European Biophysics Journal最新文献

{"title":"Anisotropy and shear stress accumulation during collective migration of epithelial cells","authors":"Ivana Pajic-Lijakovic,&nbsp;Milan Milivojevic,&nbsp;Peter V. E. McClintock","doi":"10.1007/s00249-026-01813-y","DOIUrl":"10.1007/s00249-026-01813-y","url":null,"abstract":"<div>\u0000 \u0000 <p>Anisotropy is a fundamental physical characteristic that influences efficient cell migration in biological systems. Concurrently, anisotropy serves as a primary factor contributing to a significant accumulation of mechanical stress within migrating epithelial collectives, provided that the cells maintain the strong E-cadherin-mediated cell-cell adhesion contacts that are characteristic of epithelial cells. While cells are capable of effectively enduring both compressive and tensile stress, the shear stress that can be generated during a physiological process such as collective cell migration poses a risk of: (i) disrupting the adhesion contacts among cells and between cells and the extracellular matrix, (ii) causing a partial disintegration of the lipid bilayer and cytoskeleton, (iii) triggering cellular inflammation, and (iv) inducing changes in gene expression. The principal aims of this theoretical analysis are: (i) to emphasize the main characteristics of isotropic and anisotropic wetting/de-wetting of migrating epithelial collectives as the main factor in mechanical stress generation; (ii) to formulate a constitutive model of the anisotropic viscoelasticity of migrating epithelial and mesenchymal collectives; (iii) to emphasize the physical factors related to cell sensitivity to shear stress; and (iv) to explore potential cellular strategies to mitigate shear stress, while also highlighting the associated costs of these strategies.</p>\u0000 </div>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":"55 1","pages":"21 - 39"},"PeriodicalIF":2.4,"publicationDate":"2026-02-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12929303/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146103561","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Multiscale characterization of lipid bilayer disruption induced by Methyl-β-cyclodextrin (MβCD)","authors":"Wisnu Arfian Anditya Sudjarwo,&nbsp;Jose L. Toca-Herrera","doi":"10.1007/s00249-026-01821-y","DOIUrl":"10.1007/s00249-026-01821-y","url":null,"abstract":"<div>\u0000 \u0000 <p>This study investigated the biophysical impacts of methyl-β-cyclodextrin (MβCD) on supported lipid bilayers composed of DPPC/POPE (1:1) and DPPC/POPE/Chol (1:1:2). Using Quartz Crystal Microbalance with Dissipation (QCM-D), Atomic Force Microscopy (AFM) imaging and force–distance (F–D) curve analysis, we monitored vesicle fusion, assessed bilayer symmetry, and evaluated mechanical stability before and after MβCD treatment. The DPPC/POPE bilayer initially showed a distinct “kink” in its F–D curve and a single breakthrough force, indicating a relatively asymmetric and heterogenous structure. Upon MβCD treatment, the bilayer exhibited symmetry, as evidenced by breakthrough force profiles. Similarly, the cholesterol-containing DPPC/POPE/Chol bilayers displayed two breakthrough points, signifying distinct lipid domains, higher rigidity, and heterogeneity. After one hour of MβCD treatment, these bilayers became more homogeneous and showed a single breakthrough peak—evidence of successful cholesterol or phospholipid extraction. Breakthrough force histograms reinforced these findings by revealing substantial shifts in force distributions. Complementary dynamic light scattering (DLS) and zeta potential measurements confirmed vesicle size and surface charge, while QCM detected notable mass loss in cholesterol-rich bilayers at elevated temperatures. Collectively, these findings underscore the role of cholesterol in bilayer architecture and validate MβCD as an effective modulator of bilayer composition and symmetry.</p>\u0000 </div>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":"55 :","pages":"813 - 826"},"PeriodicalIF":2.3,"publicationDate":"2026-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00249-026-01821-y.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146083680","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Predicting peptide orientation in membrane interactions: a review on transmembrane and surface-bound states","authors":"Lúcio Otávio Nunes","doi":"10.1007/s00249-025-01810-7","DOIUrl":"10.1007/s00249-025-01810-7","url":null,"abstract":"<div>\u0000 \u0000 <p>Understanding the mechanism of action of antimicrobial peptides (AMPs) is a key step in developing new antimicrobial agents. This mechanism is often linked to the peptide’s orientation upon interaction with lipid membranes—whether it inserts into the membrane or remains surface-bound. Despite its importance, the literature lacks a systematic approach to predict peptide orientation based on physicochemical characteristics. This review highlights how peptide orientation at membranes can be qualitatively predicted by integrating sequence-level features, length/effective span, amphipathicity, charge distribution, and helix propensity, with membrane/environmental variables. The approach is illustrated with representative AMPs and it is discussed how external factors (pH, anionic fraction, cholesterol, ionic strength) bias surface-bound versus transmembrane regimes. The review is built upon theoretical observations and integrates structural, thermodynamic, and electrostatic parameters drawn from experimental data in the literature. While this study does not aim to provide a definitive classification, it offers a starting point that may guide experimental validation and future refinement.</p>\u0000 </div>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":"55 1","pages":"9 - 20"},"PeriodicalIF":2.4,"publicationDate":"2026-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12929272/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146028106","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Standardization of cross-site biophysical studies of bovine insulin amyloids is challenged by structural polymorphism","authors":"Sofie Nyström,&nbsp;Davide Odino,&nbsp;Annalisa Relini,&nbsp;Claudio Canale,&nbsp;Raffaella Parlato,&nbsp;Yari Knelissen,&nbsp;Alessia Lasorsa,&nbsp;Wouter H. Roos,&nbsp;Patrick C.A. van der Wel,&nbsp;Søren V. Hoffmann,&nbsp;Nykola C. Jones,&nbsp;Vincent van Hemelryck,&nbsp;Jehan Waeytens,&nbsp;Vincent Raussens,&nbsp;Per Hammarström","doi":"10.1007/s00249-025-01811-6","DOIUrl":"10.1007/s00249-025-01811-6","url":null,"abstract":"<div>\u0000 \u0000 <p>Protein structure can be analysed using a range of different techniques. Many of the available principal techniques for assessing protein structure are developed and optimized for natively folded proteins that are soluble. Amyloids are an alternative protein fold, often associated with protein malfunction and disease but are also found as the functional fold for some proteins. While functional amyloids, just like soluble globular proteins, commonly attain one specific and precise fold to exert its function, disease associated amyloids are often poorly soluble and structurally highly variable. This is known as structural polymorphism. To investigate to what extent molecular biophysics techniques can be standardized for studies of amyloid fibrils, five sites within the Horizon 2020 funded project MOlecular-Scale Biophysics Research Infrastructure (MOSBRI) addressed this issue via a joint research activity. For this study we selected bovine insulin as a convenient, accessible, and distributable amyloid model system. The benchmark comparable techniques for observing formed amyloid fibrils at the different sites were fluorescence spectroscopy of two amyloid ligands (ThT and pFTAA) and negative stain transmission electron microscopy. The outcome of this study yielded results with a large variability between different insulin amyloid fibril preparations, between sites, and within chemically identical preparations from one site. We mainly attribute these hard to control differences to the intrinsic polymorphic behaviour of insulin amyloid fibrils. We also present a range of experimental measurement techniques to highlight their potential use for studying amyloid structure and amyloid polymorphism.</p>\u0000 </div>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":"55 :","pages":"439 - 458"},"PeriodicalIF":2.3,"publicationDate":"2026-01-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00249-025-01811-6.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146008485","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Simulation of intracellular delivery through permeabilized multivesicular vesicles","authors":"Shah Sajnin Anna,&nbsp;Shahariar Emon,&nbsp;Md. Asaduzzaman,&nbsp;Shovon Saha,&nbsp;Md. Atikur Rahman,&nbsp;Mohammad Abu Sayem Karal,&nbsp;Md Lokman Hossen,&nbsp;Samiron Kumar Saha,&nbsp;Hiromitsu Takaba,&nbsp;Md. Akhtaruzzaman,&nbsp;Md. Khorshed Alam","doi":"10.1007/s00249-026-01819-6","DOIUrl":"10.1007/s00249-026-01819-6","url":null,"abstract":"<div>\u0000 \u0000 <p>Cell permeabilization techniques are widely used to enable intracellular delivery of therapeutic molecules. Although these methods show promise for drug delivery and gene therapy, controlling and quantifying molecular transport at the nanoscale remains a significant challenge due to the structural complexity of mammalian cells. Multivesicular vesicles (MVVs), consisting of a large outer vesicle encapsulating multiple smaller vesicles, offer a simplified biomimetic platform that captures key aspects of cellular compartmentalization of mammalian cells. In this study, we employed finite element method (FEM)-based simulations using COMSOL Multiphysics to investigate passive molecular transport through permeabilized MVVs. The model incorporated biologically relevant pore sizes and three commonly used fluorescent probes of increasing molecular size: Calcein, Texas-red dextran 3000 (TRD-3k), and TRD-10k. The results reveal size-dependent accumulation kinetics. Additionally, transport efficiency was enhanced with increased pore diameter, indicating that both molecular and structural parameters influence delivery outcomes. Importantly, the simulations demonstrate that compartmentalized vesicle structures cause transport to vary across space and time. The model successfully matches experimental results seen in permeabilized vesicles and expands them to more complex nested vesicle systems. These findings highlight the role of vesicle architecture in shaping transport outcomes and provide a computational framework for exploring compartmentalization effects relevant to intracellular delivery strategies.</p>\u0000 </div>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":"55 1","pages":"89 - 99"},"PeriodicalIF":2.4,"publicationDate":"2026-01-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146008510","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Non-invasive biomechanical characterization of embryos using microfluidic cantilevers","authors":"Irene C. Turnbull,&nbsp;Tai De Li,&nbsp;Pedro Sanabria,&nbsp;Aimee Stablewski,&nbsp;Angelo Gaitas","doi":"10.1007/s00249-026-01814-x","DOIUrl":"10.1007/s00249-026-01814-x","url":null,"abstract":"<div>\u0000 \u0000 <p>Embryonic development is intricately regulated by mechanical properties such as stiffness, which influence developmental viability and implantation success – factors critical in assisted reproductive technologies (ART). Traditional embryo evaluation relies predominantly on morphology, lacking quantitative mechanical parameters that could enhance selection accuracy. Recent studies indicate that the stiffness (elasticity) of the zona pellucida (ZP) – the glycoprotein-rich extracellular matrix surrounding mammalian oocytes and embryos – correlates with embryo quality and developmental potential​. However, current biomechanical characterization techniques – including micropipette aspiration, atomic force microscopy (AFM), microtactile sensors, and microelectromechanical systems (MEMS) based sensors – either pose risks of mechanical damage or involve complex, time-consuming procedures unsuitable for clinical settings​. Here, we introduce a novel approach leveraging fluidic force microscopy cantilevers to non-invasively evaluate embryo biomechanics. Our proof-of-concept study demonstrates rapid, precise stiffness profiling of intact mouse embryos (specifically ZP elasticity). Using gentle microsuction attachment with no chemical adhesives or rigid immobilization, the method preserves embryo integrity while providing reproducible elasticity measurements. This method combines the precision of AFM with minimal invasiveness, offering a promising new quantitative biomechanical indicator to augment clinical embryo assessment and paving the way for broader applications in reproductive biology.</p>\u0000 </div>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":"55 1","pages":"111 - 118"},"PeriodicalIF":2.4,"publicationDate":"2026-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12929246/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146008471","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Impact of glucose on a Gel-A-Based polyphenol biosensor: A QCM-D study","authors":"Giorgia Tori,&nbsp;Antonella Battisti,&nbsp;Mariacristina Gagliardi,&nbsp;Marco Cecchini","doi":"10.1007/s00249-025-01807-2","DOIUrl":"10.1007/s00249-025-01807-2","url":null,"abstract":"<div>\u0000 \u0000 <p>Polyphenols play a key role in the agrifood sector, particularly in winemaking and olive oil production, where they contribute to product quality assessment. In this study, the potential interference of glucose on our previously developed Gelatin type A-based polyphenol biosensor was evaluated using Quartz Crystal Microbalance with Dissipation Monitoring (QCM-D). Since glucose is naturally present in grapes, olives, and their derivatives, its effect on the biosensor performance must be assessed to ensure reliable polyphenol detection. The biosensor response to glucose was tested across a wide concentration range (10^–6 to 3 × 10² g L⁻¹), covering typical glucose content found in musts and wines. The results showed minimal biosensor response, even at the highest glucose concentration, indicating negligible interference with the biosensor signal. These findings suggest that this biosensor can accurately detect polyphenols in real samples without significant signal distortion from glucose. Overall, the study reinforces the biosensor’s potential application in oenology and other agrifood contexts such as olive oil production.</p>\u0000 </div>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":"55 :","pages":"309 - 318"},"PeriodicalIF":2.4,"publicationDate":"2026-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146008451","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Achieving femtomolar affinities in structure-based drug design","authors":"Asta Zubrienė,&nbsp;Maija Kurtenoka,&nbsp;Vaida Paketurytė-Latvė,&nbsp;Janis Leitans,&nbsp;Elena Manakova,&nbsp;Mantas Žvirblis,&nbsp;Andris Kazaks,&nbsp;Vladislava Eimonta,&nbsp;Kaspars Tars,&nbsp;Saulius Gražulis,&nbsp;Vytautas Petrauskas,&nbsp;Jurgita Matulienė,&nbsp;Virginija Dudutienė,&nbsp;Kirill Shubin,&nbsp;Daumantas Matulis","doi":"10.1007/s00249-025-01812-5","DOIUrl":"10.1007/s00249-025-01812-5","url":null,"abstract":"<div>\u0000 \u0000 <p>Developing small-molecule compounds as effective and safe pharmaceuticals relies on their ability to bind disease-associated proteins with high affinity and selectivity. However, achieving ultra-high affinity in the femtomolar range is a major challenge in medicinal chemistry due to the inherent constraints of protein-ligand interactions. Here, we introduce a novel class of di-meta-substituted fluorinated benzenesulfonamide compounds that achieve an extraordinary dissociation constant of 44 fM for carbonic anhydrase IX (CAIX). CAIX, a transmembrane enzyme implicated in hypoxic tumor progression through the increase of microenvironment acidity, represents a promising target for anticancer therapy. Inhibiting CAIX may help suppress tumor growth and improve cancer treatment outcomes. The newly developed compounds exhibit the highest affinity for CAIX reported to date and rank among the strongest known non-covalent small-molecule inhibitors.</p>\u0000 </div>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":"55 1","pages":"55 - 62"},"PeriodicalIF":2.4,"publicationDate":"2026-01-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145996970","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Single molecule force spectroscopy for evaluating inhibitors of SARS-CoV-2 variants of concern","authors":"Rong Zhu,&nbsp;Yoo Jin Oh,&nbsp;Peter Hinterdorfer","doi":"10.1007/s00249-026-01818-7","DOIUrl":"10.1007/s00249-026-01818-7","url":null,"abstract":"<div>\u0000 \u0000 <p>The binding between the SARS-CoV-2 Spike protein and its cellular receptor ACE2 is essential for viral entry and infection and, therefore, represents a critical target for antiviral intervention. Single-molecule force spectroscopy (SMFS), conducted using atomic force microscopy (AFM), allows direct investigation of Spike–ACE2 interactions at the single-molecule level, providing insights into binding mechanisms not easily captured by conventional methods. This review discusses recent applications of SMFS to assess molecular inhibitors of Spike–ACE2 interactions, focusing specifically on soluble ACE2 and glycan-binding lectins (Clec4g, hCLEC4G, and engineered H84T-Banlec). These inhibitors demonstrated potent, concentration-dependent activity against multiple SARS-CoV-2 variants, including Delta and Omicron, achieving IC₅₀ values in the low nanomolar range (soluble ACE2: 0.25–0.38 nM; Clec4g/hCLEC4G: 36–58 nM; H84T-Banlec: 2.6–5.2 nM). Notably, single-molecule IC₅₀ measurements closely correlated with EC₅₀ values from cell-based assays, validating the physiological relevance and predictive capability of the SMFS method. Collectively, these findings underscore the utility of AFM-SMFS as a powerful approach for inhibitor evaluation and antiviral discovery, particularly for strategies targeting conserved structural features of the Spike protein to achieve broad-spectrum efficacy against current and emerging viral variants.</p>\u0000 </div>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":"55 :","pages":"877 - 885"},"PeriodicalIF":2.3,"publicationDate":"2026-01-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00249-026-01818-7.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145996947","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Factors controlling protein evolvability—at the molecular scale","authors":"Jorge A. Vila","doi":"10.1007/s00249-025-01809-0","DOIUrl":"10.1007/s00249-025-01809-0","url":null,"abstract":"<div>\u0000 \u0000 <p>This piece serves two purposes. Firstly, it aims to ascertain the extent to which the ‘principle of least action’ enables us to identify which of the potential pathways and trajectories leading to novel protein sequences have the highest evolutionary efficiency—in addition to examining how variations in factors such as protein robustness and folding rates (resulting from the inevitability of destabilizing mutations) could impact this important evolutionary process. Secondly, it seeks to elucidate how ‘epistasis’ may influence the identification of the most efficient evolutionary pathways and trajectories according to the principle of least action—as well as to determine whether the presence of ‘epistatic effects’ may stem from a yet unidentified epistatic force. The initial findings suggest that protein evolution—at a molecular level—may be more predictable than previously thought, as ‘epistasis’ and the ‘principle of least action’ collectively impose constraints on evolutionary paths and trajectories, and consequently, on protein evolvability. Thus, this work should advance our understanding of the main molecular mechanisms that underlie the evolution of mutation-driven proteins and also provide grounds to answer a fundamental evolutionary question: how does Darwinian selection regard all potential trajectories available?</p>\u0000 </div>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":"55 1","pages":"101 - 109"},"PeriodicalIF":2.4,"publicationDate":"2026-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145987788","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}