vascr: An R-based toolkit for rapid and robust analysis of cellular impedance sensing data - James J. W. Hucklesby; Charles P. Unsworth; E. Scott Graham; Catherine E. Angel (European Biophysics Journal, 2026)

A historical overview of the need for distinction between the attainment of thermodynamic equilibrium and a kinetic steady state in experimental studies - Donald J. Winzor; David J. Scott (European Biophysics Journal, 2026)
In the quantitative characterization of experimental systems the observation of a time-independent response can signify the attainment of thermodynamic equilibrium. However, there are also situations where the time-independence of experimental response merely reflects the attainment of a kinetic steady state. Although quantitative expressions derived on the basis of kinetic steady-state attainment retain validity for a system at thermodynamic equilibrium, those based on attainment of thermodynamic equilibrium do not apply to systems merely reflecting the attainment of a kinetic steady state. This survey of experimental procedures encountered during research endeavours over the past six decades has revealed many situations where the source of the time-independent instrumental response was correctly identified, but also a number where the responses were misinterpreted.

Structural evidence of thioacetate reduction by fluorescent protein mRuby - Jianshu Dong; Jiachong Xie; Qian Cao (European Biophysics Journal, 2026)

Disruption of bacterial membranes by plant extracts of celandine and dandelion: microbiological and langmuir monolayer studies - Agnieszka Gonet-Surówka; Kamil Drożdż; Anita Wnętrzak; Anna Chachaj-Brekiesz; Dawid Lupa; Sławomir Wybraniec; Łukasz Kozioł; Ewa Łopuszyńska; Monika Brzychczy-Włoch; Patrycja Dynarowicz-Latka (European Biophysics Journal, 2026)

Challenging cases for AlphaFold: two multidomain proteins with zinc-binding-, phosphorylation- or dimerization-driven conformational changes - Yinshan Yang; Hélène Déméné (European Biophysics Journal, 2026)

Bitter taste TAS2R14 and TAS2R46 receptors bound to G proteins: comparison of cryo-EM, AlphaFold, and molecular dynamics structures - Ruth Pachter; Soo-Kyung Kim; Yixin C. Xu; Gaoyuan Liu; Soohyeong Kim; William A. Goddard (European Biophysics Journal, 2026)

Homologous series of N-acylmelatonins: synthesis, biophysical studies, enhanced antioxidant, antimicrobial and anticancer activities - Surendra Pothuraju; Arya Jyothibabu Sajila; Ravi Kanth Kamlekar (European Biophysics Journal, 2026)

Tracking the rotational dynamics of Chlamydomonas reinhardtii across culture days using optical tweezers - Shurui Deng; Yanshan Lin; Domna G. Kotsifaki (European Biophysics Journal, 2026)

Process-analytical study of IL-6 refolding during batch buffer exchange - Yuichi Nakahara; Yuta Endo; Yutaka Matsuda; Shunsuke Yamazaki; Mayumi Watanabe; Yutaka Sato; Masayo Date; Naoyuki Yamada; Yoshiyuki Takahara; Kazutoshi Takahashi; Keisuke Kato; Takahiro Okasora; et al. (European Biophysics Journal, 2026)

Statistical mechanics of soft collagenous tissues: a constitutive model with damage for cerebral bridging veins - Silvia García-Vilana; David Sánchez-Molina; Hamed Abdi; Vafa Rahimi-Movaghar (European Biophysics Journal, 2026)

Antisecretory Factor in rat cerebellar granule cells augments inhibitory current via GABAA receptors: a mechanism for vertigo reduction in Menière’s disease? - Aroldo Cupello; Virginia Bazzurro; Alberto Diaspro; Elena Gatta; Kliment Gatzinsky; Eva Jennische; Stefan Lange; Mauro Robello; Elena Angeli (European Biophysics Journal, 2026)

Quantitative analysis of mucociliary activity by computational high-speed video reflection microscopy - Martin Schneiter; Julian Wyss; Jeremy Schori; Patrik Arnold; Martin Frenz; Pietro Cicuta; Stefan A. Tschanz; André Stefanov; Loretta Müller (European Biophysics Journal, 2026)

Fluorescent bionanosensor for picomolar detection of biomarkers in fluids - Aleksei Pashchenko; Marie Pospíšilová; Johana Šternová; Leontýna Varvařovská; Romana Široká; Hana Kalábová; Taťána Jarošíková; Šarka Beková; Sara Cruciani; Alois Nečas; Petr Novotný; Jiří Rulc; et al. (European Biophysics Journal, 2026)

Sedimentation velocity analytical ultracentrifugation (SV-AUC) for adeno-associated virus characterization: impact of cell alignment - Qianyi Luo; Brandon L. Doyle; Ivan L. Budyak (European Biophysics Journal, 2026)

Evidence from computational infrared spectroscopy against vibrational detection of propionate by human olfactory receptor OR51E2 - Jacob Z. Williams; Piotr E. Marszalek; Weitao Yang (European Biophysics Journal, 2026)

Charged membrane interfaces reshape the nucleation landscape of RIPK3 amyloid variants - Fátima C. Escobedo-González; Andrea Gelardo; Gustavo A. Titaux-Delgado; Miguel Mompeán (European Biophysics Journal, 2026)

Effects of synergistic/antagonistic interactions between spermidine (3+) and putrescine (2+) on gene expression through higher-order DNA structural modification - Haruto Ogawa; Takashi Nishio; Yuko Yoshikawa; Takahiro Kenmotsu; Kenichi Yoshikawa (European Biophysics Journal, 2026)

Clinical use of electrodermal activity and current developments - Ali Yucel Kara; Nazan Dolu; Ferhan Esen (European Biophysics Journal, 2026)

Structure-based identification, phosphorylation, cyclization and engineering of a self-binding peptide carboxy-terminal to EGFR kinase domain by integrating dynamics simulation, energetics calculation and fluorescence analysis - Jingjing Chen; Tianyu Wang; Lijuan Shi (European Biophysics Journal, 2026)

Perspective on 3D microfluidic eye-on-a-chip technology for ophthalmological research - Gözde Narin; Onur İnam; Mehmet Yuksekkaya (European Biophysics Journal, 2026)

Proton wave propagation along collagen fibers - Pedro Costa; Anna Maznichenko; Noam Agmon; Peter Pohl (European Biophysics Journal, 2026)
Collagen deposition and alignment in the tumor stroma stiffen the extracellular matrix and, via integrin signaling, stimulate proton extrusion by cancer cells. In aggressive tumors, migration occurs preferentially along aligned collagen fibers, where proton efflux at the leading edge acidifies and degrades the matrix to facilitate invasion. Whether directional proton diffusion along collagen fibers exacerbates invasion remains uncertain, as it is not known how far protons can travel along a fiber before being released. To characterize the release barrier, we labeled collagen lysine side chains with a pH-sensitive fluorescein derivative and introduced an interfacial proton flux by microinjecting HCl near the surface of self-assembled collagen fibers elevated above the chamber bottom. Proton wave propagation was monitored by wide-field fluorescence microscopy. Quantitative analysis of the fluorescence transients revealed that proton migration is best described by a one-dimensional diffusion model with a finite surface-to-bulk release rate. A single global parameter set consistently described all experiments. From the fitted release rate, we determined a Gibbs activation energy barrier Δ G ‡ of approximately 30 k B T , comparable to values reported for membrane–water interfaces. These results demonstrate that protons can travel tens of micrometers along collagen fibers before equilibrating with the bulk solution, suggesting that membrane-anchored collagen fibers may provide an effective pathway for directing acidification along migration tracks in tumor stroma.

Apo and substrate-bound dihydropteroate synthase crystal structures from Thermus thermophilus HB8 - Amulya Ramakrishna; Archanalakshmi Kambaru; Kuppan Gokulakrishnan; Bagautdin Bagautdinov; Sivaraman Padavattan (European Biophysics Journal, 2026)

Clustering of the T-cell receptor complex may facilitate T-cell activation by stretching of CD3$$ζ$$ cytoplasmic tails - Steven Siegl; Sebastian Fürthauer; Gerhard J. Schütz (European Biophysics Journal, 2026)
Motivated by experimental observations that T-cells can activate as a consequence of clustering of T-cell receptors, we hypothesize that steric confinement between the intracellular chains of the TCR could play a role. Using coarse-grained simulations, we show that steric interactions between TCRs are sufficient to induce appreciable stretch of the intracellular domains of CD3 $$ζ$$ chains. We propose a model, in which the difference in membrane distances between the phosphatase CD45 and the kinases lck and fyn is able to sense the clustering-induced CD3 $$ζ$$ stretch: we estimate a 1.5- to 2-fold increase in phosphorylation of immunoreceptor tyrosine-based activation motifs (ITAMs) at CD3 $$ζ$$ upon TCR clustering.

Stochastic models for cell polarization and crawling: journey from external fluctuations in reaction-diffusion system to internal noise effects - Badamasi Bashir Mikailu; Cristina Montañola-Sales; Laureano Ramírez-Piscina; Sergio Alonso (European Biophysics Journal, 2026)
The plasma membrane hosts a diverse set of proteins whose attachment, detachment, and lateral diffusion give rise to complex spatiotemporal patterns that regulate essential cellular processes. In motile eukaryotic cells, localized protein patterns at the membrane control actin organization and thereby establish a front–rear axis that drives locomotion. While persistent migration following a chemotactic signal can be captured by deterministic reaction–diffusion models coupled to a phase-field description of cell shape, amoeboid motion in cells such as neutrophils and Dictyostelium discoideum is markedly more irregular and requires the inclusion of stochastic effects. Existing modeling approaches typically introduce external noise into pattern-forming mechanisms or, alternatively, although much less frequently, they account for intrinsic fluctuations arising from the small number of participating molecules. Here, we compare and connect these two complementary modeling strategies for membrane protein dynamics driving cell locomotion in Dictyostelium discoideum . We present a stochastic reaction–diffusion model coupled to a phase field, previously calibrated to experimental data, alongside a related formulation in which fluctuations emerge intrinsically from molecular discreteness. Through systematic numerical simulations, we characterize the resulting membrane patterns and dynamical behaviors. Our results test the hypothesis that externally imposed fluctuations can be effectively reduced to intrinsic noise derived from first principles. We highlight the critical role of temporal correlation, a key feature of the original phenomenological formulation, and contrast it with the behavior of internal fluctuations. Finally, we discuss the relative strengths, differences, and physical limitations of both stochastic approaches.

Effects of gramicidin A on the deformation, membrane permeation and membrane stability of lipid vesicles by Fe3O4 nanoparticles - Tawfika Nasrin; Mir Jubair Ahamed; Md. Masum Billah; Mohammad Abu Sayem Karal (European Biophysics Journal, 2026)

Protein arginine methyltransferases as regulators of phase separation: implications in cancer and neurodegenerative diseases - Zhihang Shen; Qiubin Yu (European Biophysics Journal, 2026)

In sample pH measurement by 31P phosphate NMR: application to measure the intrinsic GTPase activity of Rab1a - David Pantoja-Uceda; Douglas V. Laurents (European Biophysics Journal, 2026)
A quick, noninvasive method based on 31 P NMR spectroscopy to measure the pH of samples containing phosphate buffer is presented. By taking advantage of all four phosphate species populated at acidic, mildly acidic, mildly alkaline and alkaline pH, the method is applicable over a wide range of pH values, from 1 to 13. This tool is most precise at pH values near the pKa values, namely from 5.8 to 8.0 and 10.6 to 13.0. To facilitate its use, a web application is presented that calculates the pH value directly from phosphate 31 P chemical shift (ppm) when sodium or potassium is the cation: ( https://rmni.iqf.csic.es/software/31phnmr/ ). In addition, the potential of this approach to monitor reactions which generate or consume H + is illustrated by following the hydrolysis of GTP catalyzed by Ras-like protein in brain 1a (Rab1a), an essential protein linked to Parkinson’s disease and tuberculosis. The intrinsic GTPase rate of Rab1a is found to be 3.3 ± 0.8·10 − 3 min at 37 °C, which places Rab1a amoung the Rabs with slow GTPase rates and the longer lived “active” GTP-bound states.

The MOlecular-Scale Biophysics Research Infrastructure (MOSBRI) Project and its Outcomes - Gregor Anderluh; Ornella Cavalleri; Patrick England; Josef Houser; Adriana Erica Miele; Bohdan Schneider; Patrick Van der Wel (European Biophysics Journal, 2026)

Synthesis and biophysical characterization of bioengineered cytochrome nanowires - M. Raquel Pacheco; Ana J. Carvalho; Marta A. Silva; Tomás Calmeiro; Nykola C. Jones; Søren V. Hoffmann; Leonor Morgado; M. Manuela A. Pereira; Elvira Fortunato; Carlos A. Salgueiro; Pedro Tavares; Alice S. Pereira (European Biophysics Journal, 2026)
Geobacter bacteria produce multiheme c -type cytochrome nanowires that are involved in long-range extracellular electron transfer. The ability of these protein nanowires to conduct electrical current makes them promising candidates for electronic devices, offering several functional and sustainable advantages over traditional materials. Therefore, this study focused on synthesizing hybrid protein fibers that mimic the natural Geobacter extracellular nanowires. To achieve this, a mutated PpcA triheme protein variant was used as the building block, with thiol-ene coupling employed to bind the protein molecules. This engineered PpcA variant (PpcAK9CK22C) maintained a structure similar to that of the native protein. Thermal denaturation studies revealed a two-state process, with a melting temperature of 62 ± 1 °C and an enthalpy change of 61 ± 2 kcal/mol. The new protein nanowires showed a lower heme group content than the precursor protein and displayed distinct secondary structure features, with a slight reduction in helical content and an increase in β-sheet and unordered structures. Their thermal stability also differed, as it could not be described by the same model applied to the PpcA variant. Despite these differences, the nanowires retained their ability to undergo redox cycling. Morphologically, they consisted of linear single-protein filaments extending over 300 nm in length.

Dynamics of viral self-assembly, viral genome packaging, and virus-cell interactions studied by optical tweezers - Yanping Gong; Dorus T. Harmsen; Wouter H. Roos (European Biophysics Journal, 2026)
Viruses are complex supramolecular assemblies that propagate their genetic material from cell to cell, thereby relying on host cell mechanisms. Employing a combination of passive and active strategies, they efficiently package, transport and release nucleic acids. While structural and biochemical techniques offer insights into certain, static aspects of the viral life cycle, recent advancements in biophysical approaches now allow for direct measurement of their inherent dynamic activities in the research field commonly referred to as physical virology. One of these methods is optical tweezers, enabling the precise measurement of force and position at the single-molecule level over time. Over the past decades, the ability to optically trap beads and to manipulate biomolecules has revolutionised medical and biophysical research. In this paper, we provide a comprehensive analysis of optical tweezers, exploring its integration with imaging modalities and review its diverse applications in the study of viruses and viral components. In particular we focus on studies that use optical tweezers to study virus-cell interactions, genome packaging using molecular motors and co-assembly of viral assembly proteins with their nucleic acid.

Flow-induced dispersion analysis for probing cyclodextrin–guest binding interactions - Josef Hamacek; Federico Perche (European Biophysics Journal, 2026)

Measuring bacterial oxygen consumption rate to probe metabolic signature and antimicrobial susceptibility - Chiara Scribani Rossi; Simone Angeli; Bruno Casciaro; Maria Rosa Loffredo; Maria Luisa Mangoni; Sharon Spizzichino; Giovanna Boumis; Manuel Espinosa-Urgel; Marzia Arese; Alessio Paone; Francesca Cutruzzolà; Serena Rinaldo (European Biophysics Journal, 2026)

Analysing the structure of antibodies using circular dichroism with an antibody augmented reference set and the algorithm SELCON - Søren Vrønning Hoffmann; Maria G. Bruque; Nykola C. Jones; Alison Rodger; Jean Aucamp; Tim R. Dafforn; Owen R. T. Thomas (European Biophysics Journal, 2026)

Biophysical insights into plasmid DNA binding by deinococcus grandis Dps nanocage - Ana J. Carvalho; M. Raquel Pacheco; João P. L. Guerra; Nykola C. Jones; Søren V. Hoffmann; Tomás Calmeiro; Elvira Fortunato; Alice S. Pereira; Pedro Tavares (European Biophysics Journal, 2026)

Weak protein–bicelle binding quantification via surface-based DNA nanolevers - Sophie Combet; Raphael Dos Santos Morais; Audrey Comte; Angélique Cheron; Emeline Barbet-Massin; Hanna Müller-Landau; Olivier Delalande; Jean-François Hubert; Jean-Baptiste Charbonnier; Paloma Fernández Varela (European Biophysics Journal, 2026)

Nitroxide spin, non-canonical amino acids and SDSL-EPR spectroscopy: a winning combination for protein dynamics studies - Maxime Bizet; Áron Balázsi; Colette Maignet-Magard; Pierre Dorlet; Emilien Etienne; Guillaume Gerbaud; Gilles Truan; Deborah Byrne; Tamás Kálai; Marlène Martinho (European Biophysics Journal, 2026)

Standardization of cross-site biophysical studies of bovine insulin amyloids is challenged by structural polymorphism - Sofie Nyström; Davide Odino; Annalisa Relini; Claudio Canale; Raffaella Parlato; Yari Knelissen; Alessia Lasorsa; Wouter H. Roos; Patrick C.A. van der Wel; Søren V. Hoffmann; Nykola C. Jones; Vincent van Hemelryck; et al. (European Biophysics Journal, 2026)

Assessment of protein incorporation into SBA-15 particles and their structural changes - Jessica A. F. Pedro; Luis C. Cides-da-Silva; Tereza S. Martins; Marcia C. A. Fantini; Jose L. S. Lopes (European Biophysics Journal, 2026)

DNA methylation enhances cooperative disentanglement by the Hfq nucleoid-associated protein - Frank Wien; Nykola C. Jones; Søren Vrønning Hoffmann; Véronique Arluison (European Biophysics Journal, 2026)

Molecular Biophysics Database (MBDB) makes raw measurements findable and reusable - Emil Dandanell Agerschou; Terezie Prchalová; Miroslav Šimek; Michal Malý; Jan Stránský; Michal Strnad; Andrea Santisteban-Veiga; Mark A. Williams; Juan Sabín; Jan Dohnálek (European Biophysics Journal, 2026)
Open science is now established as an important paradigm for publicly funded research. The main principle being that to ensure best use of research data and integrity of the scientific process the information from experiments should be made widely and freely available. However, dedicated technical infrastructure to enable useful access to comprehensive experimental information in molecular biophysics is lacking, in particular in regard to repositories for raw measurement data. The Molecular Biophysics Database (MBDB) was created to fill this gap. The MBDB provides a common and extensible framework to store and access raw measurement data from a growing number of biophysical methods, currently including bio-layer interferometry, isothermal titration calorimetry, surface plasmon resonance, and microscale thermophoresis, with additional methods planned for the future. Alongside the raw measurement data from these methods, a rich set of metadata to enable data reuse is captured in accordance with the FAIR data management principles. An overview of the data models and technologies that were used to create the MBDB is presented here.

Correction: Modifying recombinant purple acid phosphatase using computational design - Aishwarya Venkatramani; Montader Ali; Olga Predeina; Jennifer C. Molloy; Pietro Sormanni; Elizabeth A. H. Hall (European Biophysics Journal, 2026)

Modifying recombinant purple acid phosphatase using computational design - Aishwarya Venkatramani; Montader Ali; Olga Predeina; Jennifer C. Molloy; Pietro Sormanni; Elizabeth A. H. Hall (European Biophysics Journal, 2026)
Enhancing protein stability while maintaining activity is a long-standing challenge in protein engineering, as modifications that benefit one property often compromise another. In this study, we leveraged a computational design strategy, CamSol Combination, to make a first step to improve the stability of purple acid phosphatase (PAP), a metalloprotein known for its distinctive pink color. PAP serves as a challenging model for engineering due to its complex redox-active site and the incorporation of iron ions critical to its function. Five mutations were introduced—H22R, A24P, F54P, H197P, and T208R—targeted to enhance thermal stability, as suggested by the computational design pipeline, while avoiding key functional regions. Experimental validation confirmed the choice of mutations with a 5 °C increase in thermal stability and retained enzymatic activity across a slightly expanded pH range. The mutations introduced subtle shifts in the enzyme’s spectral and redox behavior, consistent with a lower energy of the oxidized state, and with dynamic light scattering data suggesting low aggregation. These results highlight the potential of computational approaches like the CamSol Combination to streamline protein engineering by enabling multi-trait optimization.

Modulation of conformational features and oligomerization of MMACHC by cobalamin variants: impact of the R161Q mutation in cblC disease - Lisa Longo; Maria Assunta Costa; Rita Carrotta; Maria Rosalia Mangione; Vincenzo Martorana; Marco Tutone; Maria Grazia Ortore; Paula M. Garcia-Franco; Sonia Vega; Adrian Velazquez-Campoy; Rosa Passantino; Silvia Vilasi (European Biophysics Journal, 2026)
Vitamin B12 (cobalamin, Cbl) is a coordination compound of the cobalt, located at the center of a corrin ring composed of four pyrrolic-like groups. The cobalt ion can be bound to a variety of upper axial ligands, which vary among different cobalamin forms, including hydroxocobalamin (OHCbl), cyanocobalamin (CNCbl), methylcobalamin (MeCbl), and adenosylcobalamin (AdoCbl). MeCbl and AdoCbl are considered the biologically active forms, serving as cofactors in the metabolism of methylmalonic acid (MMA) and homocysteine (HCY). Impaired conversion of these metabolites leads to their pathological accumulation, resulting in severe cellular damage. This is precisely what occurs in cblC deficiency, a rare inborn disorder caused by mutations in the MMACHC protein, which plays a crucial role in binding and processing the various cobalamin forms. Mutations affecting MMACHC function impair its ability to correctly handle cobalamins, leading to the disease. In this study, we evaluated the impact of various cobalamin forms, specifically AdoCbl, MeCbl, and CNCbl, on the stability and oligomeric organization of the wild type MMACHC protein, using circular dichroism spectroscopy, native gel electrophoresis, and small-angle X-ray scattering. Moreover, isothermal titration calorimetry experiments provided insights into the thermodynamic parameters governing MMACHC binding to these cobalamins. In addition, we also assessed how the R161Q mutation in MMACHC alters the affinity of this protein for the different vitamin B12 forms, leading to decreased stability and impaired homodimerization, a process likely relevant to its functional role. Our findings provide molecular insights into cblC pathogenesis and advance our understanding of MMACHC structure–function relationships.

Interaction of Pf4 tactoids with bacteria and synthetic colloidal rods - Mariana de Oliveira Silva; Iago Grobas; Abul K. Tarafder; Tanmay A. M. Bharat; Dirk G. A. L. Aarts (European Biophysics Journal, 2026)
We investigated the interaction of liquid crystal droplets, formed by a phase separating system of elongated virus particles and polymer with rod-like impurities. The virus particles were Pf4, which when mixed with sodium alginate as polymer, phase separated into an isotropic phase in coexistence with a nematic phase of the virus particles. The nematic phase appeared in the form of spindle-shaped liquid crystal droplets, which are called tactoids. We studied the interaction of this mixture with micrometer sized rods, which were either bacteria ( Bacillus subtilis or Escherichia coli ) or inert colloidal particles (made of SU8 photoresist polymer or silica). Confocal laser scanning microscopy was used to examine the mixtures and four different dominant configurations were found, classified as no attachment, partial attachment of the rod to the tactoid, a “sandwich” state, where two tactoids interact with the same rod, and lastly encapsulation of the rods by the tactoids. We categorized the results in terms of surface properties and rod geometry (size and aspect ratio). We further investigated the system through numerical calculation in a simplified two-dimensional model. Finally, we addressed the role of confining the experimental system from three dimensions to a quasi two-dimensional setup, a relevant scenario in bacteria biofilms.

Advancing Italian biophysics: insights from the 27th SIBPA congress - Silvia Caponi; Rita Carrotta; Paolo Bianchini; Velia Minicozzi; Alberto Diaspro (European Biophysics Journal, 2026)

Indenting multicellular spheroids with various tip geometries - Kajangi Gnanachandran; Ewelina Lorenc; Alessandro Podestà; Małgorzata Lekka (European Biophysics Journal, 2026)
Spheroids are of great interest in the study of cancer as they can partially mimic the tumour microenvironment, thus allowing to investigate several aspects of cell – microenvironment interactions in healthy and diseased conditions, including those pertaining to mechanobiology. Atomic Force Microscopy (AFM) is a versatile tool for studying biological samples and their mechanobiological properties. In AFM, the tip shape and dimensions determine the contact geometry between the tip and the sample and the length scales at which the mechanical properties are probed. Given the complex multiscale structure of spheroids, the choice of tip geometry and size would allow, in principle, to dissect the mechanical response of the overall system into the contributions of the constituents, from the single cell level to the cellular aggregate. In this work, we studied the mechanical properties of spheroids derived from four cell lines (A549, NHLF, HT-29, and CCD-18Co cells). Our studies revealed that using different contact geometries in the fitting procedure results in significantly different Young’s modulus values, highlighting the multiscale response of these complex cellular systems and the importance of a precise experimental design and choice of the AFM probe for the nanomechanical measurements. We observed that the location of F-actin filaments is correlated with the rigidity of the spheroids.

Magnetic field based investigation of Brugada syndrome - Martina Nicoletti; Anna Crispino; Alessandro Loppini; Alessio Gizzi; Letizia Chiodo; Christian Cherubini; Simonetta Filippi (European Biophysics Journal, 2026)
Brugada syndrome (BrS) is an inherited cardiac disorder associated with and increased risk of sudden cardiac death. The syndrome is associated with a complex current distribution and repolarization dispersion. The traditional methods for the diagnosis rely on standard electrocardiographic (ECG) assessment of the cardiac dynamics. Recent advancements in magnetocardiography suggest that the magnetic-field based investigation of cardiac electrophysiology could offer novel perspectives for the investigation of current abnormalities in BrS patients which go beyond the conventional ECG capabilities to capture intricate current distributions. In this work, we propose a framework for the magnetic analysis of action potential disturbances in Brugada syndrome. We exploit a 1D reduced-order cable geometry for analyzing the relation between the pathological electrical activity in saddleback and coved type BrS and the corresponding magnetic field. Also, we compute transmural pseudo-magnetocardiograms and demonstrate their capabilities of detecting both types of BrS. Overall, our result highlight the potential of magnetic-field oriented investigation of cardiac disturbances related to BrS.

Impact of glucose on a Gel-A-Based polyphenol biosensor: A QCM-D study - Giorgia Tori; Antonella Battisti; Mariacristina Gagliardi; Marco Cecchini (European Biophysics Journal, 2026)

Thermodynamic and kinetic considerations in DNA triplex formation revealed by ITC - Andrea Santisteban-Veiga; Sarveenah Chandrasegaran; Vicente Domínguez-Arca; Juan Sabín; Tara L. Pukala (European Biophysics Journal, 2026)

Biophysical characterization of polyphenol aggregates in Moringa oleifera leaves water extract: stability and surface exposure effect on antioxidant activity under dilution - Rita Carrotta; Fabio Librizzi; Vincenzo Martorana; Samuele Raccosta; Maria Rosalia Mangione (European Biophysics Journal, 2026)
The aqueous extract of Moringa oleifera leaves has been previously characterized for its polyphenolic composition, yet the behavior of its colloidal aggregates under dilution remains largely unexplored. In this study, we investigate the structural and chemical properties of these aggregates at room temperature, focusing on their stability and surface exposure upon dilution. Although the aggregates break up as dilution increases, they never fully dissolve within the conditions explored. Both multi-angle static light scattering and dynamic light scattering highlight aggregates fragmentation and size heterogeneity under dilution. UV–vis absorption spectroscopic data strongly suggest that the aggregates of different sizes present in the extract are homogeneously constituted, as their spectra are similar to those of the main polyphenol components. The Folin–Ciocâlteu assay reveals an increase in gallic acid equivalent values normalized for extract concentration, suggesting that fragmentation prompted by dilution enhances the exposure of reactive sites. A very basic model, considering only one kind of aggregate with uniform density, is employed to support this interpretation. Assuming this model, the Folin–Ciocâlteu assay data allow to grasp the law regulating the change of the aggregate average size under dilution, i.e., a power law. Additionally, in-liquid atomic force microscopy imaging confirms the presence of smaller but still aggregated particles at high dilution, enabling the calculation of a height distribution, that is consistent with the model prediction. These findings provide insights into the dynamic behavior of polyphenol-rich aggregates in aqueous systems and their potential implications for bioavailability and reactivity.

Optical label-free detection of SARS-CoV-2: investigating platform spectroscopic properties for oligonucleotide targeting - Silvia Maria Cristina Rotondi; Paolo Canepa; Silvia Dante; Maurizio Canepa; Ornella Cavalleri (European Biophysics Journal, 2026)
We characterized a DNA/gold interface designed for the detection of the SARS-CoV-2 RNA-dependent RNA polymerase/Helicase (RdRp/Hel) sequence. Using broadband spectroscopic ellipsometry (SE) and a difference spectra approach, we monitored molecular modifications at the interface, from probe sequence deposition to the insertion of a molecular spacer and subsequent hybridization with the target. The UV region revealed the characteristic DNA absorption peak around 260 nm, while changes in δΔ in the NIR correlated with increased optical thickness following each deposition step. The optical response was analyzed as a function of target concentration, and the binding affinity curve, derived from δΔ values at 800 nm, was fitted using a first-order Langmuir model, yielding a dissociation constant K D = (70 ± 10) nM, consistent with literature values. Selectivity studies demonstrated that the interface effectively discriminates the SARS-CoV-2 sequence from the SARS-CoV HKU variant, even in a crowded environment. A complementary platform targeting the SARS-CoV HKU sequence confirmed selective detection of HKU over SARS-CoV-2. These findings highlight the potential for parallel detection of different viral sequences.

Electron currents mediated by tonoplast cytochromes b561 - Edoardo Tosato; Elisabetta Di Franco; Sayyeda Hira Hassan; Antonella Gradogna; Laura Lagostena; Cristiana Picco; Francesca Sparla; Paolo Trost; Armando Carpaneto (European Biophysics Journal, 2026)

In silico study of cytochrome-C binding to a cardiolipin-containing membrane - Alessia Muroni; Fulvio Erba; Leonardo Domenichelli; Luisa Di Paola; Federica Sinibaldi; Giampiero Mei; Almerinda Di Venere; Velia Minicozzi (European Biophysics Journal, 2026)
Cytochrome C is a key protein involved in electron transport within the mitochondrial respiratory chain and in apoptosis mechanisms. In this work, we provide a detailed theoretical analysis of the binding mechanism between cytochrome-C and a cardiolipin-containing membrane. Molecular dynamics simulations, along with protein contact network and fractal dimension analyses were employed to investigate the structural changes in cytochrome-C during the binding process. Our results suggest that cytochrome-C follows a two-step binding mechanism, starting with a rapid initial interaction, followed by slower conformational rearrangements. We identified two different cytochrome-C conformations at the membrane: a compact, native-like structure and an extended form. The latter, stabilized by Lys72, exhibits a higher binding affinity (≈ 2 kcal/mol) compared to the former. Protein extension also correlates with increased protein-membrane contact and altered heme ring orientation, suggesting that the partial unfolding of cytochrome-C could be crucial for its peroxidase activity and its role in apoptosis. These findings enhance the understanding of the cytochrome-C’s membrane interactions and its diverse functions.

Spectroscopic secondary structure fingerprint of β-variant of SARS-CoV-2 spike glycoprotein - Rosanna Mosetti; Tiziana Mancini; Federica Bertelà; Salvatore Macis; Nicole Luchetti; Velia Minicozzi; Stefano Lupi; Annalisa D’Arco (European Biophysics Journal, 2026)
The global outbreak of COVID-19 pandemic has been accompanied by the emergence of numerous mutated forms of the SARS-CoV-2 virus, exhibiting an increasingly refined capacity to adapt to the human host. The majority of mutations affect viral proteins, particularly the Spike glycoprotein (S), leading to alterations in their physicochemical properties, in secondary structures and biological functions. In the present work, we performed, to the best of our knowledge, the first infrared spectroscopic characterization of monomeric spike glycoprotein subunits 1 (S1) of SARS-CoV-2 Beta variant at pH 7.4, combining the experimental results with Molecular Dynamic simulations, Definition of Secondary Structure of Proteins (DSSP) assignments and hydrophobicity calculations. This integrated approach has yielded valuable insights into the protein secondary structure, hydrophobic behaviour, conformational dynamics, and functional attributes, factors essential for a comprehensive understanding of the viral protein domain. Our results reveal that the SARS-CoV-2 S1 Beta variant is characterized by a secondary structure enriched with antiparallel β-sheets, as consistently supported by both experimental data and computational models. Moreover, a comparative analysis of the experimental results with hydrophobicity calculations indicates that the Beta variant exhibits a slightly more hydrophilic nature relative to the SARS-CoV-2 S1 Wild Type.

Biological applications at the AQUA beamline of the EuPRAXIA@SPARC_LAB free electron laser - Emiliano De Santis; Tomas André; Stefania Alleva; Richard Bean; Massimo Ferrario; Augusto Marcelli; Velia Minicozzi; Emiliano Principi; Nicuşor Tîmneanu; Carl Caleman; Francesco Stellato (European Biophysics Journal, 2026)
The EuPRAXIA project is a European initiative aimed at developing groundbreaking, ultra-compact accelerator research infrastructures based on novel plasma acceleration concepts. The EuPRAXIA@SPARC_LAB facility, located in the Italian National Institute for Nuclear Physics-Frascati National Laboratory, will be the first operating Free Electron Laser facility of EuPRAXIA, based on an accelerator module driven by an electron bunch driver. The Free Electron Laser will produce ultra-short photon pulses in the soft X-ray region. The photons will be delivered to an endstation, called AQUA, to perform a wide range of experiments in atomic and molecular physics, chemistry, and life sciences for both academic and industrial users. Thanks to its wavelength, which falls within the so-called ‘water window’, AQUA will be particularly well-suited for coherent imaging and ion spectroscopy measurements on biological samples at room temperature in a fully hydrated environment. This unique capability opens up innovative experimental schemes for studying biological systems in states that closely resemble their physiological conditions. This paper presents numerical simulations of coherent diffraction imaging and Coulomb explosion imaging experiments, anticipating future studies at AQUA on biological samples.

Unveiling the effect of curcumin on ion channels of SBMA motoneuron-derived cells and human IPSC-derived neurons: initial electrophysiological findings - Vera Plakhova; Ingrid Battistella; Vladimir A. Martínez-Rojas; Marta Marchioretto; Daniele Arosio; Linda Masello; Luciano Conti; Carlo Musio (European Biophysics Journal, 2026)

Image analysis tools for improved characterization of nuclear chromatin patterns by confocal fluorescence microscopy - Mohammadmehdi Roushenas; Marco Salerno; Virginia Bazzurro; Elena Gatta; Alberto Diaspro (European Biophysics Journal, 2026)
We have collected fluorescence images of fixed cell nuclei of two different types—HeLa and HepG2—with DNA labeled by a standard fluorophore, and have devised three different quantitative parameters aimed to describe the distribution of the nuclear chromatin. The parameters are the fractal dimension, associated with the intricacy and hierarchical structure of chromatin; the total perimeter of local maxima, associated with the amount of chromatin domains; and the radial distance of angularly averaged intensity profile maximum, associated with the possible occurrence of a peak density at a characteristic distance from the nucleus center. Our results suggested that it was possible to differentiate the two types of cells in the 3D space of the defined parameters. Therefore, these parameters appear promising in identifying specific functional patterns in chromatin. At the same time, the negative control of different runs of measurements on the same cell type also showed at least partial differentiation. Thus, the tool proposed here for nuclear chromatin pattern characterization is probably sensitive to the cell life cycle moment almost as much as to the cell type and should be tested further on cells synchronized at the same phase during their cycle.

Uptake of gold nanoparticles in HeLa cells observed by confocal microscopy shows dependency on particle size and shape - Kimiya Pakravanan; Virginia Bazzurro; Marco Salerno; Alberto Diaspro (European Biophysics Journal, 2026)
Uptake of gold nanoparticles by HeLa cells fixed at different incubation times of up to eight hours was investigated using 3D confocal laser scanning microscopy followed by image analysis. The cell bodies were characterized by fluorescence labeling, whereas the gold nanoparticles were identified by light scattering. The amount of nanoparticles uptaken at different times was evaluated with Fiji according to a dedicated protocol. We assessed the effect of particle size (80 and 150 nm diameter spheres) and shape (spheres vs “urchins”) on their uptake. The large spherical nanoparticles presented approximately fourfold higher levels of uptake than the nanourchins. Also, the spheres presented a clearly increasing uptake in the time profile, reaching a maximum around seven hours and then showing a slight decrease. We ascribe this behavior to a lower aptitude of the cells for taking up nanoparticles with either urchin shape or smaller size and to the possible presence of competing kinetics for exocytosis at the longest times. Live experiments confirmed for the time profile a relatively flat cell response to the urchins and an increasing response to the spheres, yet with a final plateau. However, in the live case, the internalization levels were as low for the spheres as for the urchins.

Studying SARS-CoV-2 ssRNA key sequence combining Fourier transform infrared spectroscopy and theoretical folding model - Tiziana Mancini; Federica Bertelà; Marta Di Fabrizio; Salvatore Macis; Rosanna Mosetti; Stefano Lupi; Annalisa D’Arco (European Biophysics Journal, 2026)

Structural and functional characterization of Caenorhabditis elegans cyclic GMP-activated channel TAX-4 via molecular dynamics simulations - Nicole Luchetti; Marco Lauricella; Velia Minicozzi; Grazia Cottone; Letizia Chiodo (European Biophysics Journal, 2026)
Cyclic nucleotide-gated (CNG) ion channels are crucial to the intracellular calcium dynamics in neurons and other sensory cells, in several organisms. Mutations in CNG genes are linked to various dysfunctions and diseases. In this work, we propose a theoretical investigation of the structural and functional properties of wild-type TAX-4, a non-selective CNG ion channel, expressed in various sensory neurons of Caenorhabditis elegans , and involved in the permeation of monovalent and multivalent cations. Using a recent cryo-electron microscopy structure of the open state of the channel as the starting conformation, we conduct all-atom molecular dynamics simulations of the full-length channel in a membrane/water/ions system, both in the cGMP-bound and unbound conformations. Several channel structural descriptors are examined and a first-level functional annotation is carried out, on the microsecond time scale. A comparison with the available experimental data on TAX-4 and human homologues allows us to assign the simulated bound and unbound models as the pre-open and closed conformations of TAX-4, respectively. Comparisons between the bound and unbound conformations enable us to suggest key conformational changes underlying the binding-to-gating transition.

Location of oncogene-induced DNA damage sites revealed by quantitative analysis of a DNA counterstain - Greta Paternò; Silvia Scalisi; Gaetano Ivan Dellino; Mario Faretta; Pier Giuseppe Pelicci; Alberto Diaspro; Luca Lanzanò (European Biophysics Journal, 2026)
Oncogene activation is a key driver of cancer development, inducing aberrant cellular proliferation and DNA replication stress. This in turn, leads to DNA damage—which accumulates in specific genomic regions—contributing to genomic instability in cancer. However, the interplay between oncogene-induced DNA damage and chromatin organization is still poorly understood. In this study, we introduce a QUantitative ANalysis of DNA cOunterstains (QUANDO) to investigate the subnuclear localization of DNA damage in single-cell nuclei of U937-PR9 cells, an in vitro model of acute promyelocytic leukemia (APL). Using advanced imaging techniques, including DNA intensity analysis and colocalization by image cross-correlation spectroscopy (ICCS), we map DNA damage foci and correlate them with chromatin regions of different density. QUANDO is applied to dual-color confocal images of the DNA damage marker γ-H2AX and the DNA counterstain DAPI, allowing single-cell measurements of foci distribution within areas of low or high DNA density. We find that spontaneous DNA damage and DNA damage induced by the activation of PML-RARα oncogene predominantly localize in euchromatic regions. Conversely, when DNA damage is induced by the radiomimetic agent neocarzinostatin (NCS), the foci appear more evenly distributed in euchromatic and heterochromatic regions. These findings underscore the complex interplay between oncogene activation and chromatin organization, revealing how disruptions in DNA damage distribution can contribute to genomic instability and offering new insights for targeting DNA repair mechanisms in cancer therapies.

Exploring neural networks to uncover information-richer features for protein interaction prediction - Greta Grassmann; Lorenzo Di Rienzo; Giancarlo Ruocco; Edoardo Milanetti; Mattia Miotto (European Biophysics Journal, 2026)
Moving in a crowded cellular environment, proteins have to recognize and bind to each other with high specificity. This specificity reflects in a combination of geometric and chemical complementarities at the core of interacting regions that ultimately influences binding stability. Exploiting such peculiar complementarity patterns, we recently developed CIRNet, a neural network architecture capable of identifying pairs of protein core interacting residues and assisting docking algorithms by rescaling the proposed poses. Here, we present a detailed analysis of the geometric and chemical descriptors utilized by CIRNet, investigating its decision-making process to gain deeper insights into the interactions governing protein-protein binding and their interdependence. Specifically, we quantitatively assess (i) the relative importance of chemical and physical features in network training and (ii) their interplay at protein interfaces. We show that shape and hydrophobic-hydrophilic complementarities contain the most predictive information about the classification outcome. Electrostatic complementarity alone does not achieve high classification accuracy but is required to boost learning. Ultimately, our findings suggest that identifying the most information-dense features may enhance our understanding of the mechanisms driving protein-protein interactions at core interfaces.

The sleeping bacterium: shedding light on the resuscitation mechanism - Eleonora Alfinito; Matteo Beccaria (European Biophysics Journal, 2026)
The revival mechanism in dormant bacteria is a puzzling and open issue. We propose a model of information diffusion on a regular grid where agents represent bacteria and their mutual interactions implement quorum sensing. Agents may have different metabolic characteristics corresponding to multiple phenotypes. The intra/inter phenotype cooperation is analyzed under different metabolic and productivity conditions. We study the interactions between rapidly reproducing active bacteria and non-reproducing quiescent bacteria. We highlight the conditions under which the quiescent bacteria may revive. The occurrence of revival is generally related to a change in environmental conditions. Our results support this picture showing that revival can be mediated by the presence of different catalyst bacteria that produce the necessary resources.

Molecular mechanisms of mitochondrial uncoupling: focus on 2,4-dinitrophenol - Elena E. Pohl; Olga Jovanović (European Biophysics Journal, 2026)
2,4-Dinitrophenol (DNP) is an artificial mitochondrial uncoupler that was used as an anti-obesity treatment until it was withdrawn due to high toxicity, a narrow therapeutic window, and a lack of an antidote. Despite these concerns, DNP’s efficacy surpasses that of many contemporary anti-obesity drugs, sparking renewed interest in its potential use under controlled conditions. However, the development of antidotes for their toxicity and advancement as therapeutic agents has been impeded by a critical gap in our understanding of the precise molecular mechanisms by which DNP and similar uncouplers operate within mitochondria. This review provides a brief historical overview of DNP use and explores various proposed molecular mechanisms of DNP action. It also summarizes recent results obtained using conductance measurements of artificial bilayer membranes, patch clamp of mitoplasts, in silico analysis, and cryo-electron microscopy. Continued integration of the electrophysiological, structural, and computational approaches is expected to clarify the molecular basis of DNP-mediated uncoupling, enabling the rational development of safer uncouplers and mechanism-based antidotes.

The European Biophysics Journal Prizes 2025: Recognising biophysical science at sub-cellular, cellular and tissue levels of organisation - Robert J. C. Gilbert (European Biophysics Journal, 2026)
The European Biophysics Journal Prizes for 2025, awarded at the European Biophysical Societies Association (EBSA) Congress in Rome last July, recognised three of the outstanding papers published by the Journal in 2022 and 2023. In making these awards, the Journal and EBSA again sought to recognise publications which were already proving their impact. The studies recognised are diverse and highlight the vitality of biophysical science in the 2020s. They concern studies of (i) synaptic vesicles undergoing glutamate uptake, (ii) red blood cells under pressure and the effects of mechanically triggered calcium influx, and (iii) how ciliary beating, the resulting wave effects and downstream transport processes interrelate in trachea. As such these Prizes recognise excellent biophysical science at sub-cellular, cellular and tissue levels of organisation.

Exploring the GDP binding to KRas WT, G12C, G12D, G12R, and G12V and bound with MRTX1133 using steered molecular dynamics - Abdulaziz Alamri; Showkat Ahmad Mir; Shahnawaz Khan; Irshad Ahmad; Jamoliddin Razzokov; Binata Nayak (European Biophysics Journal, 2026)

The role of heterogeneity of intersubunit interfaces in the outer membrane leaflet in maintaining GABAA receptor activity - Alexey Rossokhin (European Biophysics Journal, 2026)

Anisotropy and shear stress accumulation during collective migration of epithelial cells - Ivana Pajic-Lijakovic; Milan Milivojevic; Peter V. E. McClintock (European Biophysics Journal, 2026)
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.

Predicting peptide orientation in membrane interactions: a review on transmembrane and surface-bound states - Lúcio Otávio Nunes (European Biophysics Journal, 2026)
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.

Simulation of intracellular delivery through permeabilized multivesicular vesicles - Shah Sajnin Anna; Shahariar Emon; Md. Asaduzzaman; Shovon Saha; Md. Atikur Rahman; Mohammad Abu Sayem Karal; Md Lokman Hossen; Samiron Kumar Saha; Hiromitsu Takaba; Md. Akhtaruzzaman; Md. Khorshed Alam (European Biophysics Journal, 2026)

Non-invasive biomechanical characterization of embryos using microfluidic cantilevers - Irene C. Turnbull; Tai De Li; Pedro Sanabria; Aimee Stablewski; Angelo Gaitas (European Biophysics Journal, 2026)
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.

Achieving femtomolar affinities in structure-based drug design - Asta Zubrienė; Maija Kurtenoka; Vaida Paketurytė-Latvė; Janis Leitans; Elena Manakova; Mantas Žvirblis; Andris Kazaks; Vladislava Eimonta; Kaspars Tars; Saulius Gražulis; Vytautas Petrauskas; Jurgita Matulienė; et al. (European Biophysics Journal, 2026)

Factors controlling protein evolvability—at the molecular scale - Jorge A. Vila (European Biophysics Journal, 2026)

A look into the future - Gregor Anderluh (European Biophysics Journal, 2026)

Structural adaptability of SARS-CoV-2 Nsp1 with the host network - Monikaben Padariya; Ted Hupp; Umesh Kalathiya (European Biophysics Journal, 2026)
The SARS-CoV-2 non-structural protein 1 (Nsp1) acts at multiple points toward the host cell to trigger its mRNA cleavage and decay. Nsp1 is found binding with the 40S ribosomal subunit and inhibiting the translation process, as well as docking with different cyclophilins. Herein, we evaluated the structural physicochemical properties of SARS-CoV-2 Nsp1 protein implementing different computational techniques. The Nsp1 was found to form a structured α-helical C-terminal region, following a conformational switch at residue S166 that is necessary for binding the 40S ribosome subunit. Similarly, the presence of cyclophilins stabilizes the Nsp1 C-terminus making a tilt movement at position 166. In the 40S ribosome-Nsp1 machinery, both the ribosomal uS3 and eS30 components were found equally interacting with Nsp1, which guided construction of their pharmacophores. Among a set of studied cyclophilins, FKBP1B showed the highest affinity with Nsp1 and PPIH made least interactions. The majority of cyclophilins dock to the conserved Nsp1 loop or linker region, which connects the C-terminus to the central domain. Our findings revealed that Nsp1 has a versatile C-terminus region which changes its conformations with respect to its host binding partner. Identified novel binding sites within the Nsp1 can assist in understanding its networking (in current or future such infections), as well as support drug discovery programs aimed at targeting the coronavirus family.

Multiscale characterization of lipid bilayer disruption induced by Methyl-β-cyclodextrin (MβCD) - Wisnu Arfian Anditya Sudjarwo; Jose L. Toca-Herrera (European Biophysics Journal, 2026)
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.

Single molecule force spectroscopy for evaluating inhibitors of SARS-CoV-2 variants of concern - Rong Zhu; Yoo Jin Oh; Peter Hinterdorfer (European Biophysics Journal, 2026)
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.

Cysteine-mediated structural stabilization of the tetrameric GlpF - Christine Siligan; Sascha Gratzl; Kristyna Pluhackova; Nikolaus Goessweiner-Mohr; Peter Pohl; Andreas Horner (European Biophysics Journal, 2025)
The stability of membrane proteins depends on amino acid-specific interactions within the protein structure, its surroundings, e.g. the lipid membrane and ionic solutions, and their substrates. A molecular understanding of the factors affecting protein stability is essential for comprehending the respective structure–function relationships. This study aims to investigate the influence of native cysteine residues, ions, and glycerol on the stability of GlpF, the aqua(glycerol)porin of E. coli , under well-controlled conditions. To this end, the wild-type protein and its variant with four cysteine residues in the transmembrane helix bundle mutated to glycines were overexpressed and purified. The thermal unfolding of GlpF occurs at a transition temperature of 59.2 ± 1.4 °C, corresponding to an apparent Gibbs free energy of unfolding of approximately 10 kcal/mol. In contrast to the wild-type protein, the mutated GlpF exhibits a second unfolding transition, lowered by approximately 10 °C, and a decreased Gibbs free energy of unfolding of 5 kcal/mol. Our findings highlight that divalent ions and glycerol have a more pronounced stabilizing effect on the mutated GlpF than the wild-type protein. The structural consequences of cysteine to glycine mutations in terms of transmembrane helix rearrangement, the inter- and intra-chain H-bond network, and the reduced inter-chain interaction free energy, as well as intra-chain electrostatic energy and van der Waals energy, are revealed by molecular dynamics simulations. In conclusion, our findings illustrate the significance of cysteine residues distant from each other on protein oligomerization and stability, and the amplified impact of (de)stabilizing agents on less stable protein variants.

European Biophysics Journal - Special Issue Celebrating the 70th Anniversary of the Institute of Biophysics, Czech Academy of Sciences - Aleš Kovařík; Martin Hof; Eva Bártová (European Biophysics Journal, 2025)

Acytota and the evolution of complexity - Eduard Kejnovsky; Zdenek Kubat; Judit E. Sponer (European Biophysics Journal, 2025)

Biophysics in the Czech Republic: 70th anniversary of the institute of biophysics - Eva Bártová; Stanislav Kozubek; Aleš Kovařík (European Biophysics Journal, 2025)
Biophysics is an interdisciplinary science that applies the theories and methods of physics to understand biological systems. It encompasses a wide range of topics, from the molecular mechanisms within cells to the physical properties of organisms and ecosystems. The goal of biophysics is to uncover the physical principles underlying the structure and function of biological molecules, cells, and cellular systems, providing a deeper understanding of life itself. The Institute of Biophysics, Czech Academy of Sciences (IBP) stands as a beacon of excellence in the field of biophysical research in the Czech Republic. This article delves into its history, structure, research areas, and major scientific achievements, highlighting the role of IBP in the global scientific community.

Specific TP53 mutations impair the recruitment of 53BP1 to DNA double-strand breaks underlying the mechanism of radioresistance - Paolo Fagherazzi; Lenka Stixová; Eva Bartova (European Biophysics Journal, 2025)
The tumor suppressor p53, extensively studied for over 40 years, is a key regulator of various cellular pathways, often functioning independently of its transcriptional activity. Notably, p53 has been shown to play a crucial role in DNA repair, not only in sensing DNA damage but also in influencing repair pathway choice. This work assesses the influence of p53 on the recruitment and activity of the NHEJ mediator 53BP1, focusing specifically on common p53 hotspot mutations found in human cancers. The aim is to understand how these mutations impair DNA damage response mechanisms and contribute to genetic instability, which enhances tumor survival. Analysis of p53 missense mutations (R248W, R273C, G245S) revealed mutation-specific effects on 53BP1 and RIF1 recruitment, with G245S retaining wild-type-like 53BP1 recruitment but still exhibiting enhanced BRCA1 foci formation. Given the widespread activation of NHEJ throughout the cell cycle, especially in response to radiotherapy and chemotherapy, gaining insight into how p53 mutations affect this response is vital for developing future therapeutic strategies.

Professor Emil Paleček: seven decades with electrodes and biomolecules at the Institute of Biophysics of the CAS - Miroslav Fojta; Jan Paleček (European Biophysics Journal, 2025)

Quadruplexes with a grain of salt: influence of cation type and concentration on DNA G4 stability - Anne Cucchiarini; Filip Kledus; Yu Luo; Václav Brázda; Jean-Louis Mergny (European Biophysics Journal, 2025)
G-quadruplexes (G4) are stabilized by intra-quartet hydrogen bonds stacking between quartets, as well as specific and non-specific ionic interactions. Cation effects on G-quadruplexes differ significantly from those on duplexes, and specific cation coordination is indeed required to stabilize G4 structures. Most studies so far involve “standard” concentrations of potassium or sodium cations because of their prevalence in human cells, but several other monovalent and divalent cations may promote quadruplex formation. In addition, ionic strength may be different in other organisms such as Halophiles: the intracellular cation (potassium) concentration in salt-loving organisms such as Haloferax volcanii can be extremely high. In this study, we first performed a bioinformatics analysis of G4 propensity in halophiles and analyzed the impact of altering ionic strength or ionic balance on G4 or hairpin duplex stability. We then present a detailed and quantitative assessment of salt effect on a variety of duplex and quadruplex sequences. Over a dozen different quadruplex and duplex sequences were investigated by FRET melting and UV melting experiments. In addition, changes in sodium/potassium balance possibly occurring in human cells have a modest effect on G4-duplex competition. We also confirm that lithium is rather a “G4-indifferent” than a G4-destabilizing cation.

Fragmentation of nucleoli in senescent cancer cells is associated with increased levels of polyadenylated transcripts derived from noncoding regions of rDNA units - Jana Sochorová; Emilie Lukášová; Eva Volfová Polanská; Kateřina Řehůřková; Aleš Kovařík (European Biophysics Journal, 2025)
In this study, we investigated the behavior of rDNA loci in senescent MCF-7 mammary cancer cells induced by gamma irradiation. To analyze changes in nucleolar structure we used rDNA-FISH and immunohistochemical staining with fibrillarin and UBF transcription factor. The expression levels of rDNAs and nucleolar proteins were determined by RNA-seq of total and poly-A libraries. The cytological and molecular parameters of nucleoli were monitored throughout the 7-day interval following irradiation. Senescent cells exhibited a higher proportion of smaller nucleoli as compared to cycling cells, indicating nucleolar fragmentation. The rDNA copy number and expression of rDNA variants remained stable in cycling and senescent cells. However, the levels of polyadenylated rRNA species derived from external (5′ETS) and internal (ITS1) rDNA spacers tend to increase (c.2 fold) following irradiation. At the protein level, senescent cells showed decreased levels of fibrillarin and UBF transcription factor while localization of both proteins in the nucleolus was not impaired. We conclude that withdrawal from cell cycle does not change expression patterns of rDNA variants. However, defects in rRNA processing may lead to fragmentation of nucleoli in senescent cells.

From survival of irradiated mice to modern molecular insights: a seventy-year journey in radiobiology at the institute of biophysics, Czech academy of sciences - Jiří Toufar; Lucie Toufarová; Iva Falková; Alena Bačíková; Martin Falk (European Biophysics Journal, 2025)
This paper has been prepared to commemorate the 70th anniversary of the Institute of Biophysics of the Czech Academy of Sciences (IBP CAS), which has a long-standing tradition in researching the biological effects of ionizing radiation (IR). Radiobiology has recently gained renewed importance due to several compelling factors. The demand for a better understanding of the biological effects of both low and high doses of various types of ionizing radiation, along with improved radiation protection, is increasing—particularly in the context of critical ongoing human activities such as medical diagnostics, radiotherapy, and the operation of nuclear power plants. This demand also extends to newly emerging scenarios, including the development of hadron and FLASH radiotherapy, as well as mixed radiation field exposures related to planned manned missions to Mars. Unfortunately, there is also an urgent need to address the heightened risk of nuclear materials and weapons misuse by terrorists or even rogue states. Additionally, nuclear energy is currently the only viable alternative that can provide efficient, sustainable, and ecological coverage for the dramatically increasing current and future energy demands. Understanding the risks of IR exposure necessitates exploring how different types of IR interact with living organisms at the most fundamental level of complexity, specifically at the level of molecules and their complexes. The rising interest in radiobiology is, therefore, also driven by new experimental opportunities that enable research at previously unimaginable levels of detail and complexity. In this manuscript, we will address the important questions in radiobiology, focusing specifically on the mechanisms of radiation-induced DNA damage and repair within the context of chromatin architecture. We will emphasize the differing effects of photon and high-LET particle radiation on chromatin and DNA. Both forms of IR are encountered on Earth but are particularly significant in space.

Spectroscopic studies of sequence-dependent conformational transitions in asymmetric G/C rich double-stranded DNA - Petra Školáková; Iva Kejnovská; Daniel Renčiuk (European Biophysics Journal, 2025)
Nucleic acids, molecules essential for all life, can adopt many alternative structures besides the well-known right-handed double helix, some of which have been reported to exist and function in vivo. One of the most appropriate methods for structural studies of nucleic acids is circular dichroism spectroscopy, utilizing structure-induced chirality due to the asymmetric winding of absorbing nucleobases. Using electronic CD and absorption spectroscopies in combination with melting experiments, we analyzed a conformational equilibrium between DNA double helix and two alternative conformations of nucleic acids, cytosine i-motifs and guanine quadruplexes, as a function of the primary structure of model G/C-rich sequences, containing blocks of G and C runs in particular DNA strands. This paper is a part of special issue dedicated to 70th anniversary of the Biophysical Institute of the Czech Academy of Sciences, where circular dichroism spectroscopy of nucleic acids has been used successfully and impactfully for many years.

Mechanical properties of adherent cell sheets analyzed by deflection of supporting membrane - Yuri M. Efremov; Anastasia M. Subbot; Ivan A. Novikov; Sergei E. Avetisov; Peter S. Timashev (European Biophysics Journal, 2025)

Mitochondrial alterations induced by Macrovipera lebetina venom - Virjinia Doltchinkova; Victoria Vitkova; Milena Shkodrova; Meglena Kitanova; Vessela Lozanova; Siya Lozanova; Avgust Ivanov; Chavdar Roumenin (European Biophysics Journal, 2025)

Optimizing electroporation via pulse modulation: a molecular dynamics study - Shahariar Emon; Al Amin; Md. Hossain; Shovon Saha; Md. Asaduzzaman; Md Lokman Hossen; Mohammad Abu Sayem Karal; Hiromitsu Takaba; Md. Khorshed Alam (European Biophysics Journal, 2025)

Characterization of Aquaporin Z proteoliposome structure and functionality via microscopy and scattering methods - Zsófia Edit Szathmáry; Martin Cramer Pedersen; Alec Michels; Torsten Høybye Bak Regueira; Jacob Judas Kain Kirkensgaard (European Biophysics Journal, 2025)
Aquaporins are known for their efficient water transport capabilities and have been widely studied in the past decades. However, creating a biomimetic system mirroring natural water filtration processes still poses a challenge related to performance and stability. To study the protein reconstitution and functionality, this work presents an analytical toolkit using the model system of AqpZ reconstituted phosphatidylcholine proteoliposomes. Combining findings from dynamic light scattering, cryogenic transmission electron microscopy, laser scanning confocal microscopy, stimulated emission depletion microscopy, stopped flow-light scattering and small-angle X-ray scattering provides an assessment of structural and functional characteristics of AqpZ embedding in the bilayer of liposomes. Findings of this work reveal that the incorporation of AqpZ into liposomes promotes an increase within the hydrophobic bilayer thickness as well as within the overall size of the vesicles. AqpZ, AqpZ-GFP and AqpZ-Atto594 are studied and show distinct permeability profiles. Despite all three displaying a successful structural reconstitution into the liposomes, labeled protein variants demonstrate a loss of function. A series of protein concentrations are utilized to extract quantitative information regarding the reconstitution process, revealing constant water transport per AqpZ and thus a consistent trend of increased reconstitution and permeability as a function of AqpZ concentration, as determined by stopped flow-light scattering and detailed further via global fitting of small-angle X-ray scattering data.

Equations describing semi-confluent cell growth (II) colony formation on a flat surface - Damien Hall (European Biophysics Journal, 2025)
Individual cell growth can be affected by the presence of adjacent cells through a complex and multi-factorial biological process known alternatively as contact inhibition or confluence sensing. In a previous paper (Hall D (2024) Equations describing semi-confluent cell growth (I) Analytical approximations. Biophys Chem 307:107173), sets of differential equations (with implicit analytical solutions) were developed to describe completely symmetrical cases of multicellular colony growth affected by variable levels of contact inhibition. Here we develop a model based on a spherical cap approximation of colony growth, that is able to describe variable contact inhibition for non-symmetrical multilayer cell formation on a solid plate. Although the model is realized as a set of interrelated ordinary differential equations, it is effectively governed by two parameters and is therefore capable for use in quantitative analysis of the kinetics of cell culture parameters such as shape, colony size and receding contact angle. The model is capable of accounting for transitions from monolayer to multilayer growth in a robust fashion.

Development of novel experimental setup for hands-on cardiovascular biophysics education - Ljubica Ilić; Katarina Žikić; Zorica Nestorović; Biljana Smiljković; Dejan Žikić (European Biophysics Journal, 2025)

Voltage-sensing domains: structural and functional diversity - Martin C. Heiss; Bernhard E. Flucher (European Biophysics Journal, 2025)
Voltage-sensing domains (VSDs) are structural modules of voltage-gated ion channels, which sense changes in the membrane potential and, in response, open and close the channel’s ion conduction pore. VSDs comprise a bundle of four antiparallel transmembrane helices (S1–S4). Their basic function is well described by the sliding helix model. Upon membrane depolarization, the positively charged S4 helix slides upward and several of its positive gating charges cross the focused membrane electric field. This state transition is conformationally coupled to the opening of the channel gate. While this essential mechanism is common to all VSDs, different VSDs display a considerable structural and functional diversity, including the number of the gating charges, the nature of their countercharges, and the range, speed, and voltage dependence of the S4 movement upon activation. Here, we review these differences and discuss how they might function to determine the distinct gating properties of voltage-gated ion channels.

Proceedings of the 26th International Analytical Ultracentrifugation Workshop and Symposium - Johannes Walter; Alexander Bepperling (European Biophysics Journal, 2025)
The 26th International Analytical Ultracentrifugation Workshop and Symposium (AUC2024) took place at the scenic Banz Abbey near Bad Staffelstein, Germany, from July 22 to 27, 2024. 84 participants from 16 countries (Belgium 1, Canada 7, China 3, Colombia 1, Czech Republic 3, Finland 1, France 3, Germany 35, Israel 1, Italy 1, Japan 2, New Zealand 2, Spain 1, Switzerland 4, United Kingdom 5, United States 14) travelled to Germany to present and discuss the latest advances in the field. 40 workshop sessions were held by world-leading experts covering all aspects of AUC including experimental design, data analysis and data processing according to good manufacturing practice (GMP), but also complementary methods such as hydrodynamic modelling, isothermal titration calorimetry and small angle X-ray scattering data processing were considered. A visit to a stalactite cave in Franconian Switzerland and the Bavarian beer museum in Kulmbach offered a welcome change to the scientific program and started off the 3-day symposium. The presentations featured of course AUC, but also dynamic and static light scattering, small angle X-ray and neutron scattering, surface plasmon resonance, field flow fractionation, calorimetry, chromatography, and electron microscopy. The AUC2024 special volume provides a comprehensive overview of the sustained innovation, utility and relevance of AUC and related solution biophysical and particle technology methods across various disciplines, including biochemistry, structural biology, synthetic polymer chemistry, carbohydrate chemistry, protein and nucleic acid characterization, nano and colloids science, and macromolecular interactions.

Ribulose-1,5-bisphosphate carboxylase/oxygenase activase isoforms from diverse species show differences in oligomeric structure, thermal stability, and activity - Jeremy R. Keown; Serena A. J. Watkin; F. Grant Pearce (European Biophysics Journal, 2025)
Rubisco activase (Rca) is critical for maintaining Rubisco activity during photosynthesis by removing inhibitory sugar phosphates through ATP hydrolysis. Despite its importance, the structural and functional diversity of Rca across species remain poorly understood. This study compares the oligomeric assembly, thermal stability, and functional activities of α- and β-isoforms of Rca from cotton, creosote, Antarctic hairgrass, and Sitka spruce, representing diverse thermal and ecological adaptations. We found that cotton and creosote Rca isoforms form highly polydisperse complexes in solution, with no evidence of discrete hexamer formation, even in the presence of Mg.ATPγS. In contrast, Antarctic hairgrass α-Rca and Sitka spruce β-Rca formed stable hexamers under similar conditions. Spruce α-Rca exhibited unique redox-dependent oligomerization, forming large complexes stabilized by disulfide bonds. Thermal stability assays revealed significant nucleotide-induced stabilization in most isoforms, with hexamer formation enhancing stability and activity in select cases. Functional assays showed that hexamer-forming isoforms displayed superior Rubisco reactivation and ATP hydrolysis activities, even at low protein concentrations, while smaller oligomeric assemblies also supported activity in some species. These findings provide new insights into the structural and functional adaptations of Rca, highlighting the role of oligomeric assembly and environmental influences on its activity. This work lays a foundation for improving photosynthetic efficiency by targeting Rca isoforms tailored to specific environmental conditions.

Hydrodynamic properties of macromolecules and nanoparticles in dilute solution: a brief essay on classical and modern concepts - José García de la Torre; José G. Hernández-Cifre (European Biophysics Journal, 2025)
The theory, computational modelling and data analysis of hydrodynamic and other solution properties of macromolecules and nanoparticles in dilute solution are nowadays well-established. Along this essay, we briefly present the variety of methods which are currently available for those purposes. Although such methods embody an important complexity, they are usually presented as user-friendly tools which can be used without previous knowledge of their foundations. Some understanding of classical concepts in which modern tools are based can result in a better, more profitable, use of them and a most adequate form of presenting and discussing their results. We describe the utility of employing a systematic way of handling data and results for the solution properties in terms of equivalent radii, which indeed provide an alternative to the raw properties in their use for structural determinations. They can also be employed in the design of simulation of experiments and data analysis procedures, like in analytical ultracentrifugation as we propose finally in this paper.

Tracking reduction-induced molecular changes in pathological free light chains by SV-AUC - Florian T. Tucholski; Rebecca Sternke-Hoffmann; Thomas Pauly; Rasmus K. Norrild; Amelie Boquoi; Roland Fenk; Luitgard Nagel; Alexander K. Buell; Rainer Haas; Dieter Willbold (European Biophysics Journal, 2025)
Multiple myeloma is a blood cancer characterized by plasma cell proliferation and excessive production of monoclonal proteins, often leading to renal complications and other forms of organ damage. A set of nine immunoglobulin free light chain (FLC) samples purified from urine of multiple myeloma patients was subjected to sedimentation velocity analysis. Aim of the study was to track changes of the oligomerization state of each FLC while triggering reduction-induced aggregation into larger structures. Sedimentation velocity experiments, combined with further techniques sensitive to structural changes, were performed to determine the degree of FLC oligomerization in each patient sample under different experimental conditions. Structurally, the FLC monomers are stabilized by two intramolecular disulfide bonds, while covalent dimerization occurs through an unpaired C-terminal cysteine residue. Incubation with the reducing agent TCEP cleaves intra- and intermolecular disulfide bonds, destabilizing both monomers and dimers. Remarkably, different incubation times revealed that destabilized dimers do not dissociate into stable monomers but instead accumulate directly into oligomers and higher-order aggregates. In addition to larger aggregates, fragments with sizes around 1 S were detected with increasing TCEP incubation time. This fragmentation behavior was consistent among FLCs originating from the immunoglobulin kappa variable 1-33 gene (IGKV1-33). Sedimentation velocity-based characterization of FLCs can provide insights into the relationship between their stability and aggregation capacity. An understanding of this relationship is crucial for the development of therapeutic strategies to prevent renal complications associated with monoclonal gammopathies such as multiple myeloma.

Predictive model for evolving density and viscosity gradients in band-forming ultracentrifugation - Lukas Dobler; Emre Brookes; Piotr Grodzki; Maciej Lisicki; Borries Demeler; Helmut Cölfen; Piotr Szymczak (European Biophysics Journal, 2025)
Band-forming experiments allow the study of a wide variety of systems by overlaying two solutions with different densities in an analytical ultracentrifuge. Despite their potential benefits over other methods, these experiments are rarely used because all available fitting software encounters systematic errors, failing to account for the evolving gradient in density and viscosity due to diffusive mixing between the two layers. We develop and experimentally validate a predictive model for the purely diffusive mixing of two solutions in a cylindrical system. Capturing the space- and time-dependent evolution of density and viscosity in band-forming experiments, the model enhances their interpretation and underscores the need for analysis software to account for these dynamic changes.

Bead model hydrodynamics: an in-depth comparison between GRPY and ZENO - Emre Brookes; Pawel J. Żuk; Mattia Rocco (European Biophysics Journal, 2025)

Use of cesium chloride density gradient ultracentrifugation for the purification and characterization of recombinant adeno-associated virus - Kiichi Hirohata; Shinichiro Kino; Takuya Yamane; Karin Bandoh; Takeshi Bamba; Shawn M. Sternisha; Tetsuo Torisu; Mitsuko Fukuhara; Yuki Yamaguchi; Susumu Uchiyama (European Biophysics Journal, 2025)
Recombinant adeno-associated virus (rAAV) has been widely used as an effective delivery tool in gene therapy. One of the challenges facing the production of high-quality rAAV is optimization of the production and purification methodologies. Cesium chloride density gradient ultracentrifugation (CsCl-DGUC) has been traditionally utilized for rAAV purification; however, few studies have focused on CsCl-DGUC for rAAV purification despite this technique having a great potential for clinical-grade or large-scale rAAV production. In this study, we aimed to explore the unaddressed challenges associated with rAAV purification using CsCl-DGUC. We clarified that AAV capsids assembled by the different stoichiometries of three viral proteins (VP1, VP2, and VP3) showed heterogeneous population in the CsCl density gradient and encapsidated DNA increased the buoyant density differences of these capsids, resulting in the wider distribution. We implemented CsCl-DGUC using a vertical rotor which improved throughput and enhanced the separation of desired AAV particles from impurities. Furthermore, we examined the effect of CsCl exposure during purification, and the presence of residual CsCl in the purified rAAV. This study provides valuable insights into the application of CsCl-DGUC in the manufacturing of rAAV while ensuring adequate efficacy and safety for gene therapy.

Facilitating the simulation of sedimentation velocity data: new features of SViMULATE - Chad A. Brautigam (European Biophysics Journal, 2025)

Analytical ultracentrifugation as a tool for exploring COSAN assemblies - Hussein Fakhouri; Caroline Mas; Aline Le Roy; Estelle Marchal; Coralie Pasquier; Olivier Diat; Pierre Bauduin; Christine Ebel (European Biophysics Journal, 2025)

A method to determine confidence limits for the area, sedimentation coefficient, and molar mass of individual peaks from a SEDFIT c(s) distribution - John S. Philo (European Biophysics Journal, 2025)

Correction: SEDNTERP: a calculation and database utility to aid interpretation of analytical ultracentrifugation and light scattering data - John S. Philo (European Biophysics Journal, 2025)

A paradigm shift: analytical ultracentrifugation as a multi-attribute platform method in targeted protein degradation - Alexander E. Yarawsky; Judith A. Ronau; Tiffany A. Thibaudeau; Aaron C. Ehlinger; Gekleng Chhor; Suki M. Hyman; Michelle A. Estrada; Vladimir Stojkovic; Michael T. DeLion; Anil Vasudevan; Justin M. Reitsma; Scott E. Warder; et al. (European Biophysics Journal, 2025)

Optical trapping with nanostructured optical fibers and motility analysis of Pseudomonas aeruginosa - Eric Faudry; Jochen Fick (European Biophysics Journal, 2025)
The study of bacteria swimming behavior or their interaction with other bacteria or cells requires an efficient and flexible tool for bacteria manipulation. Optical tweezers have been shown to be perfectly adapted for this task. Here we report optical trapping of pathogen Pseudomonas aeruginosa bacteria using optical fiber tweezers with dedicated nanostructured optical fibers. Well-aligned straight chains of up to ten bacteria were observed with optical fiber tips, whereas contactless trapping was realized at distances of 100 and 45 µm for Fresnel lens fibers and TIROFs, respectively. Very efficient trapping at laser powers as low as 3.7 mW was achieved. The bacteria vitality is an important parameter in trapping experiments. Mean square displacement and speed autocorrelation methods were applied to obtain a vitality measure and to classify the free bacteria trajectories into free floating, running, and run-wrap-run categories. The high frame rates of our observation videos allow us to reveal a relation between bacteria speed and bacteria orientation oscillations.

Physical principles underpinning molecular-level protein evolution - Jorge A. Vila (European Biophysics Journal, 2025)

Biophysical and microbiological aspects of the interaction between Yersinia pestis PsaA and bacteriophage L-413C - Ilya Konyshev; Lyubov Dudina; Vladislav Belozerov; Sergey Ivanov; Svetlana Dentovskaya; Andrey Anisimov; Andrey Byvalov (European Biophysics Journal, 2025)

Amino acids hydrophobic properties in proteins are derived from their atomic polarities - Juan Cedano; Enrique Querol; Angel Mozo-Villarías (European Biophysics Journal, 2025)

Crystal structure of 4-amino-5-hydroxymethyl-2-methyl pyrimidine phosphate kinase (HMPP kinase) from Thermus thermophilus HB8 - Archanalakshmi Kambaru; Sneha Jos; Igor Lobov; Bagautdin Bagautdinov; Sivaraman Padavattan (European Biophysics Journal, 2025)

Competitive adsorption of a monoclonal antibody and amphiphilic polymers to the air–water interface - Elise J. Hingst; Michaela Blech; Dariush Hinderberger; Patrick Garidel; Christian Schwieger (European Biophysics Journal, 2025)
Understanding the structure and self-organisation of monoclonal antibodies (mAbs) at the air–water interface is crucial for the stability and efficacy of protein drug formulations. This paper investigates the competitive adsorption of mAb and two amphiphilic polymers, poloxamer 188 (P188) and polysorbate 20 (PS20), commonly used to stabilise mAb formulations. Our objective was twofold: to ascertain whether the surfactants in question are capable of preventing mAb adsorption; and to determine whether it is possible to desorb mAb molecules from the air–water interface by surfactant addition. Langmuir film balance measurements and drop shape tensiometry were used to obtain surface pressure and surface tension data. Infrared Reflection–Absorption Spectroscopy (IRRAS) provided information on the surface composition, including the amount of adsorbed molecules. The state adopted by P188 is contingent upon its surface concentration, which determines the self-assembled phases it adopts. We show that the phase state of P188 has a considerable influence on mAb adsorption. The presence of P188 in the brush phase (≥ 0.3 mg/L) consistently inhibits mAb adsorption, but addition of P188 subsequent to the formation of the mAb film does not result in mAb desorption. However, addition of PS20 results in the desorption of freshly-formed interfacial mAb layers of up to two hours’ age, whereas an aged mAb layer of 17 h was unable to be desorbed by PS20. Thus there is a time-dependent reorganisation of mAb at the air–water interface, increasing resistance to desorption, which we discuss in the context of potential intermolecular interactions within the interfacial film. Graphical abstract

The influence of the Debye–Hückel factor in estimating the distance between interacting monomers in self-assembling proteins - Angel Mozo-Villarías; Enrique Querol; Juan A. Cedano (European Biophysics Journal, 2025)

Inside the membrane: a closer look using elastic scattering techniques and friends - Michael Kaltenegger; Enrico F. Semeraro; Georg Pabst (European Biophysics Journal, 2025)
Biological membranes are highly dynamic and adaptive interfaces that define cellular compartments, posing significant challenges for detailed characterization. Among the diverse range of experimental and computational techniques, small-angle scattering emerges as a label-free, non-invasive method capable of probing membrane structures across length scales from micrometers to subnanometers. By exploiting the complementary contrasts of X-ray and neutron scattering, combined with advanced optimization algorithms, this approach has provided unique insights into membranes with well-defined lipid and protein architectures. In this review, we highlight recent studies from the Pabst Lab, including investigations of lipid domains, asymmetric lipid membranes, and intrinsic lipid curvature. Furthermore, we explore the functional implications of these findings, such as the activity of an integral membrane enzyme and the effects of antimicrobial peptides in live cells. These examples underscore the versatility of small-angle scattering techniques in elucidating membrane functions, offering valuable perspectives for understanding cellular processes and advancing pharmaceutical applications.

Microfluidics for protein interaction studies: current methods, challenges, and future perspectives - Matthias M. Schneider; Tuomas P. J. Knowles; Sandro Keller; Georg Krainer (European Biophysics Journal, 2025)
Proteins are the key molecular players of life, carrying out their functions through interactions. Microfluidic technologies have emerged as powerful tools for studying protein interactions with exquisite sensitivity, resolution, and throughput. In this review, we highlight recent advances in microfluidic approaches for protein interaction studies. We first explore continuous-flow microfluidics, which utilize diffusion-based techniques and electrophoretic methods, before examining the role of droplet microfluidics in probing protein interactions. We provide an overview of the diverse applications of these technologies in biophysical research, drug discovery, and clinical diagnostics. We conclude with a discussion of the potential of microfluidics for driving future innovations and emerging opportunities.

15th EBSA congress, June 30 – July 4, 2025, Rome, Italy – Abstracts (European Biophysics Journal, 2025)

Statistical mechanics of bone damage: a constitutive model - S. García-Vilana; D. Sánchez-Molina (European Biophysics Journal, 2025)
After the elastic regime is surpassed, cortical bone exhibits significant microcracking in its post-elastic mechanical behavior. This work develops a thermodynamically consistent, nonlinear constitutive model based on statistical mechanics, designed to predict the stress–strain relationship and the progression of inter-osteon microcracking. To assess the model’s sufficiency, precise tensile and bending tests were performed in comparison to empirical curves that illustrated theoretical predictions of constitutive relationships. Moreover, entropy increases were quantitatively assessed using model parameters refined through experimental data. A large-size sample was utilized, comprising 51 dog-bone-shaped cortical bone specimens from the 4th ribs of various subjects for uniaxial tensile tests, and 15 complete fourth ribs for bending tests. Displacement and strain fields were meticulously recorded using digital image correlation and video analysis. The model demonstrated robustness, accurately fitting the data from all experimental specimens and revealing correlations between constitutive parameters and anthropometric variables. Entropy calculations provide insights into the behavior of the bone under varying strains: microcracking is minimal at low strains with stress nearly proportional to strain, escalating significantly beyond a critical threshold, thus challenging the linear relationship between stress and strain.

Analysis of ligand binding mechanism by dimeric receptors using stopped-flow fluorimetry—application to the human decapping scavenger enzyme - Zbigniew M. Darzynkiewicz; Megerditch Kiledjian; Jan M. Antosiewicz (European Biophysics Journal, 2025)

Molecular transport through nano-sized multipores of lipid vesicles: a COMSOL simulation study - Md. Asaduzzaman; Shahariar Emon; Md. Saif Ishtiaque; Md. Imran Hossain; Mahammad Abu Sayem Karal; Md. Masum Billah; Hiromitsu Takaba; Md. Khorshed Alam (European Biophysics Journal, 2025)

Exploring the influence of water micro assemblies on protein folding, enzyme catalysis and membrane dynamics - Arturo Tozzi (European Biophysics Journal, 2025)

Extraction of geometric and transport parameters from the time constant of exocytosis transients measured by nanoscale electrodes - Sundeep Kapila; Pradeep R. Nair (European Biophysics Journal, 2025)

Molecular dynamics study of the helix-to-disorder transition in short antimicrobial peptides from Urodacus yaschenkoi - Flora Fernandez-Sánchez; Jenny Flores-Ávila; Hugo S. García; Edgar Mixcoha; Daniel Balleza (European Biophysics Journal, 2025)

Exploring the biomechanical response of human semicircular canals by a visualized bionic model - Yani Jiang; Xianhua Wen; Guangcheng Xiang; Wenxuan Zhang; Junjie Dai; Junjie Gong; Yixiang Bian (European Biophysics Journal, 2025)

Determination of the size parameters of α-synuclein amyloid precursor forms through DLS analysis - Marco A. Saraiva (European Biophysics Journal, 2025)
Currently, there is an increased interest in identifying the characteristics of amyloid aggregates in the initial stages of amyloid formation. The aggregation mechanism of the α-synuclein (Syn) amyloid protein, which has been extensively studied, is still not fully understood. I show that with conventional dynamic light scattering (DLS) technique, the measurements of the dimensions of Syn amyloid precursor forms can be done early in the protein incubation. Additionally, the early aggregation of the Syn protein was initially studied by analyzing autocorrelation functions from fit distributions up to 10 4 µs in the initial DLS measurements, specifically within the first 21 min. Investigation was conducted on the variation in the pH of the Syn solution throughout time. Based on DLS data, large Syn aggregated species formed from the monomer protein species. Afterward, I generated the autocorrelation functions based on the original DLS data, extending the fit distributions up to 10 5 µs and noticed the existence of elongated Syn amyloid precursor forms in the protein solutions. Because the length of the elongated Syn amyloid precursor forms closely matches the wavelength of the incident light, the combination of translational diffusion D t and rotational diffusion D r in the decay rates enabled the measurement of their geometric dimensions through DLS. The improved precision of the fitted distributions I offered resulted in a new interpretation for the Syn protein aggregation in the initial stages. Overall, the methodology used in this study could be an effective strategy for examining how Syn amyloid precursor forms develop over time.

The effect of C-terminal deamidation on bacterial susceptibility and resistance to modelin-5 - Sarah R. Dennison; Leslie H. G. Morton; Kamal Badiani; Frederick Harris; David A. Phoenix (European Biophysics Journal, 2025)
The C-terminal amide carried by antimicrobial peptides (AMPs) can play a variable role in their antibacterial action and here, this role is investigated here for the synthetic peptide modelin-5 (M5-NH 2 ). The peptide showed potent activity against Pseudomonas aeruginosa (MLC = 5.9 µM), with strong binding to the cytoplasmic membrane (CM) (K d = 21.5 μM) and the adoption of high levels of amphiphilic α-helical structure (80.1%) which promoted strong CM penetration (9.6 mN m −1 ) and CM lysis (89.0%). In contrast, Staphylococcus aureus was resistant to M5-NH 2 (MLC = 139.6 µM), probably due electrostatic repulsion effects mediated by Lys-PG in the organism’s CM. These effects promoted weak CM binding (K d = 120.6 μM) and the formation of low levels of amphiphilic α-helical structure (30.1%), with low levels of CM penetration (4.8 mN m −1 ) and lysis (36.4%). C-terminal deamidation had a variable influence on the antibacterial activity of M5-NH 2 , and in the case of S. aureus , loss of this structural moiety had no apparent effect on activity. The resistance of S. aureus to M5-NH 2 isoforms appeared to be facilitated by the high level of charge carried by these peptides, as well as the density and distribution of this charge. In the case of P. aeruginosa, the activity of M5-NH 2 was greatly reduced by C-terminal deamidation (MLC = 138.6 µM), primarily through decreased CM binding (K d = 118.4 μM) and amphiphilic α-helix formation (39.6%) that led to lower levels of CM penetration (5.1 mN m −1 ) and lysis (39.0%).

Changes in morphofunctional parameters of erythrocytes and oxygen-binding capacity of hemoglobin under the influence of microorganisms of various types - Elena A. Shchuplova; Sergei V. Cherkasov; Victor V. Revin; Sergei I. Pinyaev; Ilya V. Syusin (European Biophysics Journal, 2025)

DNA binding to small anionic ligands: the case of Orange G dye - Rayane M. de Oliveira; Arthur G. S. de Rezende; Daniel F. Campos; Neemias de A. Ribeiro; Márcio S. Rocha (European Biophysics Journal, 2025)

On-the-fly resolution enhancement in X-ray protein crystallography using electric field - Krishna Prasad Khakurel; Michal Nemergut; Purbaj Pant; Martin Savko; Jakob Andreasson; Gabriel Žoldák (European Biophysics Journal, 2025)
X-ray crystallography has tremendously served structural biology by routinely providing high-resolution 3D structures of macromolecules. The extent of information encoded in the X-ray crystallography is proportional to which resolution the crystals diffract and the structure can be refined to. Therefore, there is a continuous effort to obtain high-quality crystals, especially for those proteins, which are considered difficult to crystallize into high-quality protein crystals of suitable sizes for X-ray crystallography. Efforts in enhancing the resolution in X-ray crystallography have also been made by optimizing crystallization protocols using external stimuli such as an electric field and magnetic field during the crystallization. Here, we present the feasibility of on-the-fly post-crystallization resolution enhancement of the protein crystal diffraction by applying a high-voltage electric field. The electric field between 2 and 11 kV/cm, which was applied after mounting the crystals in the beamline, resulted in the enhancement of the resolution. The crystal diffraction quality improved progressively with the exposure time. Moreover, we also find that upto defined electric field threshold, the protein structure remains largely unperturbed, a conclusion further supported by molecular dynamics simulations.

A gene-encoded bioprotein second harmonic generation (SHG) probe from Autographa californica nuclear polyhedrosis virus (AcMNPV) polyhedrin for live cell imaging - Xiaoyuan Deng; Hao Liu; Heting Chen; Zuojun Yang; Yuhan Wu; Li He; Wenjing Guo (European Biophysics Journal, 2025)

EBSA at 40 – an updated history - John M. Seddon; Anthony Watts (European Biophysics Journal, 2025)

Rational design of potent phosphopeptide binders to endocrine Snk PBD domain by integrating machine learning optimization, molecular dynamics simulation, binding energetics rescoring, and in vitro affinity assay - Zhaohui Wang; Jixiao Lan; Yan Feng; Yumei Chen; Meiyuan Chen (European Biophysics Journal, 2025)

Exploring characteristic features for effective HCN1 channel inhibition using integrated analytical approaches: 3D QSAR, molecular docking, homology modelling, ADME and molecular dynamics - Shiwani Sharma; Priyanka Rana; Vijayta Dani Chadha; Neelima Dhingra; Tanzeer Kaur (European Biophysics Journal, 2024)

Quantitative characterization of non-specific interaction of two globular proteins with Dextran T70 in a binary mixture - Adedayo A. Fodeke (European Biophysics Journal, 2024)

The origin of mutational epistasis - Jorge A. Vila (European Biophysics Journal, 2024)

Time-dependent simulation of blood flow through an abdominal aorta with iliac arteries - Grzegorz Górski; Krzysztof Kucab (European Biophysics Journal, 2024)
Atherosclerosis is one of the important diseases of the circulatory system because atherosclerotic plaques cause significant disruption of blood flow. Therefore, it is very important to properly understand these processes and skillfully simulate blood flow. In our work, we consider blood flow through an abdominal aorta with iliac arteries, assuming that the right iliac artery is narrowed by an atherosclerotic lesion. Blood flow is simulated using the laminar, standard $$k-ω$$ k - ω and standard $$k-ε$$ k - ϵ models. The obtained results show that despite the use of identical initial conditions, the distribution of velocity flow and wall shear stress depends on the choice of flow simulation model. For the $$k-ε$$ k - ϵ model, we obtain higher values of speed and wall shear stress on atherosclerotic plaque than in the other two models. The laminar and $$k-ω$$ k - ω models predict larger areas where reverse blood flow occurs in the area behind the atherosclerotic lesion. This effect is associated with negative wall shear stress. These two models give very similar results. The results obtained by us, and those reported in the literature, indicate that $$k-ω$$ k - ω model is the most suitable for blood flow analysis.

Extreme enthalpy‒entropy compensation in the dimerization of small solutes in aqueous solution - David J. Scott; Donald J. Winzor (European Biophysics Journal, 2024)
This communication summarizes findings from the earliest encounters with extreme enthalpy‒entropy compensation, a phenomenon first detected in the 1950s by a reappraisal of isopiestic and calorimetric measurements on aqueous urea solutions in terms of solute self-association. Because concurrent studies of carboxylic acid association were confined to measurement of the equilibrium constant by conductance, IR spectrophotometry or potentiometric titration measurements, temperature-independence of the dimerization constant was mistakenly taken to signify a value of zero for Δ $$H^o$$ H o instead of (Δ $$H^o$$ H o ‒ TΔ $$S^o$$ S o ). In those studies of small-solute self-association the extreme enthalpy‒entropy compensation was reflecting the action of water as a reactant whose hydroxyl groups were competing for the solute carbonyl involved in self-association. Such action gives rise to a positive temperature dependence of Δ $$H^o$$ H o that could well be operating in concert with that responsible for the commonly observed negative dependence for protein‒ligand interactions exhibiting extreme enthalpy‒entropy compensation, where the solvent contribution to the energetics reflects changes in the extent of ordered water structure in hydrophobic environments.

Application of artificial neural network for the mechano-bactericidal effect of bioinspired nanopatterned surfaces - Ecren Uzun Yaylacı (European Biophysics Journal, 2024)

Structural investigation, computational analysis, and theoretical cryoprotectant approach of antifreeze protein type IV mutants - Azadeh Eskandari; Thean Chor Leow; Mohd Basyaruddin Abdul Rahman; Siti Nurbaya Oslan (European Biophysics Journal, 2024)

Computational study on the impact of linkage sequence on the structure and dynamics of lignin - Derya Vural (European Biophysics Journal, 2024)

Physical aspects of epithelial cell–cell interactions: hidden system complexities - Ivana Pajic-Lijakovic; Milan Milivojevic; Peter V. E. McClintock (European Biophysics Journal, 2024)
The maintenance of homeostasis and the retention of ordered epithelial cell self-organization are essential for morphogenesis, wound healing, and the spread of cancer across the epithelium. However, cell–cell interactions in an overcrowded environment introduce a diversity of complications. Such interactions arise from an interplay between the cell compressive and shear stress components that accompany increased cell packing density. They can lead to various kinds of cell rearrangement such as: the epithelial-to-mesenchymal cell state transition; live cell extrusion; and cell jamming. All of these scenarios of cell rearrangement under mechanical stress relate to changes in the strengths of the cell–cell and cell–matrix adhesion contacts. The objective of this review study is twofold: first, to provide a comprehensive summary of the biological and physical factors influencing the effects of cell mechanical stress on cell–cell interactions, and the consequences of these interactions for the status of cell–cell and cell–matrix adhesion contacts; and secondly, to offer a bio-physical/mathematical analysis of the aforementioned biological aspects. By presenting these two approaches in conjunction, we seek to highlight the intricate nature of biological systems, which manifests in the form of complex bio-physical/mathematical equations. Furthermore, the juxtaposition of these apparently disparate approaches underscores the importance of conducting experiments to determine the multitude of parameters that contribute to the development of these intricate bio-physical/mathematical models.

Modeling study of kinesin-13 MCAK microtubule depolymerase - Ping Xie (European Biophysics Journal, 2024)

Reciprocal effect on lateral diffusion of receptor for advanced glycation endproducts and toll-like receptor 4 in the HEK293 cell membrane - Mohammad K. I. Walid; Sharifur Rahman; Emily A. Smith (European Biophysics Journal, 2024)

Mechanisms of stationary voltage fluctuation in the neuromuscular junction endplate and corresponding denoising paradigms - Jia-Zeng Wang; Pengkun Hu; Shu Ma (European Biophysics Journal, 2024)

The Structure of the LysR-type Transcriptional Regulator, CysB, Bound to the Inducer, N-acetylserine - Koen H. G. Verschueren; Eleanor J. Dodson; Anthony J. Wilkinson (European Biophysics Journal, 2024)
In Escherichia coli and Salmonella typhimurium , cysteine biosynthesis requires the products of 20 or more cys genes co-ordinately regulated by CysB. Under conditions of sulphur limitation and in the presence of the inducer, N -acetylserine, CysB binds to cys promoters and activates the transcription of the downstream coding sequences. CysB is a homotetramer, comprising an N-terminal DNA binding domain (DBD) and a C-terminal effector binding domain (EBD). The crystal structure of a dimeric EBD fragment of CysB from Klebsiella aerogenes revealed a protein fold similar to that seen in Lac repressor but with a different symmetry in the dimer so that the mode of DNA binding was not apparent. To elucidate the subunit arrangement in the tetramer, we determined the crystal structure of intact CysB in complex with N -acetylserine. The tetramer has two subunit types that differ in the juxtaposition of their winged helix-turn-helix DNA binding domains with respect to the effector binding domain. In the assembly, the four EBDs form a core with the DNA binding domains arranged in pairs on the surface. N -acetylserine makes extensive polar interactions in an enclosed binding site, and its binding is accompanied by substantial conformational rearrangements of surrounding residues that are propagated to the protein surface where they appear to alter the arrangement of the DNA binding domains. The results are (i) discussed in relation to the extensive mutational data available for CysB and (ii) used to propose a structural mechanism of N -acetylserine induced CysB activation.

Analysis of proteins in the light of mutations - Jorge A. Vila (European Biophysics Journal, 2024)

Computational discovery of dual potential inhibitors of SARS‐CoV‐2 spike/ACE2 and Mpro: 3D-pharmacophore, docking-based virtual screening, quantum mechanics and molecular dynamics - Boris D. Bekono; Pascal Amoa Onguéné; Conrad V. Simoben; Luc C. O. Owono; Fidele Ntie-Kang (European Biophysics Journal, 2024)

The conformational properties of alamethicin in ethanol studied by NMR - Yoshinori Miura (European Biophysics Journal, 2024)

An obituary: Dr. Helmut Cölfen 1965–2023 - Borries Demeler; Denis Gebauer; Emre Brookes; Jeffrey Fagan; Johannes Walter; José García de la Torre; Juan Manuel García-Ruiz; Kristian Schilling; Mengdi Chen; Lukas Dobler; Olwyn Byron; Stephen E. Harding; et al. (European Biophysics Journal, 2024)

Two-layer elastic models for single-yeast compressibility with flat microlevers - L. Delmarre; E. Harté; A. Devin; P. Argoul; F. Argoul (European Biophysics Journal, 2024)

Site-directed mutagenesis at the Glu78 in Ec-NhaA transporter impacting ion exchange: a biophysical study - Anuradha Yadav; Dinesh Kumar; Manish Dwivedi (European Biophysics Journal, 2024)

The effect of ionic redistributions on the microwave dielectric response of cytosol water upon glucose uptake - Cindy Galindo; Leonid Livshits; Lama Tarabeih; Gregory Barshtein; Sharon Einav; Yuri Feldman (European Biophysics Journal, 2024)

Erythrocytes membrane fluidity changes induced by adenylyl cyclase cascade activation: study using fluorescence recovery after photobleaching - A. N. Semenov; A. E. Lugovtsov; S. A. Rodionov; Eu. G. Maksimov; A. V. Priezzhev; E. A. Shirshin (European Biophysics Journal, 2024)
In this study, fluorescence recovery after photobleaching (FRAP) experiments were performed on RBC labeled by lipophilic fluorescent dye CM-DiI to evaluate the role of adenylyl cyclase cascade activation in changes of lateral diffusion of erythrocytes membrane lipids. Stimulation of adrenergic receptors with epinephrine (adrenaline) or metaproterenol led to the significant acceleration of the FRAP recovery, thus indicating an elevated membrane fluidity. The effect of the stimulation of protein kinase A with membrane-permeable analog of cAMP followed the same trend but was less significant. The observed effects are assumed to be driven by increased mobility of phospholipids resulting from the weakened interaction between the intermembrane proteins and RBC cytoskeleton due to activation of adenylyl cyclase signaling cascade. Graphical abstract

Reaction of KHP with excess NaOH or TRIS as standard reactions for calibration of titration calorimeters from 0 to 60 °C - Jason D. Kenealey; Margarida Bastos; Zaid Assaf; Guangyue Bai; Wenqi Zhao; Tyler Jarrard; Colter Tower; Lee D. Hansen (European Biophysics Journal, 2024)
Calibration of titration calorimeters is an ongoing problem, particularly with calorimeters with reaction vessel volumes < 10 mL in which an electrical calibration heater is positioned outside the calorimetric vessel. Consequently, a chemical reaction with a known enthalpy change must be used to accurately calibrate these calorimeters. This work proposes the use of standard solutions of potassium acid phthalate (KHP) titrated into solutions of excess sodium hydroxide (NaOH) or excess tris(hydroxymethyl)aminomethane (TRIS) as standard reactions to determine the collective accuracy of the relevant variables in a determination of the molar enthalpy change for a reaction. KHP is readily available in high purity, weighable for easy preparation of solutions with accurately known concentrations, stable in solution, not compromised by side reactions with common contaminants such as atmospheric CO 2 , and non-corrosive to materials used in calorimeter construction. Molar enthalpy changes for these reactions were calculated from 0 to 60 °C from reliable literature data for the p K a of KHP, the molar enthalpy change for protonation of TRIS, and the molar enthalpy change for ionization of water. The feasibility of using these reactions as enthalpic standards was tested in several calorimeters; a 50 mL CSC 4300, a 185 μL NanoITC, a 1.4 mL VP-ITC, and a TAM III with 1 mL reaction vessels. The results from the 50 mL CSC 4300, which was accurately calibrated with an electric heater, verified the accuracy of the calculated standard values for the molar enthalpy changes of the proposed reactions.

Application of electron paramagnetic resonance spectroscopy for determining the relative nanoenvironment fluidity of polymeric micelles - Lusine Tonoyan; Sirazum Munira; Afsaneh Lavasanifar; Arno G. Siraki (European Biophysics Journal, 2024)

Design of inhibitor peptide sequences based on the interfacial knowledge of the protein G-IgG crystallographic complex and their binding studies with IgG - Neetu Tanwar; Rupal Ojha; Soumya Aggarwal; Vijay Kumar Prajapati; Manoj Munde (European Biophysics Journal, 2024)

Structure of a novel form of phosphopantetheine adenylyltransferase from Klebsiella pneumoniae at 2.59 Å resolution - Nabeel Ahmad; Pradeep Sharma; Sujata Sharma; Tej P. Singh (European Biophysics Journal, 2024)

Observation of magnet-induced star-like radiation of a plasma created from cancer cells in a laser trap - D. Erenso; L. Tran; I. Abualrob; M. Bushra; J. Hengstenberg; E. Muhammed; I. Endale; N. Endale; E. Endale; S. Mayhut; N. Torres; P. Sheffield; et al. (European Biophysics Journal, 2024)

Ultraviolet C intensity dependence of decontamination efficiency for pathogens as function of repacked metamaterials with screw channels - Ion Munteanu; Elena Starodub; Sergiu Bazgan; Marina Turcan; Tatiana Paslari; Diana Podoleanu; Nicolae A. Enaki (European Biophysics Journal, 2024)

BASIS: BioAnalysis SEDFIT integrated software for cGMP analysis of SV-AUC data - Alexander E. Yarawsky; Erik S. Gough; Valeria Zai-Rose; Natalya I. Figueroa; Hazel M. Cunningham; John W. Burgner; Michael T. DeLion; Lake N. Paul (European Biophysics Journal, 2024)

Vibration spectra of DNA and RNA segments - Samira Jalilvand; Hamze Mousavi (European Biophysics Journal, 2024)

Real-time tilting and twisting motions of ligand-bound states of α7 nicotinic acetylcholine receptor - Yue Yang; Tatsuya Arai; Daisuke Sasaki; Masahiro Kuramochi; Hidetoshi Inagaki; Sumiko Ohashi; Hiroshi Sekiguchi; Kazuhiro Mio; Tai Kubo; Yuji C. Sasaki (European Biophysics Journal, 2024)
The α7 nicotinic acetylcholine receptor is a member of the nicotinic acetylcholine receptor family and is composed of five α7 subunits arranged symmetrically around a central pore. It is localized in the central nervous system and immune cells and could be a target for treating Alzheimer’s disease and schizophrenia. Acetylcholine is a ligand that opens the channel, although prolonged application rapidly decreases the response. Ivermectin was reported as one of the positive allosteric modulators, since the binding of Ivermectin to the channel enhances acetylcholine-evoked α7 currents. One research has suggested that tilting motions of the nicotinic acetylcholine receptor are responsible for channel opening and activation. To verify this hypothesis applies to α7 nicotinic acetylcholine receptor, we utilized a diffracted X-ray tracking method to monitor the stable twisting and tilting motion of nAChR α7 without a ligand, with acetylcholine, with Ivermectin, and with both of them. The results show that the α7 nicotinic acetylcholine receptor twists counterclockwise with the channel transiently opening, transitioning to a desensitized state in the presence of acetylcholine and clockwise without the channel opening in the presence of Ivermectin. We propose that the conformational transition of ACh-bound nAChR α7 may be due to the collective twisting of the five α7 subunits, resulting in the compression and movement, either downward or upward, of one or more subunits, thus manifesting tilting motions. These tilting motions possibly represent the transition from the resting state to channel opening and potentially to the desensitized state.

Quenching of G4-DNA intrinsic fluorescence by ligands - Liana L. Tevonyan; Artemy D. Beniaminov; Dmitry N. Kaluzhny (European Biophysics Journal, 2024)

Swimming polarity inversion in uncultured magnetotactic cocci - Giovanny Angiolillo; Fernanda Abreu; Daniel Acosta-Avalos (European Biophysics Journal, 2024)

Probing the interactions of the HIV-1 matrix protein-derived polybasic region with lipid bilayers: insights from AFM imaging and force spectroscopy - Chinta M. Aryal; Jianjun Pan (European Biophysics Journal, 2024)

Electrophoresis, a transport technology that transitioned from moving boundary method to zone method - Tsutomu Arakawa; Masataka Nakagawa; Chiaki Sakuma; Yui Tomioka; Yasunori Kurosawa; Daisuke Ejima; Teruo Akuta (European Biophysics Journal, 2024)

Inhibitor design for TMPRSS2: insights from computational analysis of its backbone hydrogen bonds using a simple descriptor - Suraj Ugrani (European Biophysics Journal, 2024)
Transmembrane protease serine 2 (TMPRSS2) is an important drug target due to its role in the infection mechanism of coronaviruses including SARS-CoV-2. Current understanding regarding the molecular mechanisms of known inhibitors and insights required for inhibitor design are limited. This study investigates the effect of inhibitor binding on the intramolecular backbone hydrogen bonds (BHBs) of TMPRSS2 using the concept of hydrogen bond wrapping, which is the phenomenon of stabilization of a hydrogen bond in a solvent environment as a result of being surrounded by non-polar groups. A molecular descriptor which quantifies the extent of wrapping around BHBs is introduced for this. First, virtual screening for TMPRSS2 inhibitors is performed by molecular docking using the program DOCK 6 with a Generalized Born surface area (GBSA) scoring function. The docking results are then analyzed using this descriptor and its relationship to the solvent-accessible surface area term ΔG sa of the GBSA score is demonstrated with machine learning regression and principal component analysis. The effect of binding of the inhibitors camostat, nafamostat, and 4-guanidinobenzoic acid (GBA) on the wrapping of important BHBs in TMPRSS2 is also studied using molecular dynamics. For BHBs with a large increase in wrapping groups due to these inhibitors, the radial distribution function of water revealed that certain residues involved in these BHBs, like Gln438, Asp440, and Ser441, undergo preferential desolvation. The findings offer valuable insights into the mechanisms of these inhibitors and may prove useful in the design of new inhibitors.

Correction: Relation between flexibility and intrinsically disorder regions in thermosensitive TRP channels reveal allosteric effects - Abigail García‑Morales; Nancy O. Pulido; Daniel Balleza (European Biophysics Journal, 2024)

Correction to: Relation between flexibility and intrinsically disorder regions in thermosensitive TRP channels reveal allosteric effects - Abigail García‑Morales; Nancy O. Pulido; Daniel Balleza (European Biophysics Journal, 2024)

Relation between flexibility and intrinsically disorder regions in thermosensitive TRP channels reveal allosteric effects - Abigail García‑Morales; Nancy O. Pulido; Daniel Balleza (European Biophysics Journal, 2024)

Peptide-based pore formation and cell membrane deformation: European Biophysics Journal Prizes at EBSA 2023 - Robert J. C. Gilbert (European Biophysics Journal, 2023)

Drug–ionic surfactant interactions: density, sound speed, spectroscopic, and electrochemical studies - Muhammad Sohail; Hafiz Muhammad Abd Ur Rahman; Muhammad Nadeem Asghar (European Biophysics Journal, 2023)

Annexin A5 stabilizes matrix vesicle-biomimetic lipid membranes: unravelling a new role of annexins in calcification - Claudio R. Ferreira; Marcos Antônio E. Cruz; Maytê Bolean; Luiz Henrique da S. Andrilli; José Luis Millan; Ana Paula Ramos; Massimo Bottini; Pietro Ciancaglini (European Biophysics Journal, 2023)
Matrix vesicles are a special class of extracellular vesicles thought to actively contribute to both physiologic and pathologic mineralization. Proteomic studies have shown that matrix vesicles possess high amounts of annexin A5, suggesting that the protein might have multiple roles at the sites of calcification. Currently, Annexin A5 is thought to promote the nucleation of apatitic minerals close to the inner leaflet of the matrix vesicles’ membrane enriched in phosphatidylserine and Ca 2+ . Herein, we aimed at unravelling a possible additional role of annexin A5 by investigating the ability of annexin A5 to adsorb on matrix-vesicle biomimetic liposomes and Langmuir monolayers made of dipalmitoylphosphatidylserine (DPPS) and dipalmitoylphosphatidylcholine (DPPC) in the absence and in the presence of Ca 2+ . Differential scanning calorimetry and dynamic light scattering measurements showed that Ca 2+ at concentrations in the 0.5–2.0 mM range induced the aggregation of liposomes probably due to the formation of DPPS-enriched domains. However, annexin A5 avoided the aggregation of liposomes at Ca 2+ concentrations lower than 1.0 mM. Surface pressure versus surface area isotherms showed that the adsorption of annexin A5 on the monolayers made of a mixture of DPPC and DPPS led to a reduction in the area of excess compared to the theoretical values, which confirmed that the protein favored attractive interactions among the membrane lipids. The stabilization of the lipid membranes by annexin A5 was also validated by recording the changes with time of the surface pressure. Finally, fluorescence microscopy images of lipid monolayers revealed the formation of spherical lipid-condensed domains that became unshaped and larger in the presence of annexin A5. Our data support the model that annexin A5 in matrix vesicles is recruited at the membrane sites enriched in phosphatidylserine and Ca 2+ not only to contribute to the intraluminal mineral formation but also to stabilize the vesicles’ membrane and prevent its premature rupture.

Stability of multilamellar lipid tubules in excess water - Tripta Bhatia (European Biophysics Journal, 2023)

On the role of calcium diffusion and its rapid buffering in intraflagellar signaling - M. V. Satarić; T. Nemeš (European Biophysics Journal, 2023)

Physics of collective cell migration - Ivana Pajic-Lijakovic; Milan Milivojevic (European Biophysics Journal, 2023)

MIL-CELL: a tool for multi-scale simulation of yeast replication and prion transmission - Damien Hall (European Biophysics Journal, 2023)
The single-celled baker’s yeast, Saccharomyces cerevisiae , can sustain a number of amyloid-based prions, the three most prominent examples being [URE3], [PSI+], and [PIN+]. In the laboratory, haploid S. cerevisiae cells of a single mating type can acquire an amyloid prion in one of two ways (i) spontaneous nucleation of the prion within the yeast cell, and (ii) receipt via mother-to-daughter transmission during the cell division cycle. Similarly, prions can be lost due to (i) dissolution of the prion amyloid by its breakage into non-amyloid monomeric units, or (ii) preferential donation/retention of prions between the mother and daughter during cell division. Here we present a computational tool ( M onitoring I nduction and L oss of prions in Cell s; MIL-CELL) for modelling these four general processes using a multiscale approach describing both spatial and kinetic aspects of the yeast life cycle and the amyloid-prion behavior. We describe the workings of the model, assumptions upon which it is based and some interesting simulation results pertaining to the wave-like spread of the epigenetic prion elements through the yeast population. MIL-CELL is provided as a stand-alone GUI executable program for free download with the paper. MIL-CELL is equipped with a relational database allowing all simulated properties to be searched, collated and graphed. Its ability to incorporate variation in heritable properties means MIL-CELL is also capable of simulating loss of the isogenic nature of a cell population over time. The capability to monitor both chronological and reproductive age also makes MIL-CELL potentially useful in studies of cell aging.

Long-term memory in Staphylococcus aureus α-hemolysin ion channel kinetics - M. P. Silva; C. G. Rodrigues; D. C. Machado; R. A. Nogueira (European Biophysics Journal, 2023)

Energy spectrum of the ideal DNA knot on a torus - Xuguang Shi (European Biophysics Journal, 2023)

Twist-stretch relations in nucleic acids - Marco Zoli (European Biophysics Journal, 2023)

Special Issue: 18th Congress of the Polish Biophysical Society - Jan M. Antosiewicz; Robert Gilbert; Piotr E. Marszalek (European Biophysics Journal, 2023)

Diversity of hydrodynamic radii of intrinsically disordered proteins - Michał K. Białobrzewski; Barbara P. Klepka; Agnieszka Michaś; Maja K. Cieplak-Rotowska; Zuzanna Staszałek; Anna Niedźwiecka (European Biophysics Journal, 2023)
Intrinsically disordered proteins (IDPs) form an important class of biomolecules regulating biological processes in higher organisms. The lack of a fixed spatial structure facilitates them to perform their regulatory functions and allows the efficiency of biochemical reactions to be controlled by temperature and the cellular environment. From the biophysical point of view, IDPs are biopolymers with a broad configuration state space and their actual conformation depends on non-covalent interactions of its amino acid side chain groups at given temperature and chemical conditions. Thus, the hydrodynamic radius ( R h ) of an IDP of a given polymer length (N) is a sequence- and environment-dependent variable. We have reviewed the literature values of hydrodynamic radii of IDPs determined experimentally by SEC, AUC, PFG NMR, DLS, and FCS, and complement them with our FCS results obtained for a series of protein fragments involved in the regulation of human gene expression. The data collected herein show that the values of hydrodynamic radii of IDPs can span the full space between the folded globular and denatured proteins in the R h ( N ) diagram.

An intramolecular disulphide bond in human 4E-T affects its binding to eIF4E1a protein - Joanna Zuberek; Marek Warzecha; Mateusz Dobrowolski; Anna Modrak-Wojcik (European Biophysics Journal, 2023)
The cap at the 5’terminus of mRNA is a key determinant of gene expression in eukaryotic cells, which among others is required for cap dependent translation and protects mRNA from degradation. These properties of cap are mediated by several proteins. One of them is 4E-Transporter (4E-T), which plays an important role in translational repression, mRNA decay and P-bodies formation. 4E-T is also one of several proteins that interact with eukaryotic initiation factor 4E (eIF4E), a cap binding protein which is a key component of the translation initiation machinery. The molecular mechanisms underlying the interactions of these two proteins are crucial for mRNA processing. Studying the interactions between human eIF4E1a and the N-terminal fragment of 4E-T that possesses unstructured 4E-binding motifs under non-reducing conditions, we observed that 4E-T preferentially forms an intramolecular disulphide bond. This “disulphide loop” reduces affinity of 4E-T for eIF4E1a by about 300-fold. Considering that only human 4E-T possesses two cysteines located between the 4E binding motifs, we proposed that the disulphide bond may act as a switch to regulate interactions between the two proteins. Graphical Abstract

N2 modified cap analogues as translation inhibitors and substrates for preparation of therapeutic mRNA - Karol Kurpiejewski; Marzena Jankowska-Anyszka; Renata Grzela (European Biophysics Journal, 2023)
In recent years many scientists have begun to focus on the mRNA molecule’s emeregence as a new type of drug. Its fast-moving and successful career as a vaccine technology cannot be underestimated. mRNA provides new opportunities and allows for the rapid preparation of effective drugs at low cost. These extensive possibilities stem from a number of factors, but the small cap structure located at the 5′ end of the mRNA is one contributing factor. Cap protects mRNA and ensures efficient recruitment to the biosynthesis machinery. Furthermore, it allows for the easy introduction of various modifications that influence the activity of the entire mRNA. Among the many different cap analogues that have been reported, those modified at the N2 position of guanosine have been systematically developed. N2-modified caps in the form of nucleoside monophosphates or dinucleotides show favorable biological properties, as well as a high capacity to inhibit the translation process in the cell-free RRL system. Modified N2 dinucleotides are efficiently incorporated into the structure of the mRNA transcript, and in specific circumstances with the correct orientation, making them an interesting alternative for ARCA-type analogues. Moreover, mRNA transcripts containing cap structures modified within the exocyclic amino group show very high translational activity. Therefore, analogues modified at the N2 position may have future applications as therapeutics against various manifestations of cancer and as desirable tools in RNA engineering.

Mammalian Nudt15 hydrolytic and binding activity on methylated guanosine mononucleotides - Maciej Lukaszewicz; Aleksandra Ferenc-Mrozek; Julia Kokosza; Anna Stefaniuk; Janusz Stepinski; Elzbieta Bojarska; Edward Darzynkiewicz (European Biophysics Journal, 2023)
The Nudt15 enzyme of the NUDIX protein family is the subject of extensive study due to its action on thiopurine drugs used in the treatment of cancer and inflammatory diseases. In addition to thiopurines, Nudt15 is enzymatically active in vitro on several nucleotide substrates. It has also been suggested that this enzyme may play a role in 5′RNA turnover by hydrolyzing m 7 GDP, a product of mRNA decapping. However, no detailed studies on this substrate with Nudt15 are available. Here, we analyzed the enzymatic activity of Nudt15 with m 7 GDP, its triphosphate form m 7 GTP, and the trimethylated counterparts (m 3 2,2,7 GDP and m 3 2,2,7 GTP). Kinetic data revealed a moderate activity of Nudt15 toward these methylated mononucleotides compared to the dGTP substrate. However m 7 GDP and m 3 2,2,7 GDP showed a distinct stabilization of Nudt15 upon ligand binding, in the same range as dGTP, and thus these two mononucleotides may be used as leading structures in the design of small molecule binders of Nudt15.

Peptide nucleic acid conjugates and their antimicrobial applications—a mini-review - Uladzislava Tsylents; Izabela Siekierska; Joanna Trylska (European Biophysics Journal, 2023)
Peptide nucleic acid (PNA) is a nucleic acid mimic with high specificity and binding affinity to natural DNA or RNA, as well as resistance to enzymatic degradation. PNA sequences can be designed to selectively silence gene expression, which makes PNA a promising tool for antimicrobial applications. However, the poor membrane permeability of PNA remains the main limiting factor for its applications in cells. To overcome this obstacle, PNA conjugates with different molecules have been developed. This mini-review focuses on covalently linked conjugates of PNA with cell-penetrating peptides, aminosugars, aminoglycoside antibiotics, and non-peptidic molecules that were tested, primarily as PNA carriers, in antibacterial and antiviral applications. The chemistries of the conjugation and the applied linkers are also discussed.

Structure and dynamics of pteridine reductase 1: the key phenomena relevant to enzyme function and drug design - Joanna Panecka-Hofman; Ina Poehner (European Biophysics Journal, 2023)
Pteridine reductase 1 (PTR1) is a folate and pterin pathway enzyme unique for pathogenic trypanosomatids. As a validated drug target, PTR1 has been the focus of recent research efforts aimed at finding more effective treatments against human parasitic diseases such as leishmaniasis or sleeping sickness. Previous PTR1-centered structural studies highlighted the enzyme characteristics, such as flexible regions around the active site, highly conserved structural waters, and species-specific differences in pocket properties and dynamics, which likely impacts the binding of natural substrates and inhibitors. Furthermore, several aspects of the PTR1 function, such as the substrate inhibition phenomenon and the level of ligand binding cooperativity in the enzyme homotetramer, likely related to the global enzyme dynamics, are poorly known at the molecular level. We postulate that future drug design efforts could greatly benefit from a better understanding of these phenomena through studying both the local and global PTR1 dynamics. This review highlights the key aspects of the PTR1 structure and dynamics relevant to structure-based drug design that could be effectively investigated by modeling approaches. Particular emphasis is given to the perspective of molecular dynamics, what has been accomplished in this area to date, and how modeling could impact the PTR1-targeted drug design in the future.

Tautomeric equilibrium and spectroscopic properties of 8-azaguanine revealed by quantum chemistry methods - Maciej Maciejczyk; Maciej Pyrka (European Biophysics Journal, 2023)
8-azaguanine is a triazolopyrimidine nucleobase analog possessing potent antibacterial and antitumor activities, and it has been implicated as a lead molecule in cancer and malaria therapy. Its intrinsic fluorescence properties can be utilized for monitoring its interactions with biological polymers like proteins or nucleic acids. In order to better understand these interactions, it is important to know the tautomeric equilibrium of this compound. In this work, the tautomeric equilibrium of all natural neutral and anionic compound forms (except highly improbable imino-enol tautomers) as well as their methyl derivatives and ribosides was revealed by quantum chemistry methods. It was shown that, as expected, tautomers protonated at positions 1 and 9 dominate neutral forms both in gas phase and in aqueous solution. 8-azaguanines methylated at any position of the triazole ring are protonated at position 1. The computed vertical absorption and emission energies are in very good agreement with the experimental data. They confirm the validity of the assumption that replacing the proton with the methyl group does not significantly change the positions of absorption and fluorescence peaks.

The cross-correlation-based analysis to digest the conformational dynamics of the mitoBK channels in terms of their modulation by flavonoids - Agata Wawrzkiewicz-Jałowiecka; Paulina Trybek; Beata Dworakowska; Piotr Bednarczyk; Przemysław Borys (European Biophysics Journal, 2023)
The activity of mitochondrial large-conductance voltage- and $$Ca^{2+}$$ C a 2 + -activated $$K^+$$ K + channels (mitoBK) is regulated by a number of biochemical factors, including flavonoids. In particular, naringenin (Nar) and quercetin (Que) reached reasonable scientific attention due to their well-pronounced channel-activating effects. The open-reinforcing outcomes of Nar and Que on the mitoBK channel gating have been already reported. Nevertheless, the molecular picture of the corresponding channel–ligand interactions remains still to be revealed. In this work, we investigate the effects of the Nar and Que on the conformational dynamics of the mitoBK channel. In this aim, the cross-correlation-based analysis of the single-channel signals recorded by the patch-clamp method is performed. The obtained results in the form of phase space diagrams enable us to visually monitor the effects exerted by the considered flavonoids at the level of temporal characteristics of repetitive sequences of channel conformations. It turns out that the mitoBK channel activation by naringenin and quercetin does not lead to the change in the number of clusters within the phase space diagrams, which can be related to the constant number of available channel macroconformations regardless of the flavonoid administration. The localization and occupancy of the clusters of cross-correlated sequences suggest that mitoBK channel stimulation by flavonoids affects the relative stability of channel conformations and the kinetics of switching between them. For most clusters, greater net effects are observed in terms of quercetin administration in comparison with naringenin. It indicates stronger channel interaction with Que than Nar.

Choosing the right density for a concentrated protein system like gluten in a coarse-grained model - Łukasz Mioduszewski (European Biophysics Journal, 2023)
Large coarse-grained simulations are often conducted with an implicit solvent, which makes it hard to assess the water content of the sample and the effective concentration of the system. Here the number and the size of cavities and entanglements in the system, together with density profiles, are used to asses the homogeneity and interconnectedness of gluten. This is a continuation of an earlier article, "Viscoelastic properties of wheat gluten in a molecular dynamics study" (Mioduszewski and Cieplak 2021b). It turns out there is a wide range of densities (between 1 residue per cubic nanometer and 3 residues/nm $$^3$$ 3 ) where the system is interconnected, but not homogeneous: there are still large empty spaces, surrounded by an entangled protein network. Those findings should be of importance to any coarse-grained simulation of large protein systems.

On the possibility of the existence of orienting hydrodynamic steering effects in the kinetics of receptor–ligand association - Jan M. Antosiewicz (European Biophysics Journal, 2023)
In the vast majority of biologically relevant cases of receptor-ligand complex formation, the binding site of the receptor is a small part of its surface, and moreover, formation of a biologically active complex often requires a specific orientation of the ligand relative to the binding site. Before the formation of the initial form of the complex, only long-range, electrostatic and hydrodynamic interactions can act between the ligand approaching the binding site and the receptor. In this context, the question arises whether as a result of these interactions, there is a pre-orientation of the ligand towards the binding site, which to some extent would accelerate the formation of the complex. The role of electrostatic interactions in the orientation of the ligand relative to the binding site of the receptor is well documented. The analogous role of hydrodynamic interactions, although assessed as very significant by Brune and Kim (PNAS 91, 2930–2934, (1994)), is still debatable. In this article, I present the current state of knowledge on this subject and consider the possibilities of demonstrating the orienting effect of hydrodynamic interactions in the processes of receptor–ligand association, in an experimental way supported by computer simulations.

Multi intercalators FRET enhanced detection of minute amounts of DNA - Luca Ceresa; Jose Chavez; Magdalena M. Bus; Bruce Budowle; Emma Kitchner; Joseph Kimball; Ignacy Gryczynski; Zygmunt Gryczynski (European Biophysics Journal, 2023)

Proceedings of the 25th Analytical Ultracentrifugation Workshops and Symposium - Borries Demeler; Robert Gilbert; Trushar R. Patel (European Biophysics Journal, 2023)

Suitability of double-stranded DNA as a molecular standard for the validation of analytical ultracentrifugation instruments - Maduni Ranasinghe; Jonathan M. Fogg; Daniel J. Catanese; Lynn Zechiedrich; Borries Demeler (European Biophysics Journal, 2023)

Experimental support for reclassification of the light scattering second virial coefficient from macromolecular solutions as a hydrodynamic parameter - Donald J. Winzor; Vlad Dinu; David J. Scott; Stephen E. Harding (European Biophysics Journal, 2023)
This investigation examines the source of the disparity between experimental values of the light scattering second virial coefficient $${A}_{2}$$ A 2 (mL.mol/g 2 ) for proteins and those predicted on the statistical mechanical basis of excluded volume. A much better theoretical description of published results for lysozyme is obtained by considering the experimental parameters to monitor the difference between the thermodynamic excluded volume term and its hydrodynamic counterpart. This involves a combination of parameters quantifying concentration dependence of the translational diffusion coefficient obtained from dynamic light scattering measurements. That finding is shown to account for observations of a strong correlation between $${A}_{2}{M}_{2}$$ A 2 M 2 (mL/g), where M 2 is the molar mass (molecular weight) of the macromolecule and the diffusion concentration parameter $${k}_{D}$$ k D (mL/g). On the grounds that $${k}_{D}$$ k D is regarded as a hydrodynamic parameter, the same status should be accorded the light scattering second virial coefficient rather than its current incorrect thermodynamic designation as $${B}_{2}$$ B 2 (mL.mol/g 2 ), or just B , the osmotic second virial coefficient for protein self-interaction.

14th EBSA congress, July 31 – August 4, 2023, Stockholm, Sweden – Abstracts (European Biophysics Journal, 2023)

Retrospective rationalization of disparities between the concentration dependence of diffusion coefficients obtained by boundary spreading and dynamic light scattering - Donald J. Winzor; Vlad Dinu; David J. Scott; Stephen E. Harding (European Biophysics Journal, 2023)
This study establishes the existence of substantial agreement between published results from traditional boundary spreading measurements (including synthetic boundary measurements in the analytical ultracenrifuge) on two globular proteins (bovine serum albumin, ovalbumin) and the concentration dependence of diffusion coefficient predicted for experiments conducted under the operative thermodynamic constraints of constant temperature and solvent chemical potential. Although slight negative concentration dependence of the translational diffusion coefficient is the experimentally observed as well as theoretically predicted, the extent of the concentration dependence is within the limits of experimental uncertainty inherent in diffusion coefficient measurement. Attention is then directed toward the ionic strength dependence of the concentration dependence coefficient ( $${k}_{D}$$ k D ) describing diffusion coefficients obtained by dynamic light scattering, where, in principle, the operative thermodynamic constraints of constant temperature and pressure preclude consideration of results in terms of single-solute theory. Nevertheless, good agreement between predicted and published experimental ionic strength dependencies of $${k}_{D}$$ k D for lysozyme and an immunoglobulin is observed by a minor adaptation of the theoretical treatment to accommodate the fact that thermodynamic activity is monitored on the molal concentration scale because of the constraint of constant pressure that pertains in dynamic light scattering experiments.

Determination of mRNA copy number in degradable lipid nanoparticles via density contrast analytical ultracentrifugation - Alexander Bepperling; Gesa Richter (European Biophysics Journal, 2023)

Comparison of three AUC techniques for the determination of the loading status and capsid titer of AAVs - Alexander Bepperling; Janine Best (European Biophysics Journal, 2023)

SDS-induced hexameric oligomerization of myotoxin-II from Bothrops asper assessed by sedimentation velocity and nuclear magnetic resonance - Amy Henrickson; Tony Montina; Paul Hazendonk; Bruno Lomonte; Ana Gisele C. Neves-Ferreira; Borries Demeler (European Biophysics Journal, 2023)

Comparative sedimentation equilibrium analysis of two IgG1 glycoforms: IgGCri and IgGWid - Khalil Abu Hammad; Vlad Dinu; Thomas E. MacCalman; Jacob Pattem; Margaret Goodall; Richard B. Gillis; Roy Jefferis; Stephen E. Harding (European Biophysics Journal, 2023)
The solution properties of two different glycoforms of IgG1 (IgG1Cri and IgG1Wid) are compared using primarily sedimentation equilibrium analysis with two complementary analysis routines: SEDFIT-MSTAR and MULTISIG. IgGCri bears diantennary complex-type glycans on its Fc domain that are fully core fucosylated and partially sialylated, whilst on IgGWid, they are non-fucosylated, partially galactosylated and non-sialylated. IgGWid is also Fab glycosylated. Despite these differences, SEDFIT-MSTAR analysis shows similar weight average molar masses M w of ~ (150 ± 5) kDa for IgGCri and ~ (154 ± 5) kDa for IgGWid and both glycoforms show evidence of the presence of a small fraction of dimer confirmed by MULTISIG analysis and also by sedimentation coefficient distributions from supportive sedimentation velocity measurements. The closeness of the sedimentation equilibrium behaviour and sedimentation coefficient distributions with a main peak sedimentation coefficient of ~ 6.4S for both glycoforms at different concentrations suggest that the different glycosylation profiles do not significantly impact on molar mass (molecular weight) nor conformation in solution.