Biophysical reports最新文献

{"title":"Optical tweezers combined with FRET tension sensor reveal force-dependent vinculin dynamics.","authors":"Camille Dubois, Rick I Cohen, Nada N Boustany, Nathalie Westbrook","doi":"10.1016/j.bpr.2026.100267","DOIUrl":"10.1016/j.bpr.2026.100267","url":null,"abstract":"<p><p>Visualizing and quantifying molecular responses to local forces exerted at cell adhesions is crucial to elucidate how physical forces control cellular behavior. Here, we combine optical tweezers with Förster resonance energy transfer (FRET) microscopy of the vinculin tension sensor, VinTS, to measure the response of vinculin, a key mechanical load-bearing protein, to an applied force. Fibroblasts expressing VinTS formed adhesions on fibronectin-coated, 3-μm-diameter, polystyrene beads. As the beads were displaced by the cell, we applied an optical trap to counteract this movement and increase the traction force required by the cell to maintain the bead's displacement. The median bead displacement after 5 min was ∼200 nm in all trapping conditions tested, from zero (no laser) up to 0.26 pN/nm, inducing counteracting forces in the 10-100 pN range. To maintain this displacement, vinculin recruitment increased at high stiffness (up to 35% in relative intensity), while vinculin tension increased only moderately in all trapping conditions (1%-2% decrease in absolute FRET efficiency). Vinculin recruitment was governed by stiffness rather than the magnitude of the traction force and was correlated with vinculin tension at 0.26 pN/nm but not at lower stiffness. In rare instances, vinculin puncta migrated a few micrometers away from the bead, exceeding the bead's movement speed while experiencing an increase in both vinculin intensity and tension. Taken together, the results suggest that combining an optical trap with vinculin tension measurements in living cells uncovers novel vinculin dynamics in the presence of a force.</p>","PeriodicalId":72402,"journal":{"name":"Biophysical reports","volume":" ","pages":"100267"},"PeriodicalIF":2.6,"publicationDate":"2026-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13293687/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148058534","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Protein corona modulates extracellular-vesicle recognition at glycan-based nanobiointerfaces.","authors":"Tomas Bertok, Eduard Jane, Veronika Solovicova, Veronika Pinkova Gajdosova, Andrea Furdova, Matej Micusik, Monika Sramkova, Katarina Kozics, Jan Tkac","doi":"10.1016/j.bpr.2026.100281","DOIUrl":"10.1016/j.bpr.2026.100281","url":null,"abstract":"<p><p>Precise surface engineering is essential for robust characterization of extracellular vesicles and their interactions with biologically relevant interfaces. In this study, Au substrates were modified with C6 self-assembled monolayers (SAMs) bearing different terminal groups after multiple cleaning protocols to optimize monolayer compactness and interfacial quality. Surface area and functionality were further enhanced by gold nanoparticle (AuNP) deposition and secondary SAM formation, enabling layer-by-layer assembly of glycan-based polysaccharide nanostructures. Interface fabrication and growth were monitored by electrochemical methods and atomic force microscopy (AFM). Extracellular vesicles (EVs) from MDA-MB-231 breast cancer cells and benign RWPE-1 (control) cells were affinity isolated using magnetic microparticles, chromatographically preconcentrated, and subjected to protein-corona removal prior to analysis. The impact of the protein corona on antibody-mediated recognition was evaluated by ELISA and revealed markedly improved accessibility of EV surface markers following corona removal. Interactions of EVs with extracellular-matrix-mimicking glycan interfaces were investigated using surface plasmon resonance (SPR). Sensorgrams were analyzed using a physics-informed neural-network-assisted model to extract dissociation constants while reducing the influence of bulk refractive-index contributions typical of vesicle samples. The developed nanobiointerfaces enabled sensitive characterization of EV binding behavior and revealed distinct interaction phenotypes of malignant-derived and non-malignant-derived EVs toward glycan-based surfaces. These findings demonstrate that protein-corona composition and glycan-mediated interactions significantly influence EV recognition and highlight the potential of glycan-based nanobiointerfaces as tools for studying extracellular-vesicle biology, which may contribute to future liquid-biopsy development.</p>","PeriodicalId":72402,"journal":{"name":"Biophysical reports","volume":" ","pages":"100281"},"PeriodicalIF":2.6,"publicationDate":"2026-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13521020/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148686784","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cholesterol differentially regulates α-synuclein binding across membrane packing regimes.","authors":"Orianna H Kou, Brian H Kim, David H Johnson, Wade F Zeno","doi":"10.1016/j.bpr.2026.100282","DOIUrl":"10.1016/j.bpr.2026.100282","url":null,"abstract":"<p><p>α-Synuclein (αSyn) is an intrinsically disordered protein that preferentially binds anionic membranes with lipid packing defects. Cholesterol is an abundant membrane component that regulates packing and organization within membranes, yet its effect on αSyn binding remains unclear, as prior studies report both cholesterol-mediated enhancement and suppression. Here, we investigated whether these conflicting effects reflect differences in the intrinsic packing state of the phospholipid bilayer. Using a quantitative fluorescence microscopy-based binding assay, we measured αSyn binding preferences among reconstituted phosphatidylcholine/phosphatidylserine membranes with varied cholesterol content, lipid tail chemistry, and vesicle curvature. We found that cholesterol's effect depended on the underlying packing regime of the membrane. In defect-rich membranes, cholesterol reduced αSyn binding, consistent with cholesterol tightening lipid packing and reducing αSyn-accessible defects. In membranes with intermediate defect content, cholesterol enhanced binding, whereas tightly packed membranes remained largely insensitive to cholesterol except when high cholesterol content was combined with high membrane curvature. Curvature further shaped these responses, with high curvature compressing cholesterol-dependent differences between membrane compositions. These results show that cholesterol does not universally promote or inhibit αSyn binding. Instead, cholesterol regulates αSyn-membrane interactions through a packing-regime-dependent mechanism shaped by both lipid tail chemistry and membrane curvature. This framework helps reconcile opposing reports in the literature and highlights membrane physical state as a key determinant of how cholesterol modulates αSyn binding.</p>","PeriodicalId":72402,"journal":{"name":"Biophysical reports","volume":" ","pages":"100282"},"PeriodicalIF":2.6,"publicationDate":"2026-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13542602/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148708586","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The oligomeric state of chitooligosaccharide deacetylase from the marine bacterium Vibrio campbellii.","authors":"Sirikan Pongnan, Robert C Robinson, Nuntaporn Kamonsutthipaijit, Tamo Fukamizo, Wipa Suginta","doi":"10.1016/j.bpr.2026.100275","DOIUrl":"10.1016/j.bpr.2026.100275","url":null,"abstract":"<p><p>The crystal structure of a chitooligosaccharide deacetylase (COD) from the marine bacterium Vibrio campbellii (formerly V. harveyi), referred to as VhCOD, exhibits a homodimeric assembly, consistent with previously reported X-ray structures of related Vibrio CODs. Here, we investigated whether this dimeric assembly is retained in solution. Native polyacrylamide gel electrophoresis (native PAGE) analysis revealed that VhCOD is monomeric in solution, with dimeric species present only as a minor population. Small-angle X-ray scattering further indicated that VhCOD preferentially adopts a monomeric state under dilute solution conditions. Analysis of the published crystal structures using PISA/jsPISA (Protein Interfaces, Surfaces and Assemblies/JavaScript version) predicted relatively weak monomer-monomer interactions and suggested that homodimer formation occurs only at sufficiently high protein concentrations (>5 mg·mL^-1). Chemical cross-linking experiments showed that macromolecular crowding reagents promote the formation of cross-linked dimer species. Taken together, we concluded that homodimerization of Vibrio CODs arises under crowded conditions rather than representing a dominant state. This interpretation is consistent with the physiological context of VhCOD as a secretory protein that is translocated through the crowded periplasm, where transient dimerization may be relevant prior to final export across the outer membrane.</p>","PeriodicalId":72402,"journal":{"name":"Biophysical reports","volume":" ","pages":"100275"},"PeriodicalIF":2.6,"publicationDate":"2026-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13356635/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148320964","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Quantifying species-specific binding affinities of transthyretin aggregation inhibitors.","authors":"Xun Sun, H Jane Dyson, Peter E Wright","doi":"10.1016/j.bpr.2026.100274","DOIUrl":"10.1016/j.bpr.2026.100274","url":null,"abstract":"<p><p>Transthyretin (TTR) amyloidosis is one of the most common forms of systemic amyloidosis, involving deposits of pathogenic TTR aggregates in tissues and organs throughout the body. TTR aggregation is initiated by the dissociation of a native TTR tetramer into a monomeric intermediate, which subsequently misfolds and assembles into insoluble aggregates. Using an efficient ¹⁹F-NMR aggregation assay, we previously showed that designed peptide inhibitors can interact with multiple TTR species. However, quantifying species-specific binding affinities has remained difficult because the populations of these TTR species change over time and include a low-abundance monomeric intermediate. Here, we develop a quantitative method to extract species-dependent binding affinities directly from population-resolved ¹⁹F-NMR aggregation data. Using diflunisal as a model compound, we determine its binding affinities for both the tetramer and the monomeric intermediate under acidic, aggregating conditions. At acidic pH, tetramer binding becomes approximately 2-fold tighter, and monomer binding becomes 15-fold stronger, compared to neutral pH. We then apply this method to previously collected ¹⁹F-NMR aggregation data for designed peptide inhibitors. The results show that concatenating two capping peptides increases their binding affinity to both TTR tetramers and monomeric intermediates by about 2-fold, relative to the same peptides mixed separately at equal concentrations. Our method enables direct, quantitative comparison of species-dependent inhibitor binding, providing mechanistic insights useful for designing and optimizing TTR aggregation inhibitors.</p>","PeriodicalId":72402,"journal":{"name":"Biophysical reports","volume":" ","pages":"100274"},"PeriodicalIF":2.6,"publicationDate":"2026-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13355807/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148284896","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bounded multiplicative dynamics govern axonal conduction slowdown.","authors":"Shimon Marom","doi":"10.1016/j.bpr.2026.100277","DOIUrl":"10.1016/j.bpr.2026.100277","url":null,"abstract":"<p><p>Conduction velocity slows along axons, yet the right-skewed distribution of the terminal-to-initial velocity ratio ρ = v_end/v_start has length-invariant mean and variance. A bounded multiplicative framework is introduced in which local geometric and kinetic factors compound proportionally but only within a finite distal domain set by termination conditions that saturate the effective multiplicative depth. The model accounts for the observed stability of the slowdown distribution across lengths and yields discriminating experimental signatures. More generally, it suggests that robust function can emerge through constrained variability rather than structural uniformity.</p>","PeriodicalId":72402,"journal":{"name":"Biophysical reports","volume":" ","pages":"100277"},"PeriodicalIF":2.6,"publicationDate":"2026-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13452967/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148474388","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cellular membranes of the related fission yeast species differ in their dipole potential.","authors":"Bhagyashree Dasari Rao, Snezhana Oliferenko","doi":"10.1016/j.bpr.2026.100283","DOIUrl":"10.1016/j.bpr.2026.100283","url":null,"abstract":"<p><p>The dielectric environment and membrane dipole potential are key electrostatic properties of biological membranes, which modulate the function of membrane-associated proteins. If and how these properties are shaped by species-specific cellular lipid landscapes are fundamental questions. Here, we use two related fission yeast species, Schizosaccharomyces pombe (S. pombe) and Schizosaccharomyces japonicus (S. japonicus), which exhibit remarkable differences in membrane lipid composition, to address this problem. S. pombe synthesizes membranes from largely unsaturated glycerophospholipids with 18- and 16-carbon-long fatty acyl chains and the major fungal sterol ergosterol. Its relative S. japonicus produces abundant saturated asymmetrical glycerophospholipids that contain a medium-chain fatty acyl C10:0 at the sn-2 position of the glycerol backbone. Alongside ergosterol, its membranes contain the sterol mimic diplopterol, produced by a horizontally transferred squalene hopene cyclase of bacterial origin. Using fluorescence lifetime imaging of the solvatochromic dye di-4-ANEPPDHQ, we show that S. pombe and S. japonicus exhibit comparable dielectric environments. Interestingly, dipole potential measurements using the voltage-sensitive probe di-8-ANEPPS show that S. japonicus membranes have higher dipole potential than S. pombe. The in vivo measurements of sterol- and diplopterol-lacking S. japonicus mutants, supported by experiments with model membranes and S. pombe retroengineered to produce the C10-containing glycerophospholipids, indicate that both ergosterol and the saturated asymmetrical glycerophospholipids support high membrane dipole potential. Our results suggest that membrane physicochemical properties result from a combination of lipid composition, packing, and interfacial electrostatics and point to possible avenues in exploring the evolutionary differences in membrane protein function.</p>","PeriodicalId":72402,"journal":{"name":"Biophysical reports","volume":" ","pages":"100283"},"PeriodicalIF":2.6,"publicationDate":"2026-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7619421/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148835330","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effect of two-dimensional spatial confinement on platelet mechanics.","authors":"Aylin Balmes, Vincent Gidlund, Tilman E Schäffer","doi":"10.1016/j.bpr.2026.100261","DOIUrl":"10.1016/j.bpr.2026.100261","url":null,"abstract":"<p><p>Platelets are small, anucleate cells critical for hemostasis and thrombosis. Within platelet plugs and narrow capillaries, they often encounter spatially confining microenvironments. To examine how confinement influences platelet properties, we employed microcontact printing to generate fibrinogen micropatterns of varying sizes and shapes. Platelets cultured on these micropatterns adapted both their morphology and mechanical characteristics. Scanning ion conductance microscopy revealed changes in area, aspect ratio, and height, while fluorescence microscopy showed F-actin redistribution toward the periphery. Confinement reduced platelet stiffness in a size-dependent but shape-independent manner. To explore the role of intracellular signaling, we examined cyclic guanosine monophosphate (cGMP), a key inhibitor of platelet activation, adhesion, and aggregation. Treatment with a cGMP analog preserved F-actin redistribution but prevented stiffness changes in response to confinement, indicating that cGMP inhibits stiffness modulation without affecting cytoskeletal reorganization.</p>","PeriodicalId":72402,"journal":{"name":"Biophysical reports","volume":" ","pages":"100261"},"PeriodicalIF":2.6,"publicationDate":"2026-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13136703/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147663214","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A dynamic duo: Copper metalloregulators and continuous-wave electron spin resonance spectroscopy.","authors":"Alysia Mandato, Sunil Saxena, Sharon Ruthstein","doi":"10.1016/j.bpr.2026.100259","DOIUrl":"10.1016/j.bpr.2026.100259","url":null,"abstract":"<p><p>This review highlights the use of continuous-wave electron spin resonance (ESR) spectroscopy to investigate protein site-specific dynamics and metal coordination in bacterial copper metalloregulators. ESR provides direct insight into how metal binding influences conformational flexibility, revealing how similar proteins can employ distinct mechanisms of transcriptional regulation. Studies of the activator CueR and the repressor CsoR show that these systems use fundamentally different strategies to control gene expression. CueR functions as a stable dimer that activates transcription through metal-induced conformational changes rather than oligomeric transitions. In E. coli, Cu(I) binding rapidly increases dynamics in the DNA-binding domain, while in Pseudomonas aeruginosa, CueR exhibits a more gradual, DNA-dependent response that reflects adaptation to alternative copper resistance pathways. In contrast, CsoR exists in a dynamic equilibrium between dimeric and tetrameric states, with oligomerization playing a central role in its repressor mechanism. Small shifts in subunit exchange may fine-tune DNA binding and facilitate dissociation upon Cu(I) coordination. This review demonstrates how ESR spectroscopy can capture the subtle structural and dynamical differences that define metalloregulator function and highlight the diversity of bacterial strategies for maintaining metal homeostasis.</p>","PeriodicalId":72402,"journal":{"name":"Biophysical reports","volume":" ","pages":"100259"},"PeriodicalIF":2.6,"publicationDate":"2026-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13101592/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147494870","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Distinct disassembly modes shape cytoskeletal assembly and fluctuations.","authors":"Md Sorique Aziz Momin, Michaela Cohen, Lishibanya Mohapatra","doi":"10.1016/j.bpr.2026.100263","DOIUrl":"10.1016/j.bpr.2026.100263","url":null,"abstract":"<p><p>How distinct cytoskeletal structures assemble and maintain their characteristic sizes on different timescales while drawing from a shared pool of subunits remains an open question in cell biology. Experiments indicate that mechanisms promoting the disassembly of these structures and replenishing the pool may play a vital role. Here, we compare two disassembly models: one with a constant monomer loss rate and another that is size dependent, where structures lose filament fragments through severing. Using analytical calculations and simulations, we examine their effects on the assembly of two structure types, filaments and bundles composed of linear filaments, both in isolation and when co-assembling in a shared pool. We find that both models control assembly and regulate structure size in distinct ways. However, the assembly of both structures to their steady-state size is accelerated with severing, accompanied by a faster decay of autocorrelations in their length fluctuations. Moreover, we find that severing can regulate multiple structures assembling from a shared pool, constraining them to defined sizes. Our study identifies key parameters governing assembly kinetics and fluctuation dynamics associated with each disassembly mode, highlights measurable quantities such as coefficient of variation and bundle tapering that can help distinguish between different disassembly mechanisms, and reveals specific signatures of structures assembling in a limited monomer pool. Together, these results provide a framework for experiments to identify assembly-control mechanisms in cytoskeletal structures and elucidate the role specific disassembly modes can have in modulating structure formation and maintenance.</p>","PeriodicalId":72402,"journal":{"name":"Biophysical reports","volume":" ","pages":"100263"},"PeriodicalIF":2.6,"publicationDate":"2026-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13195333/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147790205","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}