Myosin-based regulation has emerged as a fundamental new concept governing both cardiac and skeletal muscle contractile function during both health and disease states. Myosin-targeted therapeutics have the potential to treat both heart failure with systolic or diastolic dysfunction based on either activating or inhibiting the function of myosin. In this study we developed a striated muscle myosin-specific

Membrane proteins play crucial roles in biological signaling and represent key targets in drug discovery, garnering significant experimental and computational attention. Recent advances in computational screening techniques have enabled the development of more accurate and efficient binding affinity calculation methods. Among these, the Molecular Mechanics Poisson Boltzmann Surface Area (MMPBSA) method

Neurotransmitter release is triggered by the fusion of synaptic vesicles with the plasma membrane, orchestrated by SNARE proteins synaptobrevin 2 (Syb2), syntaxin 1A (Stx1A), and SNAP25. Recent experimental studies showed that Stx1A palmitoylation of C271/C272 promotes spontaneous neurotransmitter release. However, the mechanistic role of SNARE transmembrane domain (TMD) palmitoylation in membrane

Ongoing improvements of genetically encoded fluorescent proteins have enhanced cellular localization studies and performance of biosensors, such as environmentally or mechanically sensitive fluorescence resonance energy transfer pairs, in cell biological and biophysical research. The brightest yellow fluorescent protein, widely used in these studies is YPet, derived from the jellyfish Aequorea victoria

For swimming bacteria near surfaces, pairwise encounters inevitably occur and impact their social behavior. However, we know little about how the encounter events influence bacterial dynamics due to the limitations in tracking interplaying bacteria in 3D. Herein, we elucidated the motions of encountering E. coli using a combination of 3D holographic tracking experiments and hydrodynamic simulations

Eukaryotic interphase chromosomes maintain a three-dimensional conformation within the nucleus and undergo fluctuations. However, the analysis of chromosome conformational fluctuations has been mainly limited to chromosome conformation capture data that record the contact frequencies between chromosomal regions. Herein, we investigated chromosome fluctuations as polymers based on experimental data

The thermodynamics of arginine-phosphate binding is key to cellular signaling, protein-nucleic acid interactions, and membrane protein dynamics. In biomolecules, monoester phosphates are typically employed as strong electrostatic anchors strategically placed in switch domains to mediate specific interactions. In the diester configuration, phosphate groups act as ubiquitous connectors in all nucleic

ATP synthase, the enzyme responsible for regenerating adenosine triphosphate (ATP) in the cell, comprises a proton-translocating motor in the cell membrane (labeled FO in bacteria, mitochondria, and chloroplasts), coupled by a common stalk to a catalytic motor F1 that synthesizes or hydrolyzes ATP, depending on the direction of rotation. The detailed mechanisms of FO, F1 and their coupling in ATP synthase

The emergence of resistance mutations in the SARS-CoV-2 spike (S) protein presents a challenge for monoclonal antibody treatments like sotrovimab. Understanding the structural, dynamic, and molecular features of these mutations is essential for therapeutic advancements. However, the intricate landscape of potential mutations and critical residues conferring resistance to mAbs like sotrovimab remains

The N-degron pathway is essential for protein quality control and cellular homeostasis. GID4, a subunit of the GID ubiquitin ligase, is the main recognition component of the Pro/N-degron pathway. It binds protein substrates through their N-terminal proline, but its binding model and recognition of nonproline residues remain unclear. In this study, we performed molecular dynamics simulations and binding

Segmented fluorescence correlation spectroscopy (FCS) improves the accuracy of FCS measurements in cells by analyzing data in short temporal segments. We have recently demonstrated the possibility of performing segmented FCS using a commercial confocal laser scanning microscope, enabling the measurement of molecular diffusion in different subcellular regions. In this study, we apply segmented FCS to

The mechanism behind osmolyte-induced protein stabilization remains elusive despite extensive research. Among various hypotheses, the associated water-modulation hypothesis has proved to be the most effective in explaining osmolyte-induced stabilization effects. Earlier, we demonstrated that osmolytes that slow down associated water dynamics enhance protein thermal stability, whereas those that accelerate

The “holy grail” of chromatin research would be to follow the chromatin configuration in individual live cells over time. One way to achieve this goal would be to track the positions of multiple loci arranged along the chromatin polymer with fluorescent labels. Using distinguishable labels would define each locus uniquely in a microscopic image but would restrict the number of loci that could be observed

Neural tissues of the central nervous system are among the softest and most fragile in the human body, protected from mechanical perturbation by the skull and the spine. In contrast, the enteric nervous system is embedded in a compliant, contractile tissue and subject to chronic, high-magnitude mechanical stress. Do neurons and glia of the enteric nervous system display specific mechanical properties

Fibrosis, marked by excessive extracellular matrix (ECM) accumulation, underlies functional decline in numerous diseases and often presents with sex-specific differences in severity. Although biochemical pathways have been widely studied, the contribution of mechanical cues—particularly ECM stiffness—to these disparities remains unclear. Here, we develop an integrative mechanobiological model to investigate

Atomic force microscope (AFM) indentation allows high-resolution spatial characterization of biomechanical properties of cells and tissues. Rapid, reproducible, and quantitative analysis of AFM force curves has been challenging due to several technical limitations, such as excessive noise and uncertainty associated with contact-point determination. Here, we propose a novel machine-learning algorithm

Cell migration through constrictions is essential for many physiological processes. During this confined cell migration, the protein nesprin-2, which links the cytoskeletal network to the nucleus, can accumulate at the front of the nucleus. However, up to now, the exact mechanism of this accumulation is unknown. Here, we further investigate this accumulation mechanism. We quantify the spatial distribution

Animal rhodopsin is a photoreceptive protein crucial for vision, with activation triggered by the cis-trans isomerization of a retinal chromophore upon light absorption. This activation involves a series of thermal intermediates, ultimately leading to G protein-mediated signal transduction. The retinal chromophore is covalently bound to the protein through a protonated Schiff base, and its deprotonation

Intracellular vesicles are typically transported by a small number of kinesin and dynein motors. However, the slow microtubule binding rate of kinesin-1 observed in in vitro biophysical studies suggests that long-range transport may require a high number of motors. To address the discrepancy in motor requirements between in vivo and in vitro studies, we reconstituted motility of 120-nm-diameter liposomes

Living cells actively regulate their volume in response to changes in the extracellular environment, such as osmolarity and chemoattractant concentration. While the basic physical mechanisms of volume regulation are understood from the classic “pump-leak” model, it does not provide an explicit expression for the volume during dynamic regulation and can benefit from further insight into the volume dynamics

Riboswitches are regulatory elements present in bacterial messenger RNA acting as sensors of small molecules and consequently playing a vital role in bacterial gene regulation. The SAM-II riboswitch is a class of riboswitches that recognizes S-adenosyl methionine. It has been previously shown that the presence of Mg2+ ions stabilizes the preexisting minor state of the riboswitch, which is structurally

Toll-like receptor 7 (TLR7), a key member of the TLR family, plays a pivotal role in innate immunity, making it an attractive therapeutic target. However, current synthetic TLR7 agonists are often associated with significant toxicity, highlighting the need for safer, naturally occurring alternatives. Our recent research identified 5′-fragments of tRNAHisGUG (5′-HisGUG) and tRNAValCAC/AAC (5′-ValCAC/AAC)

Epithelial-to-mesenchymal transition (EMT), a key process in cancer metastasis and fibrosis, disrupts cellular adhesion by replacing epithelial E-cadherin with mesenchymal N-cadherin. While, how the shift from E-cadherin to N-cadherin impacts molecular-scale adhesion mechanics and cluster dynamics—and how these changes weaken adhesion under varying mechanical and environmental conditions—remains poorly

Structural changes associated with protein aggregation are challenging to study, requiring the combination of experimental techniques providing insights at the molecular level across diverse scales, ranging from nanometers to microns. Understanding these changes is even more complex when aggregation occurs in the presence of molecular cofactors such as nucleic acids and when the resulting aggregates

Optical stimulation is emerging as a promising alternative to conventional methods for both research and therapeutic purposes due to its advantages, such as reduced energy consumption, minimal invasiveness, and exceptional spatial and temporal precision. Recently, we introduced Ziapin2, a novel light-sensitive azobenzene compound, as a tool to modulate cardiac cell excitability and contractility. The

As an essential component in generating cell contractility, F-actin plays a pivotal role in collective cell migration. However, the mechanisms by which subcellular F-actin dynamics influence the collective behaviors of cell clusters across scales remain poorly understood. In this study, we developed a mechanical model to investigate how the dynamics of stress fibers and cryptic lamellipodia, prominent

The neural code remains undiscovered and understanding synaptic input integration under in vivo-like conditions is just the initial step toward unraveling it. Synaptic signals generate fast dendritic spikes through two main modes of temporal summation: coincidence detection and integration. In coincidence detection, dendrites fire only when multiple incoming signals arrive in rapid succession, whereas

Molecular crowding influences DNA mechanics and DNA-protein interactions and is ubiquitous in living cells. Quantifying the effects of molecular crowding on DNA supercoiling is essential to relating in vitro experiments to in vivo DNA supercoiling. We use single-molecule magnetic tweezers to study DNA supercoiling in the presence of dehydrating or crowding cosolutes. To study DNA supercoiling, we apply

Helicobacter pylori infections increase the risk of noncardia gastric adenocarcinoma, and chemotaxis toward metabolites such as urea plays a key role in modulating infection. Chemotaxis studies are more insightful in strains of H. pylori that are amenable to genetic modification, such as the G27 strain. However, motility in G27 cells can be inconsistent and varies with growth conditions, raising questions

G-protein coupled receptors are critical components in cellular signaling, mediating various physiological responses to external stimuli. Here, we investigate the intricate relationship between cholesterol and the oxytocin receptor (OXTR), focusing on the binding mechanisms and the allosteric cross talk of bound cholesterol to the orthosteric ligand binding pocket. Utilizing molecular docking and molecular

Striga hermonthica is a parasitic weed that destroys billions of dollars’ worth of staple crops every year. Its rapid proliferation stems from an enhanced ability to metabolize strigolactones (SLs), plant hormones that direct root branching and shoot growth. Striga’s SL receptor, ShHTL7, bears more similarity to the staple crop karrikin receptor karrikin insensitive 2 (KAI2) than to SL receptor D14

Predicting the kinetics of drug-protein interactions is crucial for understanding drug efficacy, particularly in personalized medicine, where protein mutations can significantly alter drug residence times. This study applies replica exchange transition interface sampling and its partial path variant to investigate the dissociation kinetics of imatinib from Abelson nonreceptor tyrosine kinase (ABL)

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 (∼50 Å)

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 a flagellum. These

FtsZ, a bacterial tubulin, plays a crucial role in the cytokinesis process. It shares structural similarities with tubulin, as it consists of two domains—N-terminal and C-terminal domains. The protein assembles to form single-stranded protofilaments that exhibit a dynamic phenomenon known as treadmilling where the FtsZ filaments appear to execute a unidirectional movement even though individual monomers

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 posttranslational 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 is a visual disorder that 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 autosomal dominant retinitis

When a blood clot occludes cerebral arteries and causes 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

Förster resonance energy transfer (FRET) is a short-range distance-dependent photophysical phenomenon that allows the measurement of intra- and intermolecular 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 at

Collective migration refers to the coordinated movement of cells as a single unit during migration. Although collective migration enhances invasive and metastatic potential in cancer, the mechanisms driving this behavior and regulating tumor migration plasticity remain poorly understood. This study provides a mechanistic model explaining the emergence of different modes of collective migration under

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

We propose capturing reaction-diffusion on a molecule-by-molecule basis from the fastest acquirable timescale, namely individual photon arrivals. We illustrate our method on the intrinsically disordered human protein linker histone H1.0 and its chaperone prothymosin α, as these diffuse through an illuminated confocal spot and interact, forming larger ternary complexes on millisecond timescales. Most

The tumor suppressor p53 modulates the transcription of a variety of genes, constituting a protective barrier against anomalous cellular proliferation. High-frequency “hotspot” mutations result in loss of function by the formation of amyloid-like aggregates that correlate with cancerous progression. We show that full-length p53 undergoes spontaneous homotypic condensation at submicromolar concentrations

Tubular membrane structures are ubiquitous in cells and in the membranes of intracellular organelles such as the Golgi complex and the endoplasmic reticulum. Tubulation plays essential roles in numerous biological processes, including filopodia growth, trafficking, ion transport, and cellular motility. Understanding the fundamental mechanism of the formation of membrane tubes is thus an important problem

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

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

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