European Biophysics Journal最新文献_第2页

Modeling study of kinesin-13 MCAK microtubule depolymerase 驱动蛋白-13 MCAK 微管解聚酶的模型研究。

IF 2.2 4区生物学

European Biophysics Journal Pub Date : 2024-08-02 DOI: 10.1007/s00249-024-01718-8

Ping Xie

引用次数: 0

Reciprocal effect on lateral diffusion of receptor for advanced glycation endproducts and toll-like receptor 4 in the HEK293 cell membrane 高级糖化终产物受体和收费样受体 4 对 HEK293 细胞膜横向扩散的相互影响

IF 2.2 4区生物学

European Biophysics Journal Pub Date : 2024-07-27 DOI: 10.1007/s00249-024-01717-9

Mohammad K. I. Walid, Sharifur Rahman, Emily A. Smith

{"title":"Reciprocal effect on lateral diffusion of receptor for advanced glycation endproducts and toll-like receptor 4 in the HEK293 cell membrane","authors":"Mohammad K. I. Walid, Sharifur Rahman, Emily A. Smith","doi":"10.1007/s00249-024-01717-9","DOIUrl":"10.1007/s00249-024-01717-9","url":null,"abstract":"<div><p>Receptor for advanced glycation endproducts (RAGE) and toll-like receptor 4 (TLR4) are pattern-recognition receptors that bind to molecular patterns associated with pathogens, stress, and cellular damage. Diffusion plays an important role in receptor functionality in the cell membrane. However, there has been no prior investigation of the reciprocal effect of RAGE and TLR4 diffusion properties in the presence and absence of each receptor. This study reports how RAGE and TLR4 affect the mobility of each other in the human embryonic kidney (HEK) 293 cell membrane. Diffusion properties were measured using single-particle tracking (SPT) with quantum dots (QDs) that are selectively attached to RAGE or TLR4. The Brownian diffusion coefficients of RAGE and TLR4 are affected by the presence of the other receptor, leading to similar diffusion coefficients when both receptors coexist in the cell. When TLR4 is present, the average Brownian diffusion coefficient of RAGE increases by 40%, while the presence of RAGE decreases the average Brownian diffusion coefficient of TLR4 by 32%. Diffusion in confined membrane domains is not altered by the presence of the other receptor. The mobility of the cell membrane lipid remains constant whether one or both receptors are present. Overall, this work shows that the presence of each receptor can affect a subset of diffusion properties of the other receptor without affecting the mobility of the membrane.</p></div>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":"53 5-6","pages":"327 - 338"},"PeriodicalIF":2.2,"publicationDate":"2024-07-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141774914","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

Mechanisms of stationary voltage fluctuation in the neuromuscular junction endplate and corresponding denoising paradigms 神经肌肉接头终板的静态电压波动机制及相应的去噪范例。

IF 2.2 4区生物学

European Biophysics Journal Pub Date : 2024-07-15 DOI: 10.1007/s00249-024-01715-x

Jia-Zeng Wang, Pengkun Hu, Shu Ma

引用次数: 0

The Structure of the LysR-type Transcriptional Regulator, CysB, Bound to the Inducer, N-acetylserine 与诱导剂 N-乙酰丝氨酸结合的 LysR 型转录调节器 CysB 的结构。

IF 2.2 4区生物学

European Biophysics Journal Pub Date : 2024-07-08 DOI: 10.1007/s00249-024-01716-w

Koen H. G. Verschueren, Eleanor J. Dodson, Anthony J. Wilkinson

{"title":"The Structure of the LysR-type Transcriptional Regulator, CysB, Bound to the Inducer, N-acetylserine","authors":"Koen H. G. Verschueren, Eleanor J. Dodson, Anthony J. Wilkinson","doi":"10.1007/s00249-024-01716-w","DOIUrl":"10.1007/s00249-024-01716-w","url":null,"abstract":"<div><p>In <i>Escherichia coli</i> and <i>Salmonella typhimurium</i>, cysteine biosynthesis requires the products of 20 or more <i>cys</i> genes co-ordinately regulated by CysB. Under conditions of sulphur limitation and in the presence of the inducer, <i>N</i>-acetylserine, CysB binds to <i>cys</i> promoters and activates the transcription of the downstream coding sequences. CysB is a homotetramer, comprising an N-terminal DNA binding domain (DBD) and a C-terminal effector binding domain (EBD). The crystal structure of a dimeric EBD fragment of CysB from <i>Klebsiella aerogenes</i> revealed a protein fold similar to that seen in Lac repressor but with a different symmetry in the dimer so that the mode of DNA binding was not apparent. To elucidate the subunit arrangement in the tetramer, we determined the crystal structure of intact CysB in complex with <i>N</i>-acetylserine. The tetramer has two subunit types that differ in the juxtaposition of their winged helix-turn-helix DNA binding domains with respect to the effector binding domain. In the assembly, the four EBDs form a core with the DNA binding domains arranged in pairs on the surface. <i>N</i>-acetylserine makes extensive polar interactions in an enclosed binding site, and its binding is accompanied by substantial conformational rearrangements of surrounding residues that are propagated to the protein surface where they appear to alter the arrangement of the DNA binding domains. The results are (i) discussed in relation to the extensive mutational data available for CysB and (ii) used to propose a structural mechanism of <i>N</i>-acetylserine induced CysB activation.</p></div>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":"53 5-6","pages":"311 - 326"},"PeriodicalIF":2.2,"publicationDate":"2024-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11329422/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141553968","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

Analysis of proteins in the light of mutations 根据突变分析蛋白质。

IF 2.2 4区生物学

European Biophysics Journal Pub Date : 2024-07-02 DOI: 10.1007/s00249-024-01714-y

Jorge A. Vila

{"title":"Analysis of proteins in the light of mutations","authors":"Jorge A. Vila","doi":"10.1007/s00249-024-01714-y","DOIUrl":"10.1007/s00249-024-01714-y","url":null,"abstract":"<div><p>Proteins have evolved through mutations—amino acid substitutions—since life appeared on Earth, some 10<sup>9</sup> years ago. The study of these phenomena has been of particular significance because of their impact on protein stability, function, and structure. This study offers a new viewpoint on how the most recent findings in these areas can be used to explore the impact of mutations on protein sequence, stability, and evolvability. Preliminary results indicate that: (1) mutations can be viewed as sensitive probes to identify ‘typos’ in the amino-acid sequence, and also to assess the resistance of naturally occurring proteins to unwanted sequence alterations; (2) the presence of ‘typos’ in the amino acid sequence, rather than being an evolutionary obstacle, could promote faster evolvability and, in turn, increase the likelihood of higher protein stability; (3) the mutation site is far more important than the substituted amino acid in terms of the marginal stability changes of the protein, and (4) the unpredictability of protein evolution at the molecular level—by mutations—exists even in the absence of epistasis effects. Finally, the Darwinian concept of evolution “descent with modification” and experimental evidence endorse one of the results of this study, which suggests that some regions of any protein sequence are susceptible to mutations while others are not. This work contributes to our general understanding of protein responses to mutations and may spur significant progress in our efforts to develop methods to accurately forecast changes in protein stability, their propensity for metamorphism, and their ability to evolve.</p></div>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":"53 5-6","pages":"255 - 265"},"PeriodicalIF":2.2,"publicationDate":"2024-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141490428","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

Computational discovery of dual potential inhibitors of SARS‐CoV‐2 spike/ACE2 and Mpro: 3D-pharmacophore, docking-based virtual screening, quantum mechanics and molecular dynamics 通过计算发现 SARS-CoV-2 spike/ACE2 和 Mpro 的双重潜在抑制剂：三维药性、基于对接的虚拟筛选、量子力学和分子动力学。

IF 2.2 4区生物学

European Biophysics Journal Pub Date : 2024-06-21 DOI: 10.1007/s00249-024-01713-z

Boris D. Bekono, Pascal Amoa Onguéné, Conrad V. Simoben, Luc C. O. Owono, Fidele Ntie-Kang

{"title":"Computational discovery of dual potential inhibitors of SARS‐CoV‐2 spike/ACE2 and Mpro: 3D-pharmacophore, docking-based virtual screening, quantum mechanics and molecular dynamics","authors":"Boris D. Bekono, Pascal Amoa Onguéné, Conrad V. Simoben, Luc C. O. Owono, Fidele Ntie-Kang","doi":"10.1007/s00249-024-01713-z","DOIUrl":"10.1007/s00249-024-01713-z","url":null,"abstract":"<div><p>To find drugs against COVID-19, caused by the SARS-CoV-2, promising targets include the fusion of the viral spike with the human angiotensin-converting enzyme 2 (ACE2) as well as the main protease (M<sup>pro</sup>). These proteins are responsible for viral entry and replication, respectively. We combined several state-of-the-art computational methods, including, protein–ligand interaction fingerprint, 3D-pharmacophores, molecular-docking, MM-GBSA, DFT, and MD simulations to explore two databases: ChEMBL and NANPDB to identify molecules that could both block spike/ACE2 fusion and inhibit M<sup>pro</sup>. A total of 1,690,649 compounds from the two databases were screened using the pharmacophore model obtained from PLIF analysis. Five recent complexes of M<sup>pro</sup> co-crystallized with different ligands were used to generate the pharmacophore model, allowing 4,829 compounds that passed this prefilter. These were then submitted to molecular docking against M<sup>pro</sup>. The 5% top-ranked docking hits from docking result having scores <span>(<)</span> −8.32 kcal mol<sup>−1</sup> were selected and then docked against spike/ACE2. Only four compounds: ChEMBL244958, ChEMBL266531, ChEMBL3680003, and 1-methoxy-3-indolymethyl glucosinolate (<b>4</b>) displayed binding energies <span>(<-)</span> 8.21 kcal mol<sup>−1</sup> (for the native ligand) were considered as putative dual-target inhibitors. Furthermore, predictive ADMET, MM-GBSA and DFT/6-311G(d,p) were performed on these compounds and compared with those of well-known antivirals. DFT calculations showed that ChEMBL244958 and compound <b>4</b> had significant predicted reactivity values. Molecular dynamics simulations of the docked complexes were run for 100 ns and used to validate the stability docked poses and to confirm that these hits are putative dual binders of the spike/ACE2 and the M<sup>pro</sup>.</p></div>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":"53 5-6","pages":"277 - 298"},"PeriodicalIF":2.2,"publicationDate":"2024-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141436539","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 conformational properties of alamethicin in ethanol studied by NMR 用核磁共振法研究乙醇中阿拉米嗪的构象特性。

IF 2.2 4区生物学

European Biophysics Journal Pub Date : 2024-06-08 DOI: 10.1007/s00249-024-01711-1

Yoshinori Miura

{"title":"The conformational properties of alamethicin in ethanol studied by NMR","authors":"Yoshinori Miura","doi":"10.1007/s00249-024-01711-1","DOIUrl":"10.1007/s00249-024-01711-1","url":null,"abstract":"<div><p>Alamethicin, a peptide consisted of 20 amino acid residues, has been known to function as an antibiotic. The peptides self-associate in biological membranes, form an ion channel, and then induce cell death by leaking intracellular contents through a transmembrane pore of an ion channel. We investigated conformation and its thermal stability of alamethicin-A6 and -U6 in ethanol using proton nuclear magnetic resonance (NMR) spectroscopy; alamethicin-A6 and -U6 have the amino acid sequences of UPUAU<u>A</u>QUVUGLUPVUUQQO and UPUAU<u>U</u>QUVUGLUPVUUQQO, respectively, where U and O represent α-aminoisobutyric acid and phenylalaninol, respectively. As indicated by the under bars in the sequences, only the residue 6 differs between the alamethicins. We show that the alamethicins in ethanol form helix conformation in the region of the residues 2–11 and a non-regular conformation in the regions of the N- and C-termini, and that the helices are maintained up to 66 °C at least. Conformations in the region of the residues 12–18 of the alamethicins, however, are not well identified due to the lack of NMR data. In addition, we demonstrate that the amide proton chemical shift temperature coefficients’ method, which is known as an indicator for intramolecular hydrogen bonds in peptides and proteins in aqueous solutions, can be also applied to the alamethicins in ethanol. Further, we show that the conformation around the C-terminus of alamethicin-A6 is restrained by intramolecular hydrogen bonds, whereas that of alamethicin-U6 is either restrained or unrestrained by intramolecular hydrogen bonds; the alamethicin-U6 molecules having the restrained and unrestrained conformations coexist in ethanol. We discuss the two types of conformations using a model chain consisting of particles linked by rigid bonds called as the free jointed chain.</p></div>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":"53 5-6","pages":"267 - 276"},"PeriodicalIF":2.2,"publicationDate":"2024-06-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141287529","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

An obituary: Dr. Helmut Cölfen 1965–2023 讣告赫尔穆特-科尔芬博士 1965-2023。

IF 2.2 4区生物学

European Biophysics Journal Pub Date : 2024-06-07 DOI: 10.1007/s00249-024-01712-0

Borries Demeler, Denis Gebauer, Emre Brookes, Jeffrey Fagan, Johannes Walter, José García de la Torre, Juan Manuel García-Ruiz, Kristian Schilling, Mengdi Chen, Lukas Dobler, Olwyn Byron, Stephen E. Harding, Thomas Zemb, Tobias Kraus, Tom Laue, Trushar R. Patel

{"title":"An obituary: Dr. Helmut Cölfen 1965–2023","authors":"Borries Demeler, Denis Gebauer, Emre Brookes, Jeffrey Fagan, Johannes Walter, José García de la Torre, Juan Manuel García-Ruiz, Kristian Schilling, Mengdi Chen, Lukas Dobler, Olwyn Byron, Stephen E. Harding, Thomas Zemb, Tobias Kraus, Tom Laue, Trushar R. Patel","doi":"10.1007/s00249-024-01712-0","DOIUrl":"10.1007/s00249-024-01712-0","url":null,"abstract":"<div><p>Dr. Helmut Cölfen, an exceptional interdisciplinary scientist, mentor, colleague, and dear friend, passed away in November 2023 at the age of 58. His untimely departure is a profound loss for the fields of analytical ultracentrifugation, colloid, crystallization, and polymer research. This obituary pays tribute to Helmut, honoring his remarkable academic career and contributions to the study of nanochemistry, biophysics, and life sciences. Helmut was renowned for his pioneering research contributions in several key research areas: (1) Development of advanced analytical techniques: Helmut made major contributions to techniques such as analytical ultracentrifugation and field flow fractionation, which are widely utilized to characterize the structure of biomolecules and the growth of nanostructured crystalline materials; (2) Study of nucleation and crystallization processes: Helmut explored the early stages of crystallization which led to the discovery of pre-nucleation clusters and mesocrystal intermediates, in the presence of additives and templates; and (3) Investigation of structure and morphogenesis of mesocrystals, examining their molecular properties.</p></div>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":"53 5-6","pages":"249 - 254"},"PeriodicalIF":2.2,"publicationDate":"2024-06-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141282606","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

Two-layer elastic models for single-yeast compressibility with flat microlevers 带平面微杠杆的单酵母可压缩性双层弹性模型

IF 2.2 4区生物学

European Biophysics Journal Pub Date : 2024-05-04 DOI: 10.1007/s00249-024-01710-2

L. Delmarre, E. Harté, A. Devin, P. Argoul, F. Argoul

{"title":"Two-layer elastic models for single-yeast compressibility with flat microlevers","authors":"L. Delmarre, E. Harté, A. Devin, P. Argoul, F. Argoul","doi":"10.1007/s00249-024-01710-2","DOIUrl":"10.1007/s00249-024-01710-2","url":null,"abstract":"<div><p>Unicellular organisms such as yeast can survive in very different environments, thanks to a polysaccharide wall that reinforces their extracellular membrane. This wall is not a static structure, as it is expected to be dynamically remodeled according to growth stage, division cycle, environmental osmotic pressure and ageing. It is therefore of great interest to study the mechanics of these organisms, but they are more difficult to study than other mammalian cells, in particular because of their small size (radius of a few microns) and their lack of an adhesion machinery. Using flat cantilevers, we perform compression experiments on single yeast cells (<i>S. cerevisiae</i>) on poly-L-lysine-coated grooved glass plates, in the limit of small deformation using an atomic force microscope (AFM). Thanks to a careful decomposition of force–displacement curves, we extract local scaling exponents that highlight the non-stationary characteristic of the yeast behavior upon compression. Our multi-scale nonlinear analysis of the AFM force-displacement curves provides evidence for non-stationary scaling laws. We propose to model these phenomena based on a two-component elastic system, where each layer follows a different scaling law..</p></div>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":"53 4","pages":"205 - 224"},"PeriodicalIF":2.2,"publicationDate":"2024-05-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140847087","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 effect of ionic redistributions on the microwave dielectric response of cytosol water upon glucose uptake 葡萄糖摄取时离子再分布对细胞膜水微波介电响应的影响

IF 2.2 4区生物学

European Biophysics Journal Pub Date : 2024-04-22 DOI: 10.1007/s00249-024-01708-w

Cindy Galindo, Leonid Livshits, Lama Tarabeih, Gregory Barshtein, Sharon Einav, Yuri Feldman

{"title":"The effect of ionic redistributions on the microwave dielectric response of cytosol water upon glucose uptake","authors":"Cindy Galindo, Leonid Livshits, Lama Tarabeih, Gregory Barshtein, Sharon Einav, Yuri Feldman","doi":"10.1007/s00249-024-01708-w","DOIUrl":"10.1007/s00249-024-01708-w","url":null,"abstract":"<div><p>The sensitivity of cytosol water's microwave dielectric (MD) response to D-glucose uptake in Red Blood Cells (RBCs) allows the detailed study of cellular mechanisms as a function of controlled exposures to glucose and other related analytes like electrolytes. However, the underlying mechanism behind the sensitivity to glucose exposure remains a topic of debate. In this research, we utilize MDS within the frequency range of 0.5–40 GHz to explore how ionic redistributions within the cell impact the microwave dielectric characteristics associated with D-glucose uptake in RBC suspensions. Specifically, we compare glucose uptake in RBCs exposed to the physiological concentration of Ca<sup>2+</sup> vs. Ca-free conditions. We also investigate the potential involvement of Na<sup>+</sup>/K<sup>+</sup> redistribution in glucose-mediated dielectric response by studying RBCs treated with a specific Na<sup>+</sup>/K<sup>+</sup> pump inhibitor, ouabain. We present some insights into the MD response of cytosol water when exposed to Ca<sup>2+</sup> in the absence of D-glucose. The findings from this study confirm that ion-induced alterations in bound/bulk water balance do not affect the MD response of cytosol water during glucose uptake.</p></div>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":"53 4","pages":"183 - 192"},"PeriodicalIF":2.2,"publicationDate":"2024-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140636611","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