European Biophysics Journal最新文献_第5页

Structure of a novel form of phosphopantetheine adenylyltransferase from Klebsiella pneumoniae at 2.59 Å resolution 分辨率为 2.59 Å 的肺炎克雷伯氏菌磷酸泛硫乙胺腺苷转移酶新型结构。

IF 2.2 4区生物学

European Biophysics Journal Pub Date : 2024-03-08 DOI: 10.1007/s00249-024-01703-1

Nabeel Ahmad, Pradeep Sharma, Sujata Sharma, Tej P. Singh

{"title":"Structure of a novel form of phosphopantetheine adenylyltransferase from Klebsiella pneumoniae at 2.59 Å resolution","authors":"Nabeel Ahmad, Pradeep Sharma, Sujata Sharma, Tej P. Singh","doi":"10.1007/s00249-024-01703-1","DOIUrl":"10.1007/s00249-024-01703-1","url":null,"abstract":"<div><p>Phosphopantetheine adenylyltransferase (EC. 2.7.7.3, PPAT) catalyzes the penultimate step of the multistep reaction in the coenzyme A (CoA) biosynthesis pathway. In this step, an adenylyl group from adenosine triphosphate (ATP) is transferred to 4′-phosphopantetheine (PNS) yielding 3′-dephospho-coenzyme A (dpCoA) and pyrophosphate (PP<sub>i</sub>). PPAT from strain C3 of <i>Klebsiella pneumoniae</i> (<i>Kp</i>PPAT) was cloned, expressed and purified. It was crystallized using 0.1 M HEPES buffer and PEG10000 at pH 7.5. The crystals belonged to tetragonal space group P4<sub>1</sub>2<sub>1</sub>2 with cell dimensions of <i>a</i> = <i>b</i> = 72.82 Å and <i>c</i> = 200.37 Å. The structure was determined using the molecular replacement method and refined to values of 0.208 and 0.255 for <i>R</i><sub>cryst</sub> and <i>R</i><sub>free</sub> factors, respectively. The structure determination showed the presence of three crystallographically independent molecules A, B and C in the asymmetric unit. The molecules A and B are observed in the form of a dimer in the asymmetric unit while molecule C belongs to the second dimer whose partner is related by crystallographic twofold symmetry. The polypeptide chain of <i>Kp</i>PPAT folds into a β/α structure. The conformations of the side chains of several residues in the substrate binding site in <i>Kp</i>PPAT are significantly different from those reported in other PPATs. As a result, the modes of binding of substrates, phosphopantetheine (PNS) and adenosine triphosphate (ATP) differ considerably. The binding studies using fluorescence spectroscopy indicated a K<sub>D</sub> value of 3.45 × 10<sup>−4</sup> M for ATP which is significantly lower than the corresponding values reported for PPAT from other species.</p></div>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":"53 3","pages":"147 - 157"},"PeriodicalIF":2.2,"publicationDate":"2024-03-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140058384","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

Observation of magnet-induced star-like radiation of a plasma created from cancer cells in a laser trap 观察激光陷阱中由癌细胞产生的等离子体的磁诱导星状辐射。

IF 2.2 4区生物学

European Biophysics Journal Pub Date : 2024-03-07 DOI: 10.1007/s00249-024-01701-3

D. Erenso, L. Tran, I. Abualrob, M. Bushra, J. Hengstenberg, E. Muhammed, I. Endale, N. Endale, E. Endale, S. Mayhut, N. Torres, P. Sheffield, C. Vazquez, H. Crogman, C. Nichols, T. Dang, E. E. Hach III

引用次数: 0

Ultraviolet C intensity dependence of decontamination efficiency for pathogens as function of repacked metamaterials with screw channels 带有螺旋通道的重新封装超材料对病原体净化效率的紫外线 C 强度依赖性。

IF 2.2 4区生物学

European Biophysics Journal Pub Date : 2024-02-28 DOI: 10.1007/s00249-024-01702-2

Ion Munteanu, Elena Starodub, Sergiu Bazgan, Marina Turcan, Tatiana Paslari, Diana Podoleanu, Nicolae A. Enaki

引用次数: 0

BASIS: BioAnalysis SEDFIT integrated software for cGMP analysis of SV-AUC data BASIS：用于 SV-AUC 数据 cGMP 分析的 BioAnalysis SEDFIT 集成软件。

IF 2.2 4区生物学

European Biophysics Journal Pub Date : 2024-02-08 DOI: 10.1007/s00249-024-01700-4

Alexander E. Yarawsky, Erik S. Gough, Valeria Zai-Rose, Natalya I. Figueroa, Hazel M. Cunningham, John W. Burgner II, Michael T. DeLion, Lake N. Paul

引用次数: 0

Vibration spectra of DNA and RNA segments DNA 和 RNA 片段的振动光谱。

IF 2.2 4区生物学

European Biophysics Journal Pub Date : 2024-01-24 DOI: 10.1007/s00249-023-01699-0

Samira Jalilvand, Hamze Mousavi

{"title":"Vibration spectra of DNA and RNA segments","authors":"Samira Jalilvand, Hamze Mousavi","doi":"10.1007/s00249-023-01699-0","DOIUrl":"10.1007/s00249-023-01699-0","url":null,"abstract":"<div><p>The dispersion curves and density of states are used to analyze the vibrational characteristics of DNA and RNA segments. This is done using a harmonic Hamiltonian and the Green’s function technique. Two configurations of DNA and RNA, finite and cyclic, have been investigated and compared to their infinite counterparts. For the DNA molecule, three models, including a fishbone model, a ldder model, and a fishbone ladder model, have been employed, while the RNA molecule has been represented using a half fishbone model. To enhance the realism of DNA and RNA simulations, the unit cells within each infinite system as well as the length of the finite and cyclic cases are gradually enlarged. The connections between the sub-sites have been modeled using linear springs, where the stiffness of the vertical springs exhibits random variations throughout the length of the DNA and RNA models. Shorter DNA and RNA segments exhibit additional peaks in their density of states, resulting in more bands in dispersion curves. This indicates that as the number of building blocks grows in these segments, their curves resemble those of infinite systems. These findings have practical implications for studying the vibration characteristics of similar macro-systems.</p></div>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":"53 3","pages":"95 - 109"},"PeriodicalIF":2.2,"publicationDate":"2024-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139540916","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

Real-time tilting and twisting motions of ligand-bound states of α7 nicotinic acetylcholine receptor α7烟碱乙酰胆碱受体配体结合态的实时倾斜和扭转运动

IF 2.2 4区生物学

European Biophysics Journal Pub Date : 2024-01-17 DOI: 10.1007/s00249-023-01693-6

Yue Yang, Tatsuya Arai, Daisuke Sasaki, Masahiro Kuramochi, Hidetoshi Inagaki, Sumiko Ohashi, Hiroshi Sekiguchi, Kazuhiro Mio, Tai Kubo, Yuji C. Sasaki

{"title":"Real-time tilting and twisting motions of ligand-bound states of α7 nicotinic acetylcholine receptor","authors":"Yue Yang, Tatsuya Arai, Daisuke Sasaki, Masahiro Kuramochi, Hidetoshi Inagaki, Sumiko Ohashi, Hiroshi Sekiguchi, Kazuhiro Mio, Tai Kubo, 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}

引用次数: 0

Quenching of G4-DNA intrinsic fluorescence by ligands 配体对 G4-DNA 本征荧光的淬灭作用

IF 2.2 4区生物学

European Biophysics Journal Pub Date : 2024-01-13 DOI: 10.1007/s00249-023-01696-3

Liana L. Tevonyan, Artemy D. Beniaminov, Dmitry N. Kaluzhny

引用次数: 0

Swimming polarity inversion in uncultured magnetotactic cocci 未培养的磁性球菌的游动极性反转。

IF 2.2 4区生物学

European Biophysics Journal Pub Date : 2024-01-12 DOI: 10.1007/s00249-023-01698-1

Giovanny Angiolillo, Fernanda Abreu, Daniel Acosta-Avalos

{"title":"Swimming polarity inversion in uncultured magnetotactic cocci","authors":"Giovanny Angiolillo, Fernanda Abreu, 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}

引用次数: 0

Probing the interactions of the HIV-1 matrix protein-derived polybasic region with lipid bilayers: insights from AFM imaging and force spectroscopy 探究 HIV-1 基质蛋白衍生的多基区与脂质双分子层的相互作用：原子力显微镜成像和力谱分析的启示。

IF 2.2 4区生物学

European Biophysics Journal Pub Date : 2024-01-03 DOI: 10.1007/s00249-023-01697-2

Chinta M. Aryal, Jianjun Pan

{"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, 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}

引用次数: 0

Electrophoresis, a transport technology that transitioned from moving boundary method to zone method 电泳，一种从移动边界法过渡到区域法的传输技术

IF 2.2 4区生物学

European Biophysics Journal Pub Date : 2023-12-30 DOI: 10.1007/s00249-023-01694-5

Tsutomu Arakawa, Masataka Nakagawa, Chiaki Sakuma, Yui Tomioka, Yasunori Kurosawa, Daisuke Ejima, Teruo Akuta

引用次数: 0