European Biophysics Journal最新文献_第2页

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 2.4 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":"https://doi.org/10.1007/s00249-025-01789-1","url":null,"abstract":"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.","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2025-08-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","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":"https://doi.org/10.1007/s00249-025-01785-5","url":null,"abstract":"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.","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":" ","pages":""},"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 2.4 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

Characterization of Aquaporin Z proteoliposome structure and functionality via microscopy and scattering methods. 通过显微镜和散射方法表征水通道蛋白Z蛋白脂质体的结构和功能。

IF 2.4 4区生物学

European Biophysics Journal Pub Date : 2025-08-07 DOI: 10.1007/s00249-025-01790-8

Zsófia Edit Szathmáry, Martin Cramer Pedersen, Alec Michels, Torsten Høybye Bak Regueira, Jacob Judas Kain Kirkensgaard

{"title":"Characterization of Aquaporin Z proteoliposome structure and functionality via microscopy and scattering methods.","authors":"Zsófia Edit Szathmáry, Martin Cramer Pedersen, Alec Michels, Torsten Høybye Bak Regueira, Jacob Judas Kain Kirkensgaard","doi":"10.1007/s00249-025-01790-8","DOIUrl":"https://doi.org/10.1007/s00249-025-01790-8","url":null,"abstract":"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.","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2025-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144793111","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

Tracking reduction-induced molecular changes in pathological free light chains by SV-AUC. SV-AUC跟踪还原诱导病理性游离轻链的分子变化。

IF 2.4 4区生物学

European Biophysics Journal Pub Date : 2025-08-05 DOI: 10.1007/s00249-025-01788-2

Florian T Tucholski, Rebecca Sternke-Hoffmann, Thomas Pauly, Rasmus K Norrild, Amelie Boquoi, Roland Fenk, Luitgard Nagel, Alexander K Buell, Rainer Haas, Dieter Willbold

{"title":"Tracking reduction-induced molecular changes in pathological free light chains by SV-AUC.","authors":"Florian T Tucholski, Rebecca Sternke-Hoffmann, Thomas Pauly, Rasmus K Norrild, Amelie Boquoi, Roland Fenk, Luitgard Nagel, Alexander K Buell, Rainer Haas, Dieter Willbold","doi":"10.1007/s00249-025-01788-2","DOIUrl":"https://doi.org/10.1007/s00249-025-01788-2","url":null,"abstract":"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.","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2025-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144788028","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

In silico study of cytochrome-C binding to a cardiolipin-containing membrane. 细胞色素c与含心磷脂膜结合的硅片研究。

IF 2.2 4区生物学

European Biophysics Journal Pub Date : 2025-07-25 DOI: 10.1007/s00249-025-01783-7

Alessia Muroni, Fulvio Erba, Leonardo Domenichelli, Luisa Di Paola, Federica Sinibaldi, Giampiero Mei, Almerinda Di Venere, Velia Minicozzi

{"title":"In silico study of cytochrome-C binding to a cardiolipin-containing membrane.","authors":"Alessia Muroni, Fulvio Erba, Leonardo Domenichelli, Luisa Di Paola, Federica Sinibaldi, Giampiero Mei, Almerinda Di Venere, Velia Minicozzi","doi":"10.1007/s00249-025-01783-7","DOIUrl":"https://doi.org/10.1007/s00249-025-01783-7","url":null,"abstract":"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.","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144717231","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

Equations describing semi-confluent cell growth (II) colony formation on a flat surface. 描述半融合细胞生长的方程（II）平面上的集落形成。

IF 2.2 4区生物学

European Biophysics Journal Pub Date : 2025-07-21 DOI: 10.1007/s00249-025-01784-6

Damien Hall

引用次数: 0

Spectroscopic secondary structure fingerprint of β-variant of SARS-CoV-2 spike glycoprotein. SARS-CoV-2刺突糖蛋白β变异的光谱二级结构指纹图谱。

IF 2.2 4区生物学

European Biophysics Journal Pub Date : 2025-07-21 DOI: 10.1007/s00249-025-01782-8

Rosanna Mosetti, Tiziana Mancini, Federica Bertelà, Salvatore Macis, Nicole Luchetti, Velia Minicozzi, Stefano Lupi, Annalisa D'Arco

{"title":"Spectroscopic secondary structure fingerprint of β-variant of SARS-CoV-2 spike glycoprotein.","authors":"Rosanna Mosetti, Tiziana Mancini, Federica Bertelà, Salvatore Macis, Nicole Luchetti, Velia Minicozzi, Stefano Lupi, Annalisa D'Arco","doi":"10.1007/s00249-025-01782-8","DOIUrl":"https://doi.org/10.1007/s00249-025-01782-8","url":null,"abstract":"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.","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144681833","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

Biological applications at the AQUA beamline of the EuPRAXIA@SPARC_LAB free electron laser. EuPRAXIA@SPARC_LAB自由电子激光器AQUA光束线的生物学应用。

IF 2.2 4区生物学

European Biophysics Journal Pub Date : 2025-07-16 DOI: 10.1007/s00249-025-01778-4

Emiliano De Santis, Tomas André, Stefania Alleva, Richard Bean, Massimo Ferrario, Augusto Marcelli, Velia Minicozzi, Emiliano Principi, Nicuşor Tîmneanu, Carl Caleman, Francesco Stellato

{"title":"Biological applications at the AQUA beamline of the EuPRAXIA@SPARC_LAB free electron laser.","authors":"Emiliano De Santis, Tomas André, Stefania Alleva, Richard Bean, Massimo Ferrario, Augusto Marcelli, Velia Minicozzi, Emiliano Principi, Nicuşor Tîmneanu, Carl Caleman, Francesco Stellato","doi":"10.1007/s00249-025-01778-4","DOIUrl":"https://doi.org/10.1007/s00249-025-01778-4","url":null,"abstract":"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.","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144648167","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

Development of novel experimental setup for hands-on cardiovascular biophysics education. 心血管生物物理实践教学新型实验装置的开发。

IF 2.2 4区生物学

European Biophysics Journal Pub Date : 2025-07-15 DOI: 10.1007/s00249-025-01781-9

Ljubica Ilić, Katarina Žikić, Zorica Nestorović, Biljana Smiljković, Dejan Žikić

{"title":"Development of novel experimental setup for hands-on cardiovascular biophysics education.","authors":"Ljubica Ilić, Katarina Žikić, Zorica Nestorović, Biljana Smiljković, Dejan Žikić","doi":"10.1007/s00249-025-01781-9","DOIUrl":"https://doi.org/10.1007/s00249-025-01781-9","url":null,"abstract":"A foundational understanding of biophysics and fluid dynamics is critical for comprehending cardiovascular physiological phenomena, yet medical students often struggle with the mathematical complexity. Traditional teaching methods, including in vivo and in vitro experiments, are increasingly being replaced due to ethical concerns, leading to the adoption of in silico models. This study developed a biophysical model simulating the vascular tree using pumps and silicone vessels. Central to the model is a silicone aorta with pressure sensors, immersed in water, and connected to rubber and peristaltic pumps to generate pulse waves. Transparent silicone tubes, decreasing in diameter, mimic the vascular system, while one-way valves regulate flow. Pressure was measured via sensors at key points, with data digitized and visualized in real-time. A 40% ethyl alcohol solution, mimicking blood viscosity, was used. The exercise aimed to teach wave propagation, pressure waveform analysis, pulse wave velocity calculation, and the effects of resistance on wave propagation. Pulse wave propagation was demonstrated with manual compression of the rubber pump generating the input signal. Time delays between pressure waveforms at different sensors were used to calculate pulse wave velocity. Wave reflections were observed as the forward wave traveled to the aortic bifurcation, reflected backward, and then reflected again upon reaching a valve. Reflections were further analyzed with constrictions and added resistance in the system, with careful observation needed to discern the superimposed waves.","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144635855","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