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"Poking cells: AI can help here too". Biophys. J. (IF 3.2) Pub Date : 2025-04-22 Juanyong Li,Kristen Billiar
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tRNA kinetics on the ribosome depends non-monotonically on intersubunit rotation. Biophys. J. (IF 3.2) Pub Date : 2025-04-18 Sandra Byju,Paul C Whitford
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
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Bacteria Can Rotate while Body-Tethered to a Solid Surface. Biophys. J. (IF 3.2) Pub Date : 2025-04-18 Jordan Bell,Silverio Johnson,Brandon Pugnet,Jay X Tang
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
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Functional asymmetry in processivity clamp proteins. Biophys. J. (IF 3.2) Pub Date : 2025-04-16 Sam Mahdi,Penny J Beuning,Dmitry M Korzhnev
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
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Active and inactive pathways in the kinetic mechanism of the G51V retinitis pigmentosa mutant photoreaction. Biophys. J. (IF 3.2) Pub Date : 2025-04-16 Istvan Szundi,Weekie Yao,Eefei Chen,David S Kliger,David L Farrens
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
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Comparative Study on Efficacy of Thrombolytic Protocols: Dual Therapy against Standard tPA Regimen. Biophys. J. (IF 3.2) Pub Date : 2025-04-16 Saleheh Heydari Ghasemi,Mohammad-Taghi Ahmadian,Ahmad Assempour,Seyed Hossein Ahmadi Tafti
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
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FRET-FCS: Advancing Comprehensive Insights into Complex Biological Systems. Biophys. J. (IF 3.2) Pub Date : 2025-04-15 Anay Lazaro-Alfaro,Sterling L N Nicholas,Hugo Sanabria
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
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Synergistic effect of PIP2 and PIP3 on membrane-induced phase separation of integrin complexes. Biophys. J. (IF 3.2) Pub Date : 2025-04-14 Chiao-Peng Hsu,Arsenii Hordeichyk,Jonas Aretz,Reinhard Fässler,Andreas R Bausch
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
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SNARE complex assembly and disassembly dynamics in response to Ca2+ current activation in live cells Biophys. J. (IF 3.2) Pub Date : 2025-04-09 Qinghua Fang, Ying Zhao, Dong An, Manfred Lindau
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
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Decoding SP-D and glycan binding mechanisms using a novel computational workflow. Biophys. J. (IF 3.2) Pub Date : 2025-04-09 Deng Li,Mona S Minkara
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
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Modeling platelet P2Y1/12 pathway to integrin activation Biophys. J. (IF 3.2) Pub Date : 2025-04-08 Keshav B. Patel, Wolfgang Bergmeier, Aaron L. Fogelson
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
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Effects of curvature on growing films of microorganisms Biophys. J. (IF 3.2) Pub Date : 2025-04-07 Yuta Kuroda, Takeshi Kawasaki, Andreas M. Menzel
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
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Heterogeneous condensates of transcription factors in embryonic stem cells: Molecular simulations Biophys. J. (IF 3.2) Pub Date : 2025-04-06 Azuki Mizutani, Cheng Tan, Yuji Sugita, Shoji Takada
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
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Biophysical characterization of anion channels in mitochondrion-endoplasmic-reticulum contact sites Biophys. J. (IF 3.2) Pub Date : 2025-04-04 Shridhar Kiran Sanghvi, Denis Gabrilovich, Satish K. Raut, Ajay Gopalan, Aryan Singh, Harmeet Rireika Bhachu, Mayukha Dyta, Veronica Loyo-Celis, Jenna Thuma, Devasena Ponnalagu, Jonathan Davis, Shubha Gururaja Rao, Harpreet Singh
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
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Chromatin unfolding via loops can drive clustered transposon insertion Biophys. J. (IF 3.2) Pub Date : 2025-04-04 Roshan Prizak, Aaron Gadzekpo, Lennart Hilbert
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
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Bacteriorhodopsin proton-pumping mechanism: Successes and challenges in computational approaches Biophys. J. (IF 3.2) Pub Date : 2025-04-03 Ana-Nicoleta Bondar, Jeremy C. Smith
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
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Glycolysis model shows that allostery maintains high ATP and limits accumulation of intermediates Biophys. J. (IF 3.2) Pub Date : 2025-04-03 Mangyu Choe, Tal Einav, Rob Phillips, Denis V. Titov
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
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In silico design of foldable lasso peptides Biophys. J. (IF 3.2) Pub Date : 2025-04-03 John D.M. Nguyen, Gabriel C.A. da Hora, Marcus C. Mifflin, Andrew G. Roberts, Jessica M.J. Swanson
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
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Charge distribution and helicity tune the binding of septin's amphipathic helix domain to membranes Biophys. J. (IF 3.2) Pub Date : 2025-04-02 Christopher J. Edelmaier, Stephen J. Klawa, S. Mahsa Mofidi, Qunzhao Wang, Shreeya Bhonge, Ellysa J.D. Vogt, Brandy N. Curtis, Wenzheng Shi, Sonya M. Hanson, Daphne Klotsa, M. Gregory Forest, Amy S. Gladfelter, Ronit Freeman, Ehssan Nazockdast
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
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Comparison of BH3-dependent and BH3-independent membrane interactions of pro-apoptotic factor BAX Biophys. J. (IF 3.2) Pub Date : 2025-04-02 Mykola V. Rodnin, Victor Vasquez-Montes, Pierce T. O’Neil, Alexander Kyrychenko, Alexey S. Ladokhin
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
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Super-resolution algorithms for imaging FCS enhancement: A comparative study Biophys. J. (IF 3.2) Pub Date : 2025-04-02 Shambhavi Pandey, Nithin Pathoor, Thorsten Wohland
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
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Barrier effects on the kinetics of cohesin-mediated loop extrusion Biophys. J. (IF 3.2) Pub Date : 2025-04-02 Leiyan Chen, Zhenquan Zhang, Zihao Wang, Liu Hong, Haohua Wang, Jiajun Zhang
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
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Mechanical adaptivity of red blood cell flickering to extrinsic membrane stiffening by the solid-like biosurfactant β-Aescin Biophys. J. (IF 3.2) Pub Date : 2025-04-01 Lara H. Moleiro, Diego Herráez-Aguilar, Guillermo Solís-Fernández, Niccolo Caselli, Carina Dargel, Verónica I. Dodero, José M. Bautista, Thomas Hellweg, Francisco Monroy
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
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Single-molecule measurements of double-stranded DNA condensation Biophys. J. (IF 3.2) Pub Date : 2025-03-31 Helena Gien, Ioulia Rouzina, Michael Morse, Micah J. McCauley, Mark C. Williams
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
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Distinct roles of protrusions and collagen deformation in collective invasion of cancer cell types Biophys. J. (IF 3.2) Pub Date : 2025-03-31 Ye Lim Lee, Gregory D. Longmore, Amit Pathak
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
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Predicted functional consequences of WNT ligand mutations in colorectal cancer Biophys. J. (IF 3.2) Pub Date : 2025-03-31 Aamir Ahmed, David Shorthouse
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
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A closed-loop system for millisecond readout and control of membrane tension Biophys. J. (IF 3.2) Pub Date : 2025-03-30 Michael Sindoni, Jörg Grandl
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
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Accuracy of distance distributions and dynamics from single-molecule FRET Biophys. J. (IF 3.2) Pub Date : 2025-03-30 Mark Nüesch, Miloš T. Ivanović, Daniel Nettels, Robert B. Best, Benjamin Schuler
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
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Perspectives: Comparison of deep learning segmentation models on biophysical and biomedical data Biophys. J. (IF 3.2) Pub Date : 2025-03-28 J. Shepard Bryan IV, Pedro Pessoa, Meysam Tavakoli, Steve Pressé
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
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A discard-and-restart MD algorithm for the sampling of protein intermediate states Biophys. J. (IF 3.2) Pub Date : 2025-03-28 Alan Ianeselli, Jonathon Howard, Mark B. Gerstein
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
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Agent-based model of the human colon to investigate mechanisms of pathogen colonization resistance Biophys. J. (IF 3.2) Pub Date : 2025-03-27 Samantha Johanna Fletcher, Carly Ching, Mark Paladin Suprenant, Darash Desai, Muhammad Hamid Zaman
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
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Flow-sensitive ion channels in vascular endothelial cells: Mechanisms of activation and roles in mechanotransduction Biophys. J. (IF 3.2) Pub Date : 2025-03-27 Katie M. Beverley, Sang Joon Ahn, Irena Levitan
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
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Are cell length and volume interchangeable in cell cycle analysis? Biophys. J. (IF 3.2) Pub Date : 2025-03-26 Prathitha Kar, Ariel Amir
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
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A novel "bio-tag" for cryo-EM studies based on the small, electron-dense protein Csp1 Biophys. J. (IF 3.2) Pub Date : 2025-03-26 Weekie Yao, Adam C. Oken, David L. Farrens
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
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Reversible tuning of membrane sterol levels by cyclodextrin in a dialysis setting Biophys. J. (IF 3.2) Pub Date : 2025-03-25 Cynthia Alsayyah, Emmanuel Rodrigues, Julia Hach, Mike F. Renne, Robert Ernst
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
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Mapping the distribution and affinities of ligand interaction sites on human serum albumin Biophys. J. (IF 3.2) Pub Date : 2025-03-24 Asuka A. Orr, Agbo-Oma Uwakweh, Xun Li, Ahmad Kiani Karanji, Stephen W. Hoag, Daniel J. Deredge, Alexander D. MacKerell Jr.
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
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Fluorescence correlation spectroscopy for particle sizing: A notorious challenge Biophys. J. (IF 3.2) Pub Date : 2025-03-24 Jan-Hagen Krohn, Adam Mamot, Nastasja Kaletta, Yusuf Qutbuddin, Petra Schwille
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
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How spatial temperature gradients modulate infrared stimulation of the ex vivo rat sciatic nerve Biophys. J. (IF 3.2) Pub Date : 2025-03-24 Louis Vande Perre, Javier Chávez Cerda, Benoit Haut, Maxime Verstraeten, Romain Raffoul, Jean Delbeke, Riëm El Tahry, Simon-Pierre Gorza, Antoine Nonclercq
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
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Solid-state NMR of membrane peptides and proteins in the lipid cubic phase Biophys. J. (IF 3.2) Pub Date : 2025-03-20 Kiefer O. Ramberg, Coilin Boland, Hamed Kooshapur, Olivier Soubias, Maciej Wiktor, Chia-Ying Huang, Jonathan Bailey, Klaus Gawrisch, Martin Caffrey
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
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The Rab3 GTPase cycle modulates cardiomyocyte exocytosis and atrial natriuretic peptide release Biophys. J. (IF 3.2) Pub Date : 2025-03-20 Kobina Essandoh, Arasakumar Subramani, Sribharat Koripella, Matthew J. Brody
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
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A generalized adder for cell size homeostasis: Effects on stochastic clonal proliferation Biophys. J. (IF 3.2) Pub Date : 2025-03-20 César Nieto, César Augusto Vargas-García, Abhyudai Singh
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
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Measurement force, speed, and postmortem time affect the ratio of CNS gray-to-white-matter elasticity Biophys. J. (IF 3.2) Pub Date : 2025-03-16 Julia Monika Becker, Alexander Kevin Winkel, Eva Kreysing, Kristian Franze
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
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Buckling of red blood cell membrane in narrow capillaries induces excessive wall shear stress Biophys. J. (IF 3.2) Pub Date : 2025-03-15 Deyun Liu, Kazuyasu Sugiyama, Xiaobo Gong
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
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Structural and Hydrodynamic Characterization of Dimeric Human Oligoadenylate Synthetase 2 Biophys. J. (IF 3.2) Pub Date : 2025-03-13 Amit Koul, Danielle Gemmill, Nikhat Lubna, Markus Meier, Natalie Krahn, Evan P. Booy, Jörg Stetefeld, Trushar R. Patel, Sean A. McKenna
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Aggregation and disaggregation of red blood cells: Depletion versus bridging Biophys. J. (IF 3.2) Pub Date : 2025-03-13 Nicolas Moreno, Kirill Korneev, Alexey Semenov, Alper Topuz, Thomas John, Minne Paul Lettinga, Marco Ellero, Christian Wagner, Dmitry A. Fedosov
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
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FAIR data for optical tweezers experiments Biophys. J. (IF 3.2) Pub Date : 2025-03-12 Matthew T.J. Halma, Sowmiyaa Kumar, Jan van Eck, Sanne Abeln, Alexander Gates, Gijs J.L. Wuite
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
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Interfacial energy constraints are sufficient to align cells over large distances Biophys. J. (IF 3.2) Pub Date : 2025-03-12 Sham Tlili, Murat Shagirov, Shaobo Zhang, Timothy E. Saunders
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
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Control of cardiac waves in human iPSC-CM syncytia by a Halbach array and magnetic nanoparticles Biophys. J. (IF 3.2) Pub Date : 2025-03-12 Maria R. Pozo, Yuli W. Heinson, Christianne J. Chua, Emilia Entcheva
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
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Pair cross-correlation analysis for assessing protein co-localization Biophys. J. (IF 3.2) Pub Date : 2025-03-12 Pintu Patra, Cecilia P. Sanchez, Michael Lanzer, Ulrich S. Schwarz
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
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Electrotaxis disrupts patterns of cell-cell interactions of human corneal epithelial cells in vitro Biophys. J. (IF 3.2) Pub Date : 2025-03-11 Rebecca M. Crossley, Simon F. Martina-Perez
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
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Escherichia coli α-hemolysin induces red blood cell retention in a microfluidic spleen-like device Biophys. J. (IF 3.2) Pub Date : 2025-03-11 Nicolás Andrés Saffioti, Emilia Belén Sousa, Mickaël Marin, María Florencia Leal Denis, Mariano Aníbal Ostuni, Vanesa Herlax, Pablo Julio Schwarzbaum, Diego Pallarola
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
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The brief life-story of irreversibly sickled cells Biophys. J. (IF 3.2) Pub Date : 2025-03-10 Merav Socolovsky
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Does vitamin E behave like cholesterol? An examination of vitamin E’s effects on phospholipid membrane structure and dynamics through sum-frequency vibrational spectroscopy Biophys. J. (IF 3.2) Pub Date : 2025-03-06 Joshua M. Taylor, Kai H. Gerton, John C. Conboy
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
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Auditory cellular cooperativity probed via spontaneous otoacoustic emissions Biophys. J. (IF 3.2) Pub Date : 2025-03-03 Christopher Bergevin, Rebecca E. Whiley, Hero Wit, Geoffrey A. Manley, Pim van Dijk
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
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Flipping the switch: Illuminating inverted ligand activation of peptide-gated ion channels Biophys. J. (IF 3.2) Pub Date : 2025-03-03 Wassim Elkhatib, Adriano Senatore
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Morphological trapping of neurotransmitters in synaptic clefts: A new dimension in neural plasticity Biophys. J. (IF 3.2) Pub Date : 2025-02-28 Bugra Kaytanli, Mattia Bacca
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Further exploration of the quantitative distance-energy and contact number-energy relationships for predicting the binding affinity of protein-ligand complexes Biophys. J. (IF 3.2) Pub Date : 2025-02-27 Yong Xiao Yang, Bao Ting Zhu
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
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Developmental biophysics Biophys. J. (IF 3.2) Pub Date : 2025-02-26 Thorsten Wohland, Timothy E. Saunders, Chii Jou Chan
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Cellular teamwork in cancer invasion Biophys. J. (IF 3.2) Pub Date : 2025-02-26 Guhan Qian, Paolo P. Provenzano