalian glycolytic enzymes through allosteric feedback and mass action accomplishes various tasks of ATP homeostasis, such as controlling the rate of ATP production, maintaining high and stable ATP levels, ensuring that ATP hydrolysis generates a net excess of energy

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

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

The pro-apoptotic factor BAX is a key member of the B cell lymphoma-2 family of apoptotic regulators. BAX functions by permeating the mitochondrial outer 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

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

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

β-Aescin is a natural additive employed for treatments of vascular insufficiency, hence its impact in red blood cell (RBC) 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

Electrostatically driven double-stranded DNA (dsDNA) 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 measurements of dsDNA condensed by cationic proteins, polypeptides, and small multivalent cations. Optical tweezers (OT) measurements of dsDNA collapsed

The breast tumor microenvironment is composed of heterogeneous cell populations, including normal epithelial cells, cancer-associated fibroblasts (CAFs), 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

Mutations to wingless integration site (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 in the colorectal tract. While the structure of WNT ligands has been elucidated, little is known about how mutations in these proteins affect colorectal

Characterizing the function of force-gated ion channels is essential for understanding their molecular mechanisms and how they are affected by disease-causing mutations, lipids, or small molecules. Pressure-clamp electrophysiology is a method that is established and widely used to characterize the mechanical sensitivity of force-gated ion channels. However, the physical stimulus many force-gated ion

Single-molecule spectroscopy combined with Förster resonance energy transferis 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

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

We introduce a discard-and-restart molecular dynamics (MD) algorithm tailored for the sampling of realistic protein intermediate states. It aids computational structure-based drug discovery by reducing the simulation times to compute a "quick sketch" of folding pathways by up to 2000×. The algorithm iteratively performs short MD simulations and measures their proximity to a target state via a collective

Recent global burden of disease studies have shown that bacterial infections are responsible for over 13 million deaths worldwide, or 1 in every 8 deaths, each year. Enteric diarrheal infections, in particular, pose a significant challenge and strain on healthcare systems as many are difficult to address pharmaceutically, and thus rely primarily on the patient’s own immune system and gut microbiome

The purpose of this review is to evaluate the current knowledge about the mechanisms by which mechanosensitive ion channels are activated by fluid shear stress in endothelial cells. We focus on three classes of endothelial ion channels that are most well studied for their sensitivity to flow and roles in mechanotransduction: inwardly rectifying K+ channels, Piezo channels, and TRPV channels. We also

Cell length has been used as a proxy for cell size in cell cycle modeling studies. A previous study, however, brought into question the validity of this assumption, noting that correlations between cell lengths can be different from those involving cell volume if cell width fluctuations are taken into account. If cell volume is regulated, data analysis involving cell lengths will lead to an incorrect

Small proteins can be challenging to study by single-particle cryogenic electron microscopy (cryo-EM) techniques because they have low signal-to-noise ratios, making them difficult to identify and analyze. Here we investigated the use of Csp1, a small (∼50 kDa) tetrameric metal-binding protein, to act as a “bio-tag” to help overcome this problem. We find Csp1 is compact, stable, and exhibits enhanced

Large unilamellar vesicles are popular membrane models for studying the impact of lipids and bilayer properties on the structure and function of transmembrane proteins. However, the functional reconstitution of transmembrane proteins in liposomes can be challenging, especially if the hydrophobic thickness of the protein does not match the thickness of the lipid bilayer. Such hydrophobic mismatch causes

Ligands in many instances interact with a protein at multiple sites with a range of affinities. In this study, ligand-protein interaction sites on human serum albumin (HSA) are mapped using the site-identification by ligand competitive saturation (SILCS)-Biologics approach in conjunction with hydrogen-deuterium exchange (HDX)-mass spectrometry (MS) experiments. Ligands studied include known HSA binders

In many quantitative investigations of biological systems, including, e.g., the study of biomolecular interactions, assembly and disassembly, aggregation, micelle and vesicle formation, or drug encapsulation, accurate determination of particle sizes is of key interest. Fluorescence correlation spectroscopy (FCS), with its exceptional sensitivity for molecular diffusion properties, has long been proposed

Infrared neural stimulation (INS) uses transient near-infrared light to activate neuronal activity, likely through heat-induced thermal gradients. However, neither the effect of basal temperature nor heat accumulation has specifically been investigated. This study examines how spatial temperature gradients, varied by different laser repetition rates and the addition of a continuous wave laser, affect

Solid-state nuclear magnetic resonance (ssNMR) is a powerful technique for studying membrane protein structure and dynamics. Ideally, measurements are performed with the protein in a lipid bilayer. However, homogenous reconstitution of functional protein into intact bilayers at sufficiently high concentrations is often difficult to achieve. In this work, we investigate the suitability of the lipid

Natriuretic peptides are produced predominantly by atrial cardiomyocytes in response to cardiovascular stress and attenuate cardiac maladaptation by reducing blood pressure, blood volume, and cardiac workload primarily through activation of natriuretic peptide receptors in the kidney and vasculature. However, mechanisms underlying cardiomyocyte exocytosis and natriuretic peptide secretion remain poorly

Measurements of cell size dynamics have revealed phenomenological principles by which individual cells control their size across diverse organisms. One of the emerging paradigms of cell size homeostasis is the adder, where the cell cycle duration is established such that the cell size increase from birth to division is independent of the newborn cell size. We provide a mechanistic formulation of the

For several decades, many attempts have been made to characterize the mechanical properties of gray and white matter, which constitute the two main compartments of the central nervous system, with various methods and contradictory results. In particular, the ratio of gray-to-white-matter elasticity is sometimes larger than 1 and sometimes smaller; the reason for this apparent discrepancy is currently

The deformation of red blood cells (RBCs) in Poiseuille flows of capillary vessels is fundamental for hemodynamics in cellular scale for various physiological or pathological scenarios. However, the mechanical criterion for membrane buckling and the impact of the asymmetric deformations of cells on the hemodynamics are currently unclear. In this study, a microfluidic system with narrow tubular channels

The aggregation of red blood cells (RBCs) is a complex phenomenon that strongly impacts blood flow and tissue perfusion. Despite extensive research for more than 50 years, physical mechanisms that govern RBC aggregation are still under debate. Two proposed mechanisms are based on bridging and depletion interactions between RBCs due to the presence of macromolecules in blood plasma. The bridging hypothesis

The single-molecule biophysics community has delivered significant impacts to our understanding of fundamental biological processes, yet the field is also siloed and has fragmented data structures, which impede data sharing and limit the ability to conduct comprehensive meta-analyses. To advance the field of optical tweezers in single-molecule biophysics, it is important that the field adopts open

During development and wound healing, cells need to form long-range ordered structures to ensure precise formation of organs and repair damage. This requires cells to locate specific partner cells to which to adhere. How such cell matching reliably happens is an open problem, particularly in the presence of biological variability. Here, we use an equilibrium energy model to simulate how cell matching

The Halbach array, originally developed for particle accelerators, is a compact arrangement of permanent magnets that creates well-defined magnetic fields without heating. Here, we demonstrate its use for modulating the speed of electromechanical waves in cardiac syncytia of human stem cell-derived cardiomyocytes. At 40–50 mT magnetic field strength, a cylindrical dipolar Halbach array boosted the

Measuring co-localization of different types of molecules is essential to understand molecular organization in biological systems. The pair cross-correlation (PCC) function computed from two-color microscopy images provides a measure of co-localization between differently labeled molecules. Here, we compute a theoretical expression for the PCC function between two molecules using two-dimensional Gaussian

Electrotaxis, the process by which eukaryotic cells establish polarity and move directionally along an electric field, is a well-studied mechanism to steer the migration of cells in vitro and in vivo. Although the influence of an electric field on single cells in culture is well documented, the influence of the electric field on cell-cell interactions has not been well studied. In this work, we quantify

α-hemolysin (HlyA) is a major exotoxin secreted by uropathogenic Escherichia coli (UPEC), known for its ability to lyse red blood cells (RBCs). Although its lytic effects are well characterized, the nonlytic alterations on RBCs, such as increased permeability to Ca2+, osmotic imbalance, and morphological alterations, remain less understood and may be critical in UPEC pathogenesis. This study investigates

Vitamin E (VE) has historically been described as an antioxidant and its roles in radical species scavenging and nutrition are well studied. VE has been proposed to have secondary roles within the membrane but these roles are not as well characterized, with contradictory results emerging throughout the literature. Due to similar structural motifs, comparisons between VE and cholesterol (CHO), another

As a sound pressure detector that uses energy to boost both its sensitivity and selectivity, the inner ear is an active nonequilibrium system. The collective processes of the inner ear that give rise to this exquisite functionality remain poorly understood. One manifestation of the active ear across the animal kingdom is the presence of spontaneous otoacoustic emission (SOAE), idiosyncratic arrays

Accurate estimation of the strength of the protein-ligand interaction is important in the field of drug discovery. The binding strength can be determined by using experimental binding affinity assays which are both time and labor consuming and costly. Predicting the binding affinity/energy in silico is an alternative approach, particularly for virtual screening of large data sets. In general, the distance-based