European Biophysics Journal最新文献

{"title":"Real-time tilting and twisting motions of ligand-bound states of α7 nicotinic acetylcholine receptor","authors":"Yue Yang,&nbsp;Tatsuya Arai,&nbsp;Daisuke Sasaki,&nbsp;Masahiro Kuramochi,&nbsp;Hidetoshi Inagaki,&nbsp;Sumiko Ohashi,&nbsp;Hiroshi Sekiguchi,&nbsp;Kazuhiro Mio,&nbsp;Tai Kubo,&nbsp;Yuji C. Sasaki","doi":"10.1007/s00249-023-01693-6","DOIUrl":"10.1007/s00249-023-01693-6","url":null,"abstract":"<div><p>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.</p></div>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":"53 1-2","pages":"15 - 25"},"PeriodicalIF":2.2,"publicationDate":"2024-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00249-023-01693-6.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139482541","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}

{"title":"Quenching of G4-DNA intrinsic fluorescence by ligands","authors":"Liana L. Tevonyan,&nbsp;Artemy D. Beniaminov,&nbsp;Dmitry N. Kaluzhny","doi":"10.1007/s00249-023-01696-3","DOIUrl":"10.1007/s00249-023-01696-3","url":null,"abstract":"<div><p>G-quadruplex (G4) structures formed by the guanine-rich DNA regions exhibit several distinctive optical properties, including UV absorption and circular dichroism spectra. Some G4 DNA possess intrinsic UV fluorescence whose origin is not completely clear to date. In this work, we study the effect of TMPyP4 and Methylene Blue on the intrinsic fluorescence of the dimeric G4 DNA structure formed by two d(G₃T)₄ sequences. We demonstrate that binding of the ligands results in quenching of the intrinsic fluorescence, although the conformation of the G4 DNA and its dimeric structure remain preserved. The binding sites of the ligands were suggested by the photoinduced oxidation of guanines and analysis of binding isoterms. We discuss how DNA-ligand complexes can affect the intrinsic fluorescence of G4 DNA.</p></div>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":"53 1-2","pages":"47 - 56"},"PeriodicalIF":2.2,"publicationDate":"2024-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139460442","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}

{"title":"Swimming polarity inversion in uncultured magnetotactic cocci","authors":"Giovanny Angiolillo,&nbsp;Fernanda Abreu,&nbsp;Daniel Acosta-Avalos","doi":"10.1007/s00249-023-01698-1","DOIUrl":"10.1007/s00249-023-01698-1","url":null,"abstract":"<div><p>Magnetotactic bacteria are microorganisms that produce intracellular magnetic nanoparticles organized in chains, conferring a magnetic moment to the bacterial body that allows it to swim following the geomagnetic field lines. Magnetotactic bacteria usually display two swimming polarities in environmental samples: the South-seeking (SS) polarity and the North-seeking (NS) polarity, characterized by the bacteria swimming antiparallel or parallel to the magnetic field lines, respectively. It has been observed that in the presence of inhomogeneous magnetic fields, NS magnetotactic bacteria can change their swimming polarity to SS or vice versa. The present study analyzes populations of NS cocci obtained from SS cocci isolated in the presence of a magnet. The aim was to study differences in the swimming characteristics and magnetic moment among both populations of cocci. For that, trajectories were recorded and the velocity and angle among the velocity and the applied magnetic field were calculated. In addition, micrographs from both SS and NS cocci were obtained and their magnetosomes were measured to analyze their length, width, aspect ratio and magnetic moment, to finally obtain the magnetic moment for each coccus. The results showed the following properties of NS relative to SS cocci: higher velocities, narrow bacterial magnetic moment distribution, higher dispersion in the distribution of angles among the velocity and the applied magnetic field and lower magnetic field sensibility. Those differences cannot be explained by the simple change in magnetic polarity of the magnetosome chain and can be related to the existence of an active magnetoreceptive process in magnetotactic bacteria.</p></div>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":"53 1-2","pages":"69 - 76"},"PeriodicalIF":2.2,"publicationDate":"2024-01-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139428714","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}

{"title":"Probing the interactions of the HIV-1 matrix protein-derived polybasic region with lipid bilayers: insights from AFM imaging and force spectroscopy","authors":"Chinta M. Aryal,&nbsp;Jianjun Pan","doi":"10.1007/s00249-023-01697-2","DOIUrl":"10.1007/s00249-023-01697-2","url":null,"abstract":"<div><p>The human immunodeficiency virus type 1 (HIV-1) matrix protein contains a highly basic region, MA-HBR, crucial for various stages of viral replication. To elucidate the interactions between the polybasic peptide MA-HBR and lipid bilayers, we employed liquid-based atomic force microscopy (AFM) imaging and force spectroscopy on lipid bilayers of differing compositions. In 1-palmitoyl-2-oleoyl-<i>sn</i>-glycero-3-phosphocholine (POPC) bilayers, AFM imaging revealed the formation of annulus-shaped protrusions upon exposure to the polybasic peptide, accompanied by distinctive mechanical responses characterized by enhanced bilayer puncture forces. Importantly, our AFM-based force spectroscopy measurements unveiled that MA-HBR induces interleaflet decoupling within the cohesive bilayer organization. This is evidenced by a force discontinuity observed within the bilayer’s elastic deformation regime. In POPC/cholesterol bilayers, MA-HBR caused similar yet smaller annular protrusions, demonstrating an intriguing interplay with cholesterol-rich membranes. In contrast, in bilayers containing anionic 1-palmitoyl-2-oleoyl-<i>sn</i>-glycero-3-phospho-L-serine (POPS) lipids, MA-HBR induced unique annular protrusions, granular nanoparticles, and nanotubules, showcasing its distinctive effects in anionic lipid-enriched environments. Notably, our force spectroscopy data revealed that anionic POPS lipids weakened interleaflet adhesion within the bilayer, resulting in interleaflet decoupling, which potentially contributes to the specific bilayer perturbations induced by MA-HBR. Collectively, our findings highlight the remarkable variations in how the polybasic peptide, MA-HBR, interacts with lipid bilayers of differing compositions, shedding light on its role in host membrane restructuring during HIV-1 infection.</p></div>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":"53 1-2","pages":"57 - 67"},"PeriodicalIF":2.2,"publicationDate":"2024-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139085418","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}

{"title":"Electrophoresis, a transport technology that transitioned from moving boundary method to zone method","authors":"Tsutomu Arakawa,&nbsp;Masataka Nakagawa,&nbsp;Chiaki Sakuma,&nbsp;Yui Tomioka,&nbsp;Yasunori Kurosawa,&nbsp;Daisuke Ejima,&nbsp;Teruo Akuta","doi":"10.1007/s00249-023-01694-5","DOIUrl":"10.1007/s00249-023-01694-5","url":null,"abstract":"<div><p>Gel electrophoresis, a transport technology, is one of the most widely used experimental methods in biochemical and pharmaceutical research and development. Transport technologies are used to determine hydrodynamic or electrophoretic properties of macromolecules. Gel electrophoresis is a zone technology, where a small volume of sample is applied to a large separation gel matrix. In contrast, a seldom-used electrophoresis technology is moving boundary electrophoresis, where the sample is present throughout the separation phase or gel matrix. While the zone method gives peaks of separating macromolecular solutes, the moving boundary method gives a boundary between solute-free and solute-containing phases. We will review electrophoresis as a transport technology of zone and moving boundary methods and describe its principles and applications.</p></div>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":"53 1-2","pages":"1 - 13"},"PeriodicalIF":2.2,"publicationDate":"2023-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139069283","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}

{"title":"Inhibitor design for TMPRSS2: insights from computational analysis of its backbone hydrogen bonds using a simple descriptor","authors":"Suraj Ugrani","doi":"10.1007/s00249-023-01695-4","DOIUrl":"10.1007/s00249-023-01695-4","url":null,"abstract":"<div><p>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.</p></div>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":"53 1-2","pages":"27 - 46"},"PeriodicalIF":2.2,"publicationDate":"2023-12-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00249-023-01695-4.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139069281","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}

{"title":"Correction: Relation between flexibility and intrinsically disorder regions in thermosensitive TRP channels reveal allosteric effects","authors":"Abigail García‑Morales,&nbsp;Nancy O. Pulido,&nbsp;Daniel Balleza","doi":"10.1007/s00249-023-01692-7","DOIUrl":"10.1007/s00249-023-01692-7","url":null,"abstract":"","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":"53 1-2","pages":"93 - 93"},"PeriodicalIF":2.2,"publicationDate":"2023-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138796023","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}

{"title":"Peptide-based pore formation and cell membrane deformation: European Biophysics Journal Prizes at EBSA 2023","authors":"Robert J. C. Gilbert","doi":"10.1007/s00249-023-01691-8","DOIUrl":"10.1007/s00249-023-01691-8","url":null,"abstract":"<div><p>The European Biophysics Journal Prizes awarded at the European Biophysical Societies Association (EBSA) Congress in Stockholm in the Summer of 2023 recognised papers published in 2020 and 2021 which made use of multiple complementing experimental, theoretical and computational approaches. One of the winning papers addressed the specific role of arginine residues within antimicrobial and cell-penetrating peptides, in promoting membrane defect stabilisation and pore formation. The other winning paper described the influence of atomic force microscopy probe geometry on the measurement of surface deformability, assessed for investigation of the differing viscoelastic properties of non-malignant and cancerous cells. These papers showcase biophysical science; the importance of combining different experimental, modelling and molecular dynamics methods; and how researchers need to understand the theoretical basis and the limitations of the techniques they use. EBSA warmly congratulates the authors on their work and its subsequent recognition. Publication of these papers also demonstrates the ongoing commitment of the European Biophysics Journal to molecular scale and to systems biophysics, and to support of the international biophysical community.</p></div>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":"52 8","pages":"619 - 623"},"PeriodicalIF":2.0,"publicationDate":"2023-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138294475","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}

{"title":"Drug–ionic surfactant interactions: density, sound speed, spectroscopic, and electrochemical studies","authors":"Muhammad Sohail,&nbsp;Hafiz Muhammad Abd Ur Rahman,&nbsp;Muhammad Nadeem Asghar","doi":"10.1007/s00249-023-01689-2","DOIUrl":"10.1007/s00249-023-01689-2","url":null,"abstract":"<div><p>The failure of antibiotics against infectious diseases has become a global health issue due to the incessant use of antibiotics in the community and a lack of entry of new antibacterial drugs onto the market. The limited knowledge of biophysical interactions of existing antibiotics with bio-membranes is one of the major hurdles to design and develop more effective antibiotics. Surfactant systems are the simplest biological membrane models that not only mimic the cell membrane functions but are also used to investigate the biophysical interactions between pharmaceutical drugs and bio-membranes at the molecular level. In this work, volumetric and acoustic studies were used to investigate the molecular interactions of moxifloxacin (MXF), a potential antibacterial drug, with ionic surfactants (dodecyl-tri-methyl-ammonium bromide (DTAB), a cationic surfactant and sodium dodecyl sulfate (SDS), an anionic surfactant) under physiological conditions (phosphate buffer, pH 7.4) at <i>T</i> = 298.15–313.15 K at an interval of 5 K. Various volumetric and acoustic parameters were computed from the density and sound speed data and interpreted in terms of MXF–ionic surfactant interaction using electrostriction effect and co-sphere overlap model. Absorption spectroscopy and cyclic voltammetry were further used to determine the binding, partitioning, and related free energies of MXF with ionic micelles.</p></div>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":"52 8","pages":"735 - 747"},"PeriodicalIF":2.0,"publicationDate":"2023-11-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71520145","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}

{"title":"Annexin A5 stabilizes matrix vesicle-biomimetic lipid membranes: unravelling a new role of annexins in calcification","authors":"Claudio R. Ferreira,&nbsp;Marcos Antônio E. Cruz,&nbsp;Maytê Bolean,&nbsp;Luiz Henrique da S. Andrilli,&nbsp;José Luis Millan,&nbsp;Ana Paula Ramos,&nbsp;Massimo Bottini,&nbsp;Pietro Ciancaglini","doi":"10.1007/s00249-023-01687-4","DOIUrl":"10.1007/s00249-023-01687-4","url":null,"abstract":"<div><p>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 Ca²⁺. 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 Ca²⁺. Differential scanning calorimetry and dynamic light scattering measurements showed that Ca²⁺ 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 Ca²⁺ 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 Ca²⁺ not only to contribute to the intraluminal mineral formation but also to stabilize the vesicles’ membrane and prevent its premature rupture.</p></div>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":"52 8","pages":"721 - 733"},"PeriodicalIF":2.0,"publicationDate":"2023-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00249-023-01687-4.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71476752","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}