European Biophysics Journal最新文献_第2页

Effects of gramicidin A on the deformation, membrane permeation and membrane stability of lipid vesicles by Fe₃O₄ nanoparticles. 革兰西菌素A对Fe3O4纳米颗粒脂质囊泡变形、膜渗透和膜稳定性的影响。

IF 2.3 4区生物学

European Biophysics Journal Pub Date : 2026-07-27 DOI: 10.1007/s00249-026-01862-3

Tawfika Nasrin, Mir Jubair Ahamed, Md Masum Billah, Mohammad Abu Sayem Karal

{"title":"Effects of gramicidin A on the deformation, membrane permeation and membrane stability of lipid vesicles by Fe3O4 nanoparticles.","authors":"Tawfika Nasrin, Mir Jubair Ahamed, Md Masum Billah, Mohammad Abu Sayem Karal","doi":"10.1007/s00249-026-01862-3","DOIUrl":"https://doi.org/10.1007/s00249-026-01862-3","url":null,"abstract":"Magnetite nanoparticles (MNPs, Fe3O4) have gained considerable interest for various biomedical applications. Gramicidin A (GrA) is a linear pentadecapeptide that plays an important role in modifying the biophysical and biological properties of membranes. Elucidating how GrA modulates the interaction between MNPs and biomembranes is essential for deepening our understanding of membrane biophysics and guiding the development of nanomedicine. We investigated the effects of GrA on anionic MNPs-induced deformation, membrane permeation, and the stability of cell-mimetic giant unilamellar vesicles (GUVs) under physiological conditions. The membranes of the GUVs were prepared using a combination of negatively charged lipid, neutral lipid, and varying GrA. The degree of deformation (e.g., compactness) decreased with increasing GrA. The leakage of encapsulated calcein from the GUVs indicated membrane poration caused by the adsorption of MNPs into the membranes. The leakage rate initially decreased and then increased as GrA rose. To assess membrane stability, we examined constant tension-induced rupture of GUVs by varying GrA using the micropipette technique. The rupture rate constant also showed a biphasic response, initially decreasing and then increasing with the increase of GrA at a constant membrane tension. Thus, GrA modulates the mechanical stability of membranes, along with MNPs-induced vesicle deformation and lipid membrane poration.","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":" ","pages":""},"PeriodicalIF":2.3,"publicationDate":"2026-07-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148590105","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

Apo and substrate-bound dihydropteroate synthase crystal structures from Thermus thermophilus HB8. 嗜热热菌HB8的载子和底物结合二氢嘌呤合酶晶体结构。

IF 2.3 4区生物学

European Biophysics Journal Pub Date : 2026-07-27 DOI: 10.1007/s00249-026-01857-0

Amulya Ramakrishna, Archanalakshmi Kambaru, Kuppan Gokulakrishnan, Bagautdin Bagautdinov, Sivaraman Padavattan

{"title":"Apo and substrate-bound dihydropteroate synthase crystal structures from Thermus thermophilus HB8.","authors":"Amulya Ramakrishna, Archanalakshmi Kambaru, Kuppan Gokulakrishnan, Bagautdin Bagautdinov, Sivaraman Padavattan","doi":"10.1007/s00249-026-01857-0","DOIUrl":"https://doi.org/10.1007/s00249-026-01857-0","url":null,"abstract":"Folate biosynthesis is essential for the survival of bacteria and other lower organisms, yet absent in mammals, making its enzymes promising targets for selective antimicrobial therapy. Dihydropteroate synthase (DHPS) catalyzes a key step in this pathway by condensing para-aminobenzoate (pABA) with 6-hydroxymethyl-7,8-dihydropterin pyrophosphate (DHPPP) to generate dihydropteroate. DHPS is also the cellular target of sulfonamide antibiotics, and the emergence of sulfonamide resistance underscores the need for detailed structural insights into substrate recognition and inhibitor design. Here, we report high-resolution crystal structures of Thermus thermophilus HB8 DHPS (TtDHPS) in its apo form (at 1.65 Å resolution) and in complex with pABA (at 1.9 Å resolution) and the pterin substrate analogue 6-hydroxymethyl-7,8-dihydropterin pyrophosphate (6-HMPPP) (at 1.9 Å resolution). TtDHPS adopts a classical TIM-barrel fold and forms a biologically relevant dimer stabilized by C-terminal α-helices. Comparative analysis of the apo and ligand-bound forms reveals substrate-induced ordering of flexible loop regions that, together with residues from the barrel core, define the pterin- and pABA-binding pockets. Structural and sequence analyses with DHPS homologs from Escherichia coli and Mycobacterium tuberculosis highlight conserved catalytic features, as well as variable loop conformations and phosphate-binding residues that may contribute to differential sulfonamide sensitivity. Collectively, these structures shed light on DHPS catalysis and may prove helpful in the study of inhibitors associated with sulfonamide resistance.","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":" ","pages":""},"PeriodicalIF":2.3,"publicationDate":"2026-07-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148590054","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

Protein arginine methyltransferases as regulators of phase separation: implications in cancer and neurodegenerative diseases. 蛋白精氨酸甲基转移酶作为相分离的调节因子：在癌症和神经退行性疾病中的意义。

IF 2.3 4区生物学

European Biophysics Journal Pub Date : 2026-07-22 DOI: 10.1007/s00249-026-01859-y

Zhihang Shen, Qiubin Yu

引用次数: 0

A historical overview of the need for distinction between the attainment of thermodynamic equilibrium and a kinetic steady state in experimental studies 在实验研究中需要区分热力学平衡和动力学稳定状态的历史概述。

IF 2.3 4区生物学

European Biophysics Journal Pub Date : 2026-07-22 DOI: 10.1007/s00249-026-01847-2

Donald J. Winzor, David J. Scott

引用次数: 0

Structural evidence of thioacetate reduction by fluorescent protein mRuby 荧光蛋白mRuby还原硫乙酸的结构证据。

IF 2.3 4区生物学

European Biophysics Journal Pub Date : 2026-07-09 DOI: 10.1007/s00249-026-01855-2

Jianshu Dong, Jiachong Xie, Qian Cao

引用次数: 0

Disruption of bacterial membranes by plant extracts of celandine and dandelion: microbiological and langmuir monolayer studies 白屈碱和蒲公英植物提取物对细菌膜的破坏：微生物学和朗缪尔单层研究。

IF 2.3 4区生物学

European Biophysics Journal Pub Date : 2026-06-30 DOI: 10.1007/s00249-026-01853-4

Agnieszka Gonet-Surówka, Kamil Drożdż, Anita Wnętrzak, Anna Chachaj-Brekiesz, Dawid Lupa, Sławomir Wybraniec, Łukasz Kozioł, Ewa Łopuszyńska, Monika Brzychczy-Włoch, Patrycja Dynarowicz-Latka

{"title":"Disruption of bacterial membranes by plant extracts of celandine and dandelion: microbiological and langmuir monolayer studies","authors":"Agnieszka Gonet-Surówka, Kamil Drożdż, Anita Wnętrzak, Anna Chachaj-Brekiesz, Dawid Lupa, Sławomir Wybraniec, Łukasz Kozioł, Ewa Łopuszyńska, Monika Brzychczy-Włoch, Patrycja Dynarowicz-Latka","doi":"10.1007/s00249-026-01853-4","DOIUrl":"10.1007/s00249-026-01853-4","url":null,"abstract":"<div>The article presents a study on the disruption of the bacterial membrane by celandine (CME) and dandelion (TOE) extracts containing bioactive compounds responsible for their antibacterial activity. The in vitro microbiological tests showed antibacterial effect both on Gram-positive (Staphylococcus aureus and Streptococcus pyogenes) and Gram-negative (Escherichia coli and Pseudomonas aeruginosa) pathogenic bacteria species. However, in the case of celandine herb extract, the effect was stronger, especially for Gram-positive bacteria. For a deeper understanding of the mechanism of antibacterial action, both studied extracts were subjected to biophysical studies on artificial bacterial lipid membranes, modeled with the Langmuir monolayers technique. The monolayer investigations were performed using two approaches: (i) monitoring the penetration of extracts injected into the aqueous subphase beneath a compressed lipid film, and (ii) comparing surface pressure–area isotherms recorded on a subphase with and without addition of extracts. These experiments confirmed the activity of TOE and CME at the membrane level, demonstrating the penetration of extract components into the membranes and their fluidizing effect. AFM analysis of the domain structures of the films transferred onto solid supports (Langmuir-Blodgett) revealed differences in film topography induced by the extracts and are in a good agreement with the results of biological tests and analytical analyses of the tested extracts. These findings confirm that the stronger antibacterial effect of CME, associated with a higher content of bioactive compounds, exerts a more destructive effect on the bacterial lipid membranes compared to TOE.</div>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":"55 4","pages":"757 - 776"},"PeriodicalIF":2.3,"publicationDate":"2026-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148350185","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

Challenging cases for AlphaFold: two multidomain proteins with zinc-binding-, phosphorylation- or dimerization-driven conformational changes AlphaFold具有挑战性的案例：两个多结构域蛋白与锌结合，磷酸化或二聚化驱动的构象变化。

IF 2.3 4区生物学

European Biophysics Journal Pub Date : 2026-06-29 DOI: 10.1007/s00249-026-01854-3

Yinshan Yang, Hélène Déméné

引用次数: 0

In sample pH measurement by ³¹P phosphate NMR: application to measure the intrinsic GTPase activity of Rab1a. 用31P磷酸核磁共振测定样品pH值：应用于测定Rab1a的内在GTPase活性。

IF 2.3 4区生物学

European Biophysics Journal Pub Date : 2026-06-25 DOI: 10.1007/s00249-026-01850-7

David Pantoja-Uceda, Douglas V Laurents

{"title":"In sample pH measurement by 31P phosphate NMR: application to measure the intrinsic GTPase activity of Rab1a.","authors":"David Pantoja-Uceda, Douglas V Laurents","doi":"10.1007/s00249-026-01850-7","DOIUrl":"https://doi.org/10.1007/s00249-026-01850-7","url":null,"abstract":"A quick, noninvasive method based on 31P 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 31P 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.","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":" ","pages":""},"PeriodicalIF":2.3,"publicationDate":"2026-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148315106","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

The MOlecular-Scale Biophysics Research Infrastructure (MOSBRI) Project and its Outcomes 分子尺度生物物理研究基础设施（MOSBRI）项目及其成果。

IF 2.3 4区生物学

European Biophysics Journal Pub Date : 2026-06-11 DOI: 10.1007/s00249-026-01851-6

Gregor Anderluh, Ornella Cavalleri, Patrick England, Josef Houser, Adriana Erica Miele, Bohdan Schneider, Patrick Van der Wel

引用次数: 0

Bitter taste TAS2R14 and TAS2R46 receptors bound to G proteins: comparison of cryo-EM, AlphaFold, and molecular dynamics structures 结合G蛋白的苦味TAS2R14和TAS2R46受体：冷冻电镜、AlphaFold和分子动力学结构的比较。

IF 2.3 4区生物学

European Biophysics Journal Pub Date : 2026-06-05 DOI: 10.1007/s00249-026-01841-8

Ruth Pachter, Soo-Kyung Kim, Yixin C. Xu, Gaoyuan Liu, Soohyeong Kim, William A. Goddard

{"title":"Bitter taste TAS2R14 and TAS2R46 receptors bound to G proteins: comparison of cryo-EM, AlphaFold, and molecular dynamics structures","authors":"Ruth Pachter, Soo-Kyung Kim, Yixin C. Xu, Gaoyuan Liu, Soohyeong Kim, William A. Goddard","doi":"10.1007/s00249-026-01841-8","DOIUrl":"10.1007/s00249-026-01841-8","url":null,"abstract":"<div>Bitter taste type 2 G protein-coupled receptors (TAS2R GPCRs) detect bitter substances on the tongue, but they are also prevalent in tissues throughout the human body that play a role in cancer and other diseases, making them targets for pharmacological research. However, structural information on G protein (GP)-bound TAS2R complexes resolved by cryogenic electron microscopy (cryo-EM) is available for only 4 of the 25 TAS2Rs. Herein, we show that AlphaFold (AF) predictions of GP-bound TAS2R14 and TAS2R46 agree well with cryo-EM structure determinations, thus suggesting that the AF2 predicted structures for all 25 TAS2Rs could be used as starting points for drug development. Although useful starting points, we show that Molecular Dynamics (MD) studies are needed to refine the AF2 structures to get sufficient accuracy for drug design. We find that the MD simulations agree well with the cryo-EM structures at 85 K, but significant changes occur in the MD structures at 310 K that arise from thermal fluctuations frozen-out in the cryo-EM structure, making them far less pronounced at 85 K. We conclude that for TAS2Rs for which cryo-EM structures are not available, AF2 predicted structures followed by MD at 310 K provide a basis for TAS2R drug discovery.</div>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":"55 4","pages":"731 - 745"},"PeriodicalIF":2.3,"publicationDate":"2026-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148161398","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