European Biophysics Journal最新文献_第3页

Site-directed mutagenesis at the Glu78 in Ec-NhaA transporter impacting ion exchange: a biophysical study 影响离子交换的 Ec-NhaA 转运体 Glu78 的定点突变：一项生物物理研究

IF 2.2 4区生物学

European Biophysics Journal Pub Date : 2024-04-22 DOI: 10.1007/s00249-024-01709-9

Anuradha Yadav, Dinesh Kumar, Manish Dwivedi

{"title":"Site-directed mutagenesis at the Glu78 in Ec-NhaA transporter impacting ion exchange: a biophysical study","authors":"Anuradha Yadav, Dinesh Kumar, Manish Dwivedi","doi":"10.1007/s00249-024-01709-9","DOIUrl":"10.1007/s00249-024-01709-9","url":null,"abstract":"<div><p>Na<sup>+</sup>/H<sup>+</sup> antiporters facilitate the exchange of Na<sup>+</sup> for H<sup>+</sup> across the cytoplasmic membrane in prokaryotic and eukaryotic cells. These transporters are crucial to maintain the homeostasis of sodium ions, consequently pH, and volume of the cells. Therefore, sodium/proton antiporters are considered promising therapeutic targets in humans. The Na<sup>+</sup>/H<sup>+</sup> antiporter in <i>Escherichia coli</i> (<i>Ec</i>-NhaA), a prototype of cation–proton antiporter (CPA) family, transports two protons and one sodium (or Li<sup>+</sup>) in opposite direction. Previous mutagenesis experiments on Ec-NhaA have proposed Asp164, Asp163, and Asp133 amino acids with the significant implication in functional and structural integrity and create site for ion-binding. However, the mechanism and the sites for the binding of the two protons remain unknown and controversial which could be critical for pH regulation. In this study, we have explored the role of Glu78 in the regulation of pH by <i>Ec</i>-NhaA. Although we have created various mutants, E78C has shown a considerable effect on the stoichiometry of NhaA and presented comparable phenotypes. The ITC experiment has shown the binding of ~ 5 protons in response to the transport of one lithium ion. The phenotype analysis on selective medium showed a significant expression compared to WT <i>Ec</i>-NhaA. This represents the importance of Glu78 in transporting the H<sup>+</sup> across the membrane where a single mutation with Cys amino acid alters the number of H<sup>+</sup> significantly maintaining the activity of the protein.</p></div>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":"53 4","pages":"193 - 203"},"PeriodicalIF":2.2,"publicationDate":"2024-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140636292","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

Erythrocytes membrane fluidity changes induced by adenylyl cyclase cascade activation: study using fluorescence recovery after photobleaching 腺苷酸环化酶级联激活诱导的红细胞膜流动性变化：利用光漂白后荧光恢复进行的研究

IF 2.2 4区生物学

European Biophysics Journal Pub Date : 2024-04-16 DOI: 10.1007/s00249-024-01707-x

A. N. Semenov, A. E. Lugovtsov, S. A. Rodionov, Eu. G. Maksimov, A. V. Priezzhev, E. A. Shirshin

{"title":"Erythrocytes membrane fluidity changes induced by adenylyl cyclase cascade activation: study using fluorescence recovery after photobleaching","authors":"A. N. Semenov, A. E. Lugovtsov, S. A. Rodionov, Eu. G. Maksimov, A. V. Priezzhev, E. A. Shirshin","doi":"10.1007/s00249-024-01707-x","DOIUrl":"10.1007/s00249-024-01707-x","url":null,"abstract":"<div><p>In this study, fluorescence recovery after photobleaching (FRAP) experiments were performed on RBC labeled by lipophilic fluorescent dye CM-DiI to evaluate the role of adenylyl cyclase cascade activation in changes of lateral diffusion of erythrocytes membrane lipids. Stimulation of adrenergic receptors with epinephrine (adrenaline) or metaproterenol led to the significant acceleration of the FRAP recovery, thus indicating an elevated membrane fluidity. The effect of the stimulation of protein kinase A with membrane-permeable analog of cAMP followed the same trend but was less significant. The observed effects are assumed to be driven by increased mobility of phospholipids resulting from the weakened interaction between the intermembrane proteins and RBC cytoskeleton due to activation of adenylyl cyclase signaling cascade.</p><h3>Graphical abstract</h3><div><figure><div><div><picture><source><img></source></picture></div></div></figure></div></div>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":"53 4","pages":"239 - 247"},"PeriodicalIF":2.2,"publicationDate":"2024-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00249-024-01707-x.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140611270","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

Reaction of KHP with excess NaOH or TRIS as standard reactions for calibration of titration calorimeters from 0 to 60 °C 将 KHP 与过量 NaOH 或 TRIS 反应作为校准 0 至 60 °C 滴定热量计的标准反应

IF 2.2 4区生物学

European Biophysics Journal Pub Date : 2024-04-13 DOI: 10.1007/s00249-024-01705-z

Jason D. Kenealey, Margarida Bastos, Zaid Assaf, Guangyue Bai, Wenqi Zhao, Tyler Jarrard, Colter Tower, Lee D. Hansen

{"title":"Reaction of KHP with excess NaOH or TRIS as standard reactions for calibration of titration calorimeters from 0 to 60 °C","authors":"Jason D. Kenealey, Margarida Bastos, Zaid Assaf, Guangyue Bai, Wenqi Zhao, Tyler Jarrard, Colter Tower, Lee D. Hansen","doi":"10.1007/s00249-024-01705-z","DOIUrl":"10.1007/s00249-024-01705-z","url":null,"abstract":"<div><p>Calibration of titration calorimeters is an ongoing problem, particularly with calorimeters with reaction vessel volumes < 10 mL in which an electrical calibration heater is positioned outside the calorimetric vessel. Consequently, a chemical reaction with a known enthalpy change must be used to accurately calibrate these calorimeters. This work proposes the use of standard solutions of potassium acid phthalate (KHP) titrated into solutions of excess sodium hydroxide (NaOH) or excess tris(hydroxymethyl)aminomethane (TRIS) as standard reactions to determine the collective accuracy of the relevant variables in a determination of the molar enthalpy change for a reaction. KHP is readily available in high purity, weighable for easy preparation of solutions with accurately known concentrations, stable in solution, not compromised by side reactions with common contaminants such as atmospheric CO<sub>2</sub>, and non-corrosive to materials used in calorimeter construction. Molar enthalpy changes for these reactions were calculated from 0 to 60 °C from reliable literature data for the p<i>K</i><sub>a</sub> of KHP, the molar enthalpy change for protonation of TRIS, and the molar enthalpy change for ionization of water. The feasibility of using these reactions as enthalpic standards was tested in several calorimeters; a 50 mL CSC 4300, a 185 μL NanoITC, a 1.4 mL VP-ITC, and a TAM III with 1 mL reaction vessels. The results from the 50 mL CSC 4300, which was accurately calibrated with an electric heater, verified the accuracy of the calculated standard values for the molar enthalpy changes of the proposed reactions.</p></div>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":"53 4","pages":"225 - 238"},"PeriodicalIF":2.2,"publicationDate":"2024-04-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00249-024-01705-z.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140595681","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

Application of electron paramagnetic resonance spectroscopy for determining the relative nanoenvironment fluidity of polymeric micelles 应用电子顺磁共振波谱测定聚合物胶束的相对纳米环境流动性

IF 2.2 4区生物学

European Biophysics Journal Pub Date : 2024-04-10 DOI: 10.1007/s00249-024-01706-y

Lusine Tonoyan, Sirazum Munira, Afsaneh Lavasanifar, Arno G. Siraki

{"title":"Application of electron paramagnetic resonance spectroscopy for determining the relative nanoenvironment fluidity of polymeric micelles","authors":"Lusine Tonoyan, Sirazum Munira, Afsaneh Lavasanifar, Arno G. Siraki","doi":"10.1007/s00249-024-01706-y","DOIUrl":"10.1007/s00249-024-01706-y","url":null,"abstract":"<p>Polymeric micelles are nanocarriers for drug, protein and gene delivery due to their unique core/shell structure, which encapsulates and protects therapeutic cargos with diverse physicochemical properties. However, information regarding the micellar nanoenvironment's fluidity can provide unique insight into their makeup. In this study, we used electron paramagnetic resonance (EPR) spectroscopy to study free radical spin probe (5-doxylstearate methyl ester, 5-MDS, and 16-doxylstearic acid, 16-DS) behaviour in methoxy-poly(ethylene oxide)-poly(α-benzyl carboxylate-ε-caprolactone) (PEO-PBCL) and methoxy-poly(ethylene oxide)-poly(ε-caprolactone) (PEO-PCL) polymeric micelles. Spin probes provided information about the spectroscopic rotational correlation time (τ, s) and the spectroscopic partition parameter F. We hypothesized that spin probes would partition into the polymeric micelles, and these parameters would be calculated. The results showed that both 5-MDS and 16-DS spectra were modulated in the presence of polymeric micelles. Based on τ values, 5-MDS revealed that PEO-PCL (τ = 3.92 ± 0.26 × 10<sup>−8</sup> s) was more fluid than PEO-PBCL (τ = 7.15 ± 0.63 × 10<sup>−8</sup> s). The F parameter, however, could not be calculated due to the rotational hindrance of the probe within the micelles. With 16-DS, more probe rotation was observed, and although the F parameter could be calculated, it was not helpful to distinguish the micelles' fluidity. Also, doxorubicin-loading interfered with the spin probes, particularly for 16-DS. However, using simulations, we could distinguish the hydrophilic and hydrophobic components of the 16-DS probe. The findings suggest that EPR spectroscopy is a valuable method for determining core fluidity in polymeric micelles.</p>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":"53 4","pages":"171 - 181"},"PeriodicalIF":2.2,"publicationDate":"2024-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140595984","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

Design of inhibitor peptide sequences based on the interfacial knowledge of the protein G-IgG crystallographic complex and their binding studies with IgG 根据蛋白质 G-IgG 晶体复合物的界面知识设计抑制剂肽序列，并与 IgG 进行结合研究。

IF 2.2 4区生物学

European Biophysics Journal Pub Date : 2024-03-17 DOI: 10.1007/s00249-024-01704-0

Neetu Tanwar, Rupal Ojha, Soumya Aggarwal, Vijay Kumar Prajapati, Manoj Munde

{"title":"Design of inhibitor peptide sequences based on the interfacial knowledge of the protein G-IgG crystallographic complex and their binding studies with IgG","authors":"Neetu Tanwar, Rupal Ojha, Soumya Aggarwal, Vijay Kumar Prajapati, Manoj Munde","doi":"10.1007/s00249-024-01704-0","DOIUrl":"10.1007/s00249-024-01704-0","url":null,"abstract":"<div><p>Protein–protein interactions (PPI) have emerged as valuable targets in medicinal chemistry due to their key roles in important biological processes. The modulation of PPI by small peptides offers an excellent opportunity to develop drugs against human diseases. Here, we exploited the knowledge of the binding interface of the IgG-protein G complex (PDB:1FCC) for designing peptides that can inhibit these complexes. Herein, we have designed several closely related peptides, and the comparison of results from experiments and computational studies indicated that all the peptides bind close to the expected binding site on IgG and the complexes are stable. A minimal sequence consisting of 11 amino acids (P5) with binding constants in the range of 100 nM was identified. We propose that the main affinity differences across the series of peptides arose from the presence of polar amino acid residues. Further, the molecular dynamic studies helped to understand the dynamic properties of complexes in terms of flexibility of residues and structural stability at the interface. The ability of P5 to compete with the protein G in recognizing IgG can help in the detection and purification of antibodies. Further, it can serve as a versatile tool for a better understanding of protein–protein interactions.</p></div>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":"53 3","pages":"159 - 170"},"PeriodicalIF":2.2,"publicationDate":"2024-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140142604","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

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