European Biophysics Journal最新文献_第2页

Changes in morphofunctional parameters of erythrocytes and oxygen-binding capacity of hemoglobin under the influence of microorganisms of various types 不同类型微生物影响下红细胞形态功能参数及血红蛋白氧结合能力的变化

IF 2.2 4区生物学

European Biophysics Journal Pub Date : 2025-02-08 DOI: 10.1007/s00249-025-01736-0

Elena A. Shchuplova, Sergei V. Cherkasov, Victor V. Revin, Sergei I. Pinyaev, Ilya V. Syusin

{"title":"Changes in morphofunctional parameters of erythrocytes and oxygen-binding capacity of hemoglobin under the influence of microorganisms of various types","authors":"Elena A. Shchuplova, Sergei V. Cherkasov, Victor V. Revin, Sergei I. Pinyaev, Ilya V. Syusin","doi":"10.1007/s00249-025-01736-0","DOIUrl":"10.1007/s00249-025-01736-0","url":null,"abstract":"<div><p>When bacteria interact with red blood cells, the plasma membrane receives signals from the microorganism adhesins, and the functional work of the erythrocyte as a whole depends on the biomembrane phospholipid condition. However, the microorganism effect on the structural and functional properties of the red blood cell membrane, as well as on the hemoglobin oxygen-binding ability has not been studied enough. Given the foregoing, we sought to study these issues in our work. The study used the “bacteria–red blood cells” model, using archival microbial strains (<i>Staphylococcus aureus, Escherichia coli, Mycolicibacterium rutilum,</i> and <i>M. iranicum)</i> and donor erythrocytes. The structural and functional properties of the red blood cell membrane phospholipids and the spectral characteristics of the hemoglobin molecule were studied using Raman spectroscopy. To study changes in red blood cell (RBC) morphology under the impact of microorganisms, laser interference microscopy was used. The results show that various types of microorganisms affected the conformational structure of the RBCs membrane phospholipid bonds, which contributed to changes in the morphological characteristics of cells, resulting in functional changes in both the red blood cell as a whole and the main RBC oxygen transport protein—hemoglobin.</p></div>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":"54 1-2","pages":"73 - 87"},"PeriodicalIF":2.2,"publicationDate":"2025-02-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143373707","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

DNA binding to small anionic ligands: the case of Orange G dye DNA与小阴离子配体的结合：橙色G染料的例子。

IF 2.2 4区生物学

European Biophysics Journal Pub Date : 2025-02-07 DOI: 10.1007/s00249-025-01733-3

Rayane M. de Oliveira, Arthur G. S. de Rezende, Daniel F. Campos, Neemias de A. Ribeiro, Márcio S. Rocha

{"title":"DNA binding to small anionic ligands: the case of Orange G dye","authors":"Rayane M. de Oliveira, Arthur G. S. de Rezende, Daniel F. Campos, Neemias de A. Ribeiro, Márcio S. Rocha","doi":"10.1007/s00249-025-01733-3","DOIUrl":"10.1007/s00249-025-01733-3","url":null,"abstract":"<div><p>Here we advance in the understanding of nucleic acids interactions with small anionic ligands by characterizing the binding of the Orange G (OG) dye to double-stranded DNA via single molecule force spectroscopy. While there is no detectable interaction at low ionic strengths, we found that for [<span>(hbox {Na}^+)</span>] = 150 mM OG was able to interact with the double-helix via groove binding in a non-cooperative way, with a relatively high equilibrium association constant (<span>(sim)</span> <span>(10^5)</span> <span>(hbox {M}^{-1})</span>) that is compatible to other classic DNA small ligands. Furthermore, experiments performed with a fixed OG concentration at various ionic strengths clearly show that the binding can be turned “on / off” by regulating the concentration of available counterions, a result that can guide the development of new synthetic ligands and shows how to modulate their interactions with nucleic acids. The present work therefore advances in evaluating the fundamental role of the ionic strength on the DNA interactions with small anionic ligands.</p></div>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":"54 1-2","pages":"65 - 71"},"PeriodicalIF":2.2,"publicationDate":"2025-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143370224","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

On-the-fly resolution enhancement in X-ray protein crystallography using electric field 利用电场增强x射线蛋白质晶体学的动态分辨率。

IF 2.2 4区生物学

European Biophysics Journal Pub Date : 2025-01-22 DOI: 10.1007/s00249-025-01731-5

Krishna Prasad Khakurel, Michal Nemergut, Purbaj Pant, Martin Savko, Jakob Andreasson, Gabriel Žoldák

{"title":"On-the-fly resolution enhancement in X-ray protein crystallography using electric field","authors":"Krishna Prasad Khakurel, Michal Nemergut, Purbaj Pant, Martin Savko, Jakob Andreasson, Gabriel Žoldák","doi":"10.1007/s00249-025-01731-5","DOIUrl":"10.1007/s00249-025-01731-5","url":null,"abstract":"<div><p>X-ray crystallography has tremendously served structural biology by routinely providing high-resolution 3D structures of macromolecules. The extent of information encoded in the X-ray crystallography is proportional to which resolution the crystals diffract and the structure can be refined to. Therefore, there is a continuous effort to obtain high-quality crystals, especially for those proteins, which are considered difficult to crystallize into high-quality protein crystals of suitable sizes for X-ray crystallography. Efforts in enhancing the resolution in X-ray crystallography have also been made by optimizing crystallization protocols using external stimuli such as an electric field and magnetic field during the crystallization. Here, we present the feasibility of on-the-fly post-crystallization resolution enhancement of the protein crystal diffraction by applying a high-voltage electric field. The electric field between 2 and 11 kV/cm, which was applied after mounting the crystals in the beamline, resulted in the enhancement of the resolution. The crystal diffraction quality improved progressively with the exposure time. Moreover, we also find that upto defined electric field threshold, the protein structure remains largely unperturbed, a conclusion further supported by molecular dynamics simulations.</p></div>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":"54 1-2","pages":"89 - 95"},"PeriodicalIF":2.2,"publicationDate":"2025-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00249-025-01731-5.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142998246","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

A gene-encoded bioprotein second harmonic generation (SHG) probe from Autographa californica nuclear polyhedrosis virus (AcMNPV) polyhedrin for live cell imaging 一种用于活细胞成像的基因编码生物蛋白二谐代（SHG）探针，来自加利福尼亚自签名核多角体病毒（AcMNPV）多角体蛋白。

IF 2.2 4区生物学

European Biophysics Journal Pub Date : 2025-01-15 DOI: 10.1007/s00249-024-01728-6

Xiaoyuan Deng, Hao Liu, Heting Chen, Zuojun Yang, Yuhan Wu, Li He, Wenjing Guo

{"title":"A gene-encoded bioprotein second harmonic generation (SHG) probe from Autographa californica nuclear polyhedrosis virus (AcMNPV) polyhedrin for live cell imaging","authors":"Xiaoyuan Deng, Hao Liu, Heting Chen, Zuojun Yang, Yuhan Wu, Li He, Wenjing Guo","doi":"10.1007/s00249-024-01728-6","DOIUrl":"10.1007/s00249-024-01728-6","url":null,"abstract":"<p>Compared to fluorescence, second harmonic generation (SHG) has recently emerged as an excellent signal for imaging probes due to its unmatched advantages in terms of no photobleaching, no phototoxicity, no signal saturation, as well as the superior imaging accuracy with excellent avoidance of background noise. Existing SHG probes are constructed from heavy metals and are cellular exogenous, presenting with high cytotoxicity, difficult cellular uptake, and the limitation of non-heritability. We, therefore, initially propose an innovative gene-encoded bioprotein SHG probe derived from <i>Autographa californica</i> nuclear polyhedrosis virus (AcMNPV) polyhedrin. The primitive gene of AcMNPV polyhedrin was codon-optimized and mutated in its nuclear localization sequence to achieve cytoplasmic expression in mammalian cells. While providing strong SHG signals, this gene-modified AcMNPV (GM-AcMNPV) polyhedrin could be utilized as an SHG probe for cell imaging. Our experimental results demonstrated successful expression of GM-AcMNPV polyhedrin in the cytoplasm of HEK293T cells and bone mesenchymal stem cells (BMSCs), and verified its characteristic features as an SHG probe. Such SHG probes exhibit high biocompatibility and showed no hindering of central physiological activities such as the differentiation of stem cells. Most importantly, our SHG probes may be successfully used for imaging in living cells. This work will inspire the development of gene encoding-derived bioprotein SHG probes, for long-term tracing of cells/stem cells along with their division, to understand stem cell cycles, reveal stem cell-based therapy mechanisms in regenerative medicine, and unravel cell lineage origins and fates in developmental biology, among other potential applications.</p>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":"54 1-2","pages":"21 - 32"},"PeriodicalIF":2.2,"publicationDate":"2025-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142982464","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

EBSA at 40 – an updated history 40岁的EBSA -更新的历史。

IF 2.2 4区生物学

European Biophysics Journal Pub Date : 2025-01-11 DOI: 10.1007/s00249-024-01730-y

John M. Seddon, Anthony Watts

引用次数: 0

Rational design of potent phosphopeptide binders to endocrine Snk PBD domain by integrating machine learning optimization, molecular dynamics simulation, binding energetics rescoring, and in vitro affinity assay 结合机器学习优化、分子动力学模拟、结合能重测定和体外亲和力测定，合理设计内分泌Snk PBD结构域的强效磷酸肽结合物。

IF 2.2 4区生物学

European Biophysics Journal Pub Date : 2024-11-29 DOI: 10.1007/s00249-024-01729-5

Zhaohui Wang, Jixiao Lan, Yan Feng, Yumei Chen, Meiyuan Chen

{"title":"Rational design of potent phosphopeptide binders to endocrine Snk PBD domain by integrating machine learning optimization, molecular dynamics simulation, binding energetics rescoring, and in vitro affinity assay","authors":"Zhaohui Wang, Jixiao Lan, Yan Feng, Yumei Chen, Meiyuan Chen","doi":"10.1007/s00249-024-01729-5","DOIUrl":"10.1007/s00249-024-01729-5","url":null,"abstract":"<div><p>Human Snk is an evolutionarily conserved serine/threonine kinase essential for the maintenance of endocrine stability. The protein consists of a N-terminal catalytic domain and a C-terminal polo-box domain (PBD) that determines subcellular localization and substrate specificity. Here, an integrated strategy is described to explore the vast structural diversity space of Snk PBD-binding phosphopeptides at a molecular level using machine learning modeling, annealing optimization, dynamics simulation, and energetics rescoring, focusing on the recognition specificity and motif preference of the Snk PBD domain. We further performed a systematic rational design of potent phosphopeptide ligands for the domain based on the harvested knowledge, from which a few potent binders were also confirmed by fluorescence-based assays. A phosphopeptide PP17 was designed as a good binder with affinity improvement by 6.7-fold relative to the control PP0, while the other three designed phosphopeptides PP7, PP13, and PP15 exhibit a comparable potency with PP0. In addition, a basic recognition motif that divides potent Snk PBD-binding sequences into four residue blocks was defined, namely [Χ<sub>-5</sub>Χ-<sub>4</sub>]<sub>block1</sub>–[Ω<sub>-3</sub>Ω<sub>-2</sub>Ω<sub>-1</sub>]<sub>block2</sub>–[pS<sub>0</sub>/pT<sub>0</sub>]<sub>block3</sub>–[Ψ<sub>+1</sub>]<sub>block4</sub>, where the X represents any amino acid, Ω indicates polar amino acid, Ψ denotes hydrophobic amino acid, and pS<sub>0</sub>/pT<sub>0</sub> is the anchor phosphoserine/phosphothreonine at reference residue position 0.</p></div>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":"54 1-2","pages":"33 - 43"},"PeriodicalIF":2.2,"publicationDate":"2024-11-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142749777","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

Exploring characteristic features for effective HCN1 channel inhibition using integrated analytical approaches: 3D QSAR, molecular docking, homology modelling, ADME and molecular dynamics 利用综合分析方法探索有效抑制 HCN1 通道的特征：3D QSAR、分子对接、同源建模、ADME 和分子动力学。

IF 2.2 4区生物学

European Biophysics Journal Pub Date : 2024-11-03 DOI: 10.1007/s00249-024-01726-8

Shiwani Sharma, Priyanka Rana, Vijayta Dani Chadha, Neelima Dhingra, Tanzeer Kaur

{"title":"Exploring characteristic features for effective HCN1 channel inhibition using integrated analytical approaches: 3D QSAR, molecular docking, homology modelling, ADME and molecular dynamics","authors":"Shiwani Sharma, Priyanka Rana, Vijayta Dani Chadha, Neelima Dhingra, Tanzeer Kaur","doi":"10.1007/s00249-024-01726-8","DOIUrl":"10.1007/s00249-024-01726-8","url":null,"abstract":"<div><p>Neuropathic pain (NP) is characterized by hyperalgesia, allodynia, and spontaneous pain. Hyperpolarization-activated cyclic nucleotide-gated (HCN) channel involved in neuronal hyperexcitability, has emerged as an important target for the drug development of NP. HCN channels exist in four different isoforms, where HCN1 is majorly expressed in dorsal root ganglion having an imperative role in NP pathophysiology. A specific HCN1 channel inhibitor will hold the better potential to treat NP without disturbing the physiological roles of other HCN isoforms. The main objective is to identify and analyze the chemical properties of scaffolds with higher HCN1 channel specificity. The 3D-QSAR studies highlight the hydrophobic & hydrogen bond donor groups enhance specificity towards the HCN1 channel. Further, the molecular interaction of the scaffolds with the HCN1 pore was studied by generating an open-pore model of the HCN1 channel using homology modelling and then docking the molecules with it. In addition, the important residues involved in the interaction between HCN1 pore and scaffolds were also identified. Moreover, ADME predictions revealed that compounds had good oral bioavailability and solubility characteristics. Subsequently, molecular dynamics simulation studies revealed the better stability of the lead molecules A7 and A9 during interactions and ascertained them as potential drug candidates. Cumulative studies provided the important structural features for enhancing HCN1 channel-specific inhibition, paving the way to design and develop novel specific HCN1 channel inhibitors.</p></div>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":"53 7-8","pages":"447 - 464"},"PeriodicalIF":2.2,"publicationDate":"2024-11-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142563489","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

Quantitative characterization of non-specific interaction of two globular proteins with Dextran T70 in a binary mixture 二元混合物中两种球状蛋白质与右旋糖酐 T70 非特异性相互作用的定量表征。

IF 2.2 4区生物学

European Biophysics Journal Pub Date : 2024-10-25 DOI: 10.1007/s00249-024-01727-7

Adedayo A. Fodeke

引用次数: 0

The origin of mutational epistasis 突变外显的起源

IF 2.2 4区生物学

European Biophysics Journal Pub Date : 2024-10-23 DOI: 10.1007/s00249-024-01725-9

Jorge A. Vila

{"title":"The origin of mutational epistasis","authors":"Jorge A. Vila","doi":"10.1007/s00249-024-01725-9","DOIUrl":"10.1007/s00249-024-01725-9","url":null,"abstract":"<div><p>The interconnected processes of protein folding, mutations, epistasis, and evolution have all been the subject of extensive analysis throughout the years due to their significance for structural and evolutionary biology. The origin (molecular basis) of epistasis—the non-additive interactions between mutations—is still, nonetheless, unknown. The existence of a new perspective on protein folding, a problem that needs to be conceived as an ‘analytic whole’, will enable us to shed light on the origin of mutational epistasis at the simplest level—within proteins—while also uncovering the reasons why the genetic background in which they occur, a key component of molecular evolution, could foster changes in epistasis effects. Additionally, because mutations are the source of epistasis, more research is needed to determine the impact of post-translational modifications, which can potentially increase the proteome’s diversity by several orders of magnitude, on mutational epistasis and protein evolvability. Finally, a protein evolution thermodynamic-based analysis that does not consider specific mutational steps or epistasis effects will be briefly discussed. Our study explores the complex processes behind the evolution of proteins upon mutations, clearing up some previously unresolved issues, and providing direction for further research.</p></div>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":"53 7-8","pages":"473 - 480"},"PeriodicalIF":2.2,"publicationDate":"2024-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00249-024-01725-9.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142492569","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

Time-dependent simulation of blood flow through an abdominal aorta with iliac arteries 随时间变化的腹主动脉与髂动脉血流模拟。

IF 2.2 4区生物学

European Biophysics Journal Pub Date : 2024-10-18 DOI: 10.1007/s00249-024-01724-w

Grzegorz Górski, Krzysztof Kucab

{"title":"Time-dependent simulation of blood flow through an abdominal aorta with iliac arteries","authors":"Grzegorz Górski, Krzysztof Kucab","doi":"10.1007/s00249-024-01724-w","DOIUrl":"10.1007/s00249-024-01724-w","url":null,"abstract":"<div><p>Atherosclerosis is one of the important diseases of the circulatory system because atherosclerotic plaques cause significant disruption of blood flow. Therefore, it is very important to properly understand these processes and skillfully simulate blood flow. In our work, we consider blood flow through an abdominal aorta with iliac arteries, assuming that the right iliac artery is narrowed by an atherosclerotic lesion. Blood flow is simulated using the laminar, standard <span>(k-omega)</span> and standard <span>(k-epsilon)</span> models. The obtained results show that despite the use of identical initial conditions, the distribution of velocity flow and wall shear stress depends on the choice of flow simulation model. For the <span>(k-epsilon)</span> model, we obtain higher values of speed and wall shear stress on atherosclerotic plaque than in the other two models. The laminar and <span>(k-omega)</span> models predict larger areas where reverse blood flow occurs in the area behind the atherosclerotic lesion. This effect is associated with negative wall shear stress. These two models give very similar results. The results obtained by us, and those reported in the literature, indicate that <span>(k-omega)</span> model is the most suitable for blood flow analysis.</p></div>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":"53 7-8","pages":"429 - 445"},"PeriodicalIF":2.2,"publicationDate":"2024-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00249-024-01724-w.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142455353","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