European Biophysics Journal最新文献_第8页

Mitochondrial alterations induced by Macrovipera lebetina venom 大毒蛇毒液诱导线粒体改变。

IF 2.4 4区生物学

European Biophysics Journal Pub Date : 2025-09-14 DOI: 10.1007/s00249-025-01796-2

Virjinia Doltchinkova, Victoria Vitkova, Milena Shkodrova, Meglena Kitanova, Vessela Lozanova, Siya Lozanova, Avgust Ivanov, Chavdar Roumenin

{"title":"Mitochondrial alterations induced by Macrovipera lebetina venom","authors":"Virjinia Doltchinkova, Victoria Vitkova, Milena Shkodrova, Meglena Kitanova, Vessela Lozanova, Siya Lozanova, Avgust Ivanov, Chavdar Roumenin","doi":"10.1007/s00249-025-01796-2","DOIUrl":"10.1007/s00249-025-01796-2","url":null,"abstract":"<div><p>The development of snake venom-based therapeutics and antivenoms is closely linked to understanding how snake venoms modulate the physicochemical properties of biological membranes. In this study, we investigated the effects of <i>Macrovipera lebetina</i> venom on the surface electrical characteristics of rat liver mitochondrial membranes in vitro. A combination of electrokinetic and mechanical techniques was employed, including measurements of mitochondrial electrophoretic mobility and the bending elasticity of phosphatidylcholine membrane models. Exposure to <i>Macrovipera lebetina</i> venom significantly increased the net surface charge of mitochondria, while adenosine triphosphatase (ATPase) activity remained unchanged. Morphological alterations and vesicle aggregation, observed via light scattering and fluorescence microscopy, indicated reduced binding of α-D-mannosyl and α-D-glucosyl residues to the outer mitochondrial membrane in the presence of venom. In addition, malondialdehyde assays revealed elevated levels of oxidized lipid species in venom-treated mitochondria. A pronounced softening of model phosphatidylcholine membranes was also observed, likely associated with lipid oxidation induced by the venom. It states that the effect of the venom of the Macrovipera lebetina on the surface electrical charge of rat liver mitochondria is being studied in vitro. The surface charge is a physicochemical characteristic of the mitochondrial membrane.</p><h3>Graphical abstract</h3><div><figure><div><div><picture><source><img></source></picture></div></div></figure></div></div>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":"54 7","pages":"491 - 510"},"PeriodicalIF":2.4,"publicationDate":"2025-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145058267","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Voltage-sensing domains: structural and functional diversity 电压传感领域：结构和功能的多样性。

IF 2.3 4区生物学

European Biophysics Journal Pub Date : 2025-09-13 DOI: 10.1007/s00249-025-01797-1

Martin C. Heiss, Bernhard E. Flucher

引用次数: 0

Ribulose-1,5-bisphosphate carboxylase/oxygenase activase isoforms from diverse species show differences in oligomeric structure, thermal stability, and activity 不同物种的核酮糖-1,5-二磷酸羧化酶/加氧酶激活酶异构体在寡聚物结构、热稳定性和活性方面存在差异。

IF 2.4 4区生物学

European Biophysics Journal Pub Date : 2025-09-11 DOI: 10.1007/s00249-025-01794-4

Jeremy R. Keown, Serena A. J. Watkin, F. Grant Pearce

{"title":"Ribulose-1,5-bisphosphate carboxylase/oxygenase activase isoforms from diverse species show differences in oligomeric structure, thermal stability, and activity","authors":"Jeremy R. Keown, Serena A. J. Watkin, F. Grant Pearce","doi":"10.1007/s00249-025-01794-4","DOIUrl":"10.1007/s00249-025-01794-4","url":null,"abstract":"<div><p>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.</p></div>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":"54 :","pages":"403 - 414"},"PeriodicalIF":2.4,"publicationDate":"2025-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00249-025-01794-4.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145038900","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Biophysical characterization of polyphenol aggregates in Moringa oleifera leaves water extract: stability and surface exposure effect on antioxidant activity under dilution 辣木叶水提物中多酚聚集体的生物物理特性：稀释条件下稳定性及表面暴露对抗氧化活性的影响。

IF 2.4 4区生物学

European Biophysics Journal Pub Date : 2025-09-03 DOI: 10.1007/s00249-025-01786-4

Rita Carrotta, Fabio Librizzi, Vincenzo Martorana, Samuele Raccosta, Maria Rosalia Mangione

{"title":"Biophysical characterization of polyphenol aggregates in Moringa oleifera leaves water extract: stability and surface exposure effect on antioxidant activity under dilution","authors":"Rita Carrotta, Fabio Librizzi, Vincenzo Martorana, Samuele Raccosta, Maria Rosalia Mangione","doi":"10.1007/s00249-025-01786-4","DOIUrl":"10.1007/s00249-025-01786-4","url":null,"abstract":"<div><p>The aqueous extract of <i>Moringa oleifera</i> 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.</p></div>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":"55 :","pages":"283 - 292"},"PeriodicalIF":2.4,"publicationDate":"2025-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00249-025-01786-4.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144991119","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Hydrodynamic properties of macromolecules and nanoparticles in dilute solution: a brief essay on classical and modern concepts 大分子和纳米颗粒在稀溶液中的流体动力学性质：古典和现代概念的简要介绍。

IF 2.4 4区生物学

European Biophysics Journal Pub Date : 2025-08-24 DOI: 10.1007/s00249-025-01791-7

José García de la Torre, José G. Hernández-Cifre

{"title":"Hydrodynamic properties of macromolecules and nanoparticles in dilute solution: a brief essay on classical and modern concepts","authors":"José García de la Torre, José G. Hernández-Cifre","doi":"10.1007/s00249-025-01791-7","DOIUrl":"10.1007/s00249-025-01791-7","url":null,"abstract":"<div><p>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.</p></div>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":"54 :","pages":"331 - 349"},"PeriodicalIF":2.4,"publicationDate":"2025-08-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00249-025-01791-7.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144938001","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Optimizing electroporation via pulse modulation: a molecular dynamics study 通过脉冲调制优化电穿孔：分子动力学研究。

IF 2.4 4区生物学

European Biophysics Journal Pub Date : 2025-08-21 DOI: 10.1007/s00249-025-01793-5

Shahariar Emon, Al Amin, Md. Hossain, Shovon Saha, Md. Asaduzzaman, Md Lokman Hossen, Mohammad Abu Sayem Karal, Hiromitsu Takaba, Md. Khorshed Alam

{"title":"Optimizing electroporation via pulse modulation: a molecular dynamics study","authors":"Shahariar Emon, Al Amin, Md. Hossain, Shovon Saha, Md. Asaduzzaman, Md Lokman Hossen, Mohammad Abu Sayem Karal, Hiromitsu Takaba, Md. Khorshed Alam","doi":"10.1007/s00249-025-01793-5","DOIUrl":"10.1007/s00249-025-01793-5","url":null,"abstract":"<div><p>Efficient molecular transport via reversible electroporation requires sustained existence of the pore without causing irreversible cellular damage. In this study, we used molecular dynamics simulations to investigate pore formation during electroporation, and we characterized the transition to hydrophilic pores. Our simulations reveal that during the hydrophilic state, the reapplication of an electric field, even at reduced magnitudes, extends the pore duration while maintaining structural integrity. Furthermore, we established that the pore size can be controlled by regulating the intervals between successive electric field pulses, offering precise control over membrane permeabilization. These findings provide a foundation for fine-tuning electroporation protocols, enabling customized permeabilization strategies based on the properties of the molecules to be delivered. This approach has the potential to significantly improve the efficacy of targeted drug delivery and gene therapy. It also creates new possibilities for precise and controlled cellular manipulation in therapeutic contexts.</p></div>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":"54 7","pages":"477 - 490"},"PeriodicalIF":2.4,"publicationDate":"2025-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144938027","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Optical label-free detection of SARS-CoV-2: investigating platform spectroscopic properties for oligonucleotide targeting 光学无标记检测SARS-CoV-2：寡核苷酸靶向平台光谱特性研究

IF 2.4 4区生物学

European Biophysics Journal Pub Date : 2025-08-11 DOI: 10.1007/s00249-025-01787-3

Silvia Maria Cristina Rotondi, Paolo Canepa, Silvia Dante, Maurizio Canepa, Ornella Cavalleri

{"title":"Optical label-free detection of SARS-CoV-2: investigating platform spectroscopic properties for oligonucleotide targeting","authors":"Silvia Maria Cristina Rotondi, Paolo Canepa, Silvia Dante, Maurizio Canepa, Ornella Cavalleri","doi":"10.1007/s00249-025-01787-3","DOIUrl":"10.1007/s00249-025-01787-3","url":null,"abstract":"<div><p>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<sub>D</sub> = (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.</p></div>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":"55 :","pages":"209 - 216"},"PeriodicalIF":2.4,"publicationDate":"2025-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00249-025-01787-3.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144820311","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Molecular Biophysics Database (MBDB) makes raw measurements findable and reusable 分子生物物理数据库（MBDB）使原始测量可查找和可重复使用。

IF 2.3 4区生物学

European Biophysics Journal Pub Date : 2025-08-10 DOI: 10.1007/s00249-025-01789-1

Emil Dandanell Agerschou, Terezie Prchalová, Miroslav Šimek, Michal Malý, Jan Stránský, Michal Strnad, Andrea Santisteban-Veiga, Mark A. Williams, Juan Sabín, Jan Dohnálek

{"title":"Molecular Biophysics Database (MBDB) makes raw measurements findable and reusable","authors":"Emil Dandanell Agerschou, Terezie Prchalová, Miroslav Šimek, Michal Malý, Jan Stránský, Michal Strnad, Andrea Santisteban-Veiga, Mark A. Williams, Juan Sabín, Jan Dohnálek","doi":"10.1007/s00249-025-01789-1","DOIUrl":"10.1007/s00249-025-01789-1","url":null,"abstract":"<div><p>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.</p></div>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":"55 :","pages":"335 - 345"},"PeriodicalIF":2.3,"publicationDate":"2025-08-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00249-025-01789-1.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144811582","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Electron currents mediated by tonoplast cytochromes b561 细胞质细胞色素b561介导的电子电流。

IF 2.4 4区生物学

European Biophysics Journal Pub Date : 2025-08-09 DOI: 10.1007/s00249-025-01785-5

Edoardo Tosato, Elisabetta Di Franco, Sayyeda Hira Hassan, Antonella Gradogna, Laura Lagostena, Cristiana Picco, Francesca Sparla, Paolo Trost, Armando Carpaneto

{"title":"Electron currents mediated by tonoplast cytochromes b561","authors":"Edoardo Tosato, Elisabetta Di Franco, Sayyeda Hira Hassan, Antonella Gradogna, Laura Lagostena, Cristiana Picco, Francesca Sparla, Paolo Trost, Armando Carpaneto","doi":"10.1007/s00249-025-01785-5","DOIUrl":"10.1007/s00249-025-01785-5","url":null,"abstract":"<div><p>Ascorbate (ASC) is a key redox buffer in plant cells, whose antioxidant capacity depends on its balance with monodehydroascorbate (MDHA), its one-electron oxidation product. In the cytoplasm of Arabidopsis mesophyll cells, ASC is present at high concentrations and interacts with enzymes that oxidize it to MDHA, such as ascorbate peroxidases, as well as with enzymes that regenerate it, like NAD(P)H-dependent MDHA oxidoreductases (MDHAR) and glutathione-dependent dehydroascorbate reductases (DHAR). In vacuoles, ASC is found at lower concentrations and vacuoles lack these enzymes, but it can still undergo non-enzymatic oxidation by phenoxy radicals generated by class III peroxidases. It has been discovered that vacuoles isolated from Arabidopsis mesophyll cells contain an electron transport system that functionally connects the cytoplasmic and vacuolar ASC pools, acting as a transmembrane MDHA oxidoreductase dependent on Asc. Patch-clamp measurements have shown that electron currents across the tonoplast depend on the presence of ASC as an electron donor and MDHA or ferricyanide as electron acceptors on opposite sides of the membrane. These electron currents are catalyzed by cytochrome b561 isoform A (CYB561A), a tonoplast redox protein with ASC-binding sites in both the cytoplasm and the vacuole, electrically connected by two heme b groups. The recent functional characterization of other members of the cytochrome b561 family underscores how these proteins are essential for cellular redox balance and metabolism, facilitating electron transport across membranes and supporting processes such as iron homeostasis, stress defence, and cell wall modifications, highlighting their fundamental role in plant physiology.</p></div>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":"55 :","pages":"275 - 282"},"PeriodicalIF":2.4,"publicationDate":"2025-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144803235","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Correction: Modifying recombinant purple acid phosphatase using computational design 修正：利用计算设计修改重组紫色酸性磷酸酶。

IF 2.3 4区生物学

European Biophysics Journal Pub Date : 2025-08-09 DOI: 10.1007/s00249-025-01792-6

Aishwarya Venkatramani, Montader Ali, Olga Predeina, Jennifer C. Molloy, Pietro Sormanni, Elizabeth A. H. Hall

引用次数: 0