European Biophysics Journal最新文献_第2页

Biophysical and microbiological aspects of the interaction between Yersinia pestis PsaA and bacteriophage L-413C. 鼠疫耶尔森菌PsaA与噬菌体L-413C相互作用的生物物理和微生物学方面的研究。

IF 2.4 4区生物学

European Biophysics Journal Pub Date : 2025-07-01 Epub Date: 2025-06-16 DOI: 10.1007/s00249-025-01768-6

Ilya Konyshev, Lyubov Dudina, Vladislav Belozerov, Sergey Ivanov, Svetlana Dentovskaya, Andrey Anisimov, Andrey Byvalov

{"title":"Biophysical and microbiological aspects of the interaction between Yersinia pestis PsaA and bacteriophage L-413C.","authors":"Ilya Konyshev, Lyubov Dudina, Vladislav Belozerov, Sergey Ivanov, Svetlana Dentovskaya, Andrey Anisimov, Andrey Byvalov","doi":"10.1007/s00249-025-01768-6","DOIUrl":"10.1007/s00249-025-01768-6","url":null,"abstract":"There has been a great interest in developing the phage-containing remedy against plague caused by antimicrobial resistant strains of Yersinia pestis, which have been increasingly isolated in recent years from sick humans and animals. Studies thus are under way to develop a \"phage cocktail\", which is expected to be effective against a wide range of pathogenic strains. Our paper sheds light on the role of Y. pestis antigen PsaA in reception of the phage L-413C, which might be a possible component of such a \"cocktail\". Using optical trapping (OT) and atomic force microscopy (AFM), we showed that PsaA-positive cells and PsaA-coated beads or cantilevers bound more effectively to a substrate coated with L-413C rather than Pokrovskaya phage. Comparing two isogenic strains of Y. pestis (EV and EV∆psaA), we found that when bacteria and phages are co-incubated under slightly acidic pH, as if in a eukaryotic cell, PsaA-positive cells bound the phage L-413C more effectively. There is good evidence to say that L-413C may become a component of a new anti-plague therapy due to its high ability to interact with the pili-forming protein PsaA from the outer membrane of Y. pestis.","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":" ","pages":"267-276"},"PeriodicalIF":2.4,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144309396","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 trapping with nanostructured optical fibers and motility analysis of Pseudomonas aeruginosa. 纳米结构光纤的光捕获及铜绿假单胞菌的动力学分析。

IF 2.4 4区生物学

European Biophysics Journal Pub Date : 2025-07-01 Epub Date: 2025-07-08 DOI: 10.1007/s00249-025-01775-7

Eric Faudry, Jochen Fick

引用次数: 0

Physical principles underpinning molecular-level protein evolution. 支撑分子水平蛋白质进化的物理原理。

IF 2.4 4区生物学

European Biophysics Journal Pub Date : 2025-07-01 Epub Date: 2025-06-26 DOI: 10.1007/s00249-025-01776-6

Jorge A Vila

{"title":"Physical principles underpinning molecular-level protein evolution.","authors":"Jorge A Vila","doi":"10.1007/s00249-025-01776-6","DOIUrl":"10.1007/s00249-025-01776-6","url":null,"abstract":"Since protein mutations are the main driving force of evolution at a molecular level, a proper analysis of the factors controlling them-such as the proteins' robustness, the evolutionary pathways, the number of ancestors, the epistasis, the post-translational modifications, and the location and the order of mutations-will enable us to find a response to several crucial queries in evolutionary biology. Among them, we highlight the following: At the molecular level, what factors determine whether protein evolution is repeatable? Aiming at finding an answer to this and several other significant questions behind protein evolvability, we distinguish two evolutionary models in our analysis: convergent and divergent, based on whether or not a \"target sequence\" needs to be reached after n mutational steps beginning with a wild-type protein sequence (from an unknown ancestor). Preliminary results suggest-regardless of whether the evolution is convergent or divergent-a tight relationship between the thermodynamic hypothesis (or Anfinsen's dogma) and the protein evolution at the molecular level. This conjecture will allow us to uncover how fundamental physical principles guide protein evolution and to gain a deeper grasp of mutationally driven evolutionary processes and the factors that influence them. Breaking down complex evolutionary problems into manageable pieces-without compromising the vision of the problem as a whole-could lead to effective solutions to critical evolutionary biology challenges, paving the way for further progress in this field.","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":" ","pages":"201-211"},"PeriodicalIF":2.4,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144504421","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

Amino acids hydrophobic properties in proteins are derived from their atomic polarities. 蛋白质中氨基酸的疏水性是由它们的原子极性决定的。

IF 2.4 4区生物学

European Biophysics Journal Pub Date : 2025-07-01 Epub Date: 2025-06-13 DOI: 10.1007/s00249-025-01764-w

Juan Cedano, Enrique Querol, Angel Mozo-Villarías

{"title":"Amino acids hydrophobic properties in proteins are derived from their atomic polarities.","authors":"Juan Cedano, Enrique Querol, Angel Mozo-Villarías","doi":"10.1007/s00249-025-01764-w","DOIUrl":"10.1007/s00249-025-01764-w","url":null,"abstract":"Knowledge of the hydrophobicity of amino acids is essential to understanding the structure and function of proteins. One of the most useful tools for this purpose has been the use of hydrophobicity scales. In these scales, each amino acid is attributed with a numerical value that characterizes its hydrophobic or hydrophilic behavior in a protein. These values depend on the particular methodologies used to obtain them. In the present work, we present a way to infer a hydrophobicity scale for all the amino acids from their partial atomic charge from the uniCHARMM force field. All amino acids are more or less soluble in water as they need to be easily bioavailable in the cell medium. It is during the folding process of a polypeptide chain, that an amino acid goes from a soluble state to be part of a folded protein within a cohesive hydrophobic core. In the present work, we have implemented a model and a formula that considers hydrophilicity as the ability of the atoms of amino acids to interact with water, being proportional to the accessibility to the solvent and its partial charge, depending on its sign. On the other hand, hydrophobicity is considered to be more intense the lower the charge on the atom and also proportional to the accessibility of the atom. This procedure improves the accuracy of protein hydrophobicity calculations down to the atomic level.","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":" ","pages":"257-265"},"PeriodicalIF":2.4,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144281880","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

Competitive adsorption of a monoclonal antibody and amphiphilic polymers to the air-water interface. 单克隆抗体和两亲性聚合物在空气-水界面上的竞争吸附。

IF 2.4 4区生物学

European Biophysics Journal Pub Date : 2025-07-01 Epub Date: 2025-05-22 DOI: 10.1007/s00249-025-01752-0

Elise J Hingst, Michaela Blech, Dariush Hinderberger, Patrick Garidel, Christian Schwieger

{"title":"Competitive adsorption of a monoclonal antibody and amphiphilic polymers to the air-water interface.","authors":"Elise J Hingst, Michaela Blech, Dariush Hinderberger, Patrick Garidel, Christian Schwieger","doi":"10.1007/s00249-025-01752-0","DOIUrl":"10.1007/s00249-025-01752-0","url":null,"abstract":"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.","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":" ","pages":"213-229"},"PeriodicalIF":2.4,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144126208","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

Modulation of conformational features and oligomerization of MMACHC by cobalamin variants: impact of the R161Q mutation in cblC disease. 钴胺素变异对MMACHC构象特征和寡聚化的调节：R161Q突变对cblC疾病的影响

IF 2.2 4区生物学

European Biophysics Journal Pub Date : 2025-06-27 DOI: 10.1007/s00249-025-01777-5

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

{"title":"Modulation of conformational features and oligomerization of MMACHC by cobalamin variants: impact of the R161Q mutation in cblC disease.","authors":"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","doi":"10.1007/s00249-025-01777-5","DOIUrl":"https://doi.org/10.1007/s00249-025-01777-5","url":null,"abstract":"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.","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144504420","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

Inside the membrane: a closer look using elastic scattering techniques and friends. 薄膜内部：使用弹性散射技术和朋友更近距离观察。

IF 2.2 4区生物学

European Biophysics Journal Pub Date : 2025-06-26 DOI: 10.1007/s00249-025-01761-z

Michael Kaltenegger, Enrico F Semeraro, Georg Pabst

{"title":"Inside the membrane: a closer look using elastic scattering techniques and friends.","authors":"Michael Kaltenegger, Enrico F Semeraro, Georg Pabst","doi":"10.1007/s00249-025-01761-z","DOIUrl":"https://doi.org/10.1007/s00249-025-01761-z","url":null,"abstract":"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.","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144493357","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

Quadruplexes with a grain of salt: influence of cation type and concentration on DNA G4 stability. 带盐颗粒的四联体：阳离子类型和浓度对DNA G4稳定性的影响。

IF 2.2 4区生物学

European Biophysics Journal Pub Date : 2025-06-25 DOI: 10.1007/s00249-025-01772-w

Anne Cucchiarini, Filip Kledus, Yu Luo, Václav Brázda, Jean-Louis Mergny

{"title":"Quadruplexes with a grain of salt: influence of cation type and concentration on DNA G4 stability.","authors":"Anne Cucchiarini, Filip Kledus, Yu Luo, Václav Brázda, Jean-Louis Mergny","doi":"10.1007/s00249-025-01772-w","DOIUrl":"https://doi.org/10.1007/s00249-025-01772-w","url":null,"abstract":"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.","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144482774","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

Professor Emil Paleček: seven decades with electrodes and biomolecules at the Institute of Biophysics of the CAS. Emil paleek教授：在中国科学院生物物理研究所从事电极和生物分子研究70年。

IF 2.2 4区生物学

European Biophysics Journal Pub Date : 2025-06-25 DOI: 10.1007/s00249-025-01771-x

Miroslav Fojta, Jan Paleček

{"title":"Professor Emil Paleček: seven decades with electrodes and biomolecules at the Institute of Biophysics of the CAS.","authors":"Miroslav Fojta, Jan Paleček","doi":"10.1007/s00249-025-01771-x","DOIUrl":"https://doi.org/10.1007/s00249-025-01771-x","url":null,"abstract":"This year we celebrate seventy years since the establishment of the Institute of Biophysics of the Czechoslovak Academy of Sciences (IBP) (founded on January 1, 1955). If we look into the biography of Professor Emil Paleček (born on October 3, 1930), one of the most world-recognized personalities associated with the Institute and one of the most cited Czech scientists, known as the founder of nucleic acids electrochemistry, we are drawn to the same year, i.e. 1955, as the year in which Emil Paleček finished his studies in biochemistry and joined the IBP, where he worked with admirable vitality, enthusiasm and dedication until his death (October 30, 2018). In the context of celebration of founding of the Institute, we would like to commemorate in this article a personality who significantly influenced the history of the Institute alongside the important discoveries and research directions that defined his extremely successful career. We prefer this form, which is a sort of a mini-review of the most important results of the laboratory obtained under EP's leadership over 63 years, presented in mutual context and natural relations. For his life's work, Professor Paleček received many prestigious awards, with the Czech Head Award in 2014 and the Neuron Foundation Award in 2017 being the most distinguished.","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144493358","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

Image analysis tools for improved characterization of nuclear chromatin patterns by confocal fluorescence microscopy. 通过共聚焦荧光显微镜改进核染色质模式表征的图像分析工具。

IF 2.2 4区生物学

European Biophysics Journal Pub Date : 2025-06-23 DOI: 10.1007/s00249-025-01770-y

Mohammadmehdi Roushenas, Marco Salerno, Virginia Bazzurro, Elena Gatta, Alberto Diaspro

{"title":"Image analysis tools for improved characterization of nuclear chromatin patterns by confocal fluorescence microscopy.","authors":"Mohammadmehdi Roushenas, Marco Salerno, Virginia Bazzurro, Elena Gatta, Alberto Diaspro","doi":"10.1007/s00249-025-01770-y","DOIUrl":"https://doi.org/10.1007/s00249-025-01770-y","url":null,"abstract":"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.","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144473636","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