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.
蛋白质-蛋白质相互作用(PPI)在重要的生物过程中发挥着关键作用,因此已成为药物化学领域的重要靶点。小肽对 PPI 的调节为开发防治人类疾病的药物提供了绝佳的机会。在这里,我们利用 IgG 蛋白 G 复合物(PDB:1FCC)结合界面的知识来设计能抑制这些复合物的多肽。我们设计了几种密切相关的多肽,实验结果和计算研究结果的比较表明,所有多肽都能与 IgG 上的预期结合位点密切结合,而且复合物是稳定的。我们确定了一个由 11 个氨基酸组成的最小序列(P5),其结合常数在 100 nM 范围内。我们认为,不同系列肽的主要亲和力差异来自极性氨基酸残基的存在。此外,分子动力学研究有助于从残基的灵活性和界面结构稳定性的角度了解复合物的动态特性。P5 能够与蛋白质 G 竞争识别 IgG,这有助于抗体的检测和纯化。此外,它还可以作为一种多功能工具,帮助人们更好地了解蛋白质与蛋白质之间的相互作用。
{"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":null,"pages":null},"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}
Pub Date : 2024-03-08DOI: 10.1007/s00249-024-01703-1
Nabeel Ahmad, Pradeep Sharma, Sujata Sharma, Tej P. Singh
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 (PPi). PPAT from strain C3 of Klebsiella pneumoniae (KpPPAT) 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 P41212 with cell dimensions of a = b = 72.82 Å and c = 200.37 Å. The structure was determined using the molecular replacement method and refined to values of 0.208 and 0.255 for Rcryst and Rfree 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 KpPPAT folds into a β/α structure. The conformations of the side chains of several residues in the substrate binding site in KpPPAT 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 KD value of 3.45 × 10−4 M for ATP which is significantly lower than the corresponding values reported for PPAT from other species.
磷泛硫乙氨酸腺苷基转移酶(EC. 2.7.7.3,PPAT)催化辅酶 A(CoA)生物合成途径中多步反应的倒数第二步。在这一步中,来自三磷酸腺苷(ATP)的腺苷酸基转移到 4'-磷泛硫乙氨酸(PNS)上,生成 3'-去磷辅酶 A(dpCoA)和焦磷酸(PPi)。克隆、表达和纯化了肺炎克雷伯氏菌 C3 菌株中的 PPAT(KpPPAT)。在 pH 值为 7.5 时,使用 0.1 M HEPES 缓冲液和 PEG10000 对其进行结晶。晶体属于四方空间群 P41212,晶胞尺寸为 a = b = 72.82 Å 和 c = 200.37 Å。采用分子置换法确定了其结构,并将 Rcryst 和 Rfree 因子的值分别细化为 0.208 和 0.255。结构测定结果表明,在不对称单元中存在三个晶体学上独立的分子 A、B 和 C。分子 A 和 B 在不对称单元中以二聚体的形式存在,而分子 C 则属于第二个二聚体,其伙伴与结晶学上的二重对称性有关。KpPPAT 的多肽链折叠成 β/α 结构。KpPPAT 底物结合位点中几个残基侧链的构象与其他 PPAT 的侧链构象明显不同。因此,底物磷酸泛硫乙烷(PNS)和三磷酸腺苷(ATP)的结合模式也大不相同。利用荧光光谱进行的结合研究表明,ATP 的 KD 值为 3.45 × 10-4 M,明显低于其他物种 PPAT 的相应值。
{"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":null,"pages":null},"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}
Pub Date : 2024-03-07DOI: 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
We present a new phenomenon resulting from the interaction of magnetic beads with cancer cells in a laser trap formed on a slide containing a depression 16.5 mm in diameter and 0.78 mm of maximum depth. This phenomenon includes the apparent formation and expansion of a dark bubble that attracts and incinerates surrounding matter when it explodes, which leads to a plasma emitting intense radiation that has the appearance of a star on a microscopic scale. We have observed the star-like phenomenon for more than 4 years, and the intensity depends on the laser’s power. Measuring the laser power of the dark bubble shows the entrapment of electromagnetic energy as it expands.
{"title":"Observation of magnet-induced star-like radiation of a plasma created from cancer cells in a laser trap","authors":"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","doi":"10.1007/s00249-024-01701-3","DOIUrl":"10.1007/s00249-024-01701-3","url":null,"abstract":"<div><p>We present a new phenomenon resulting from the interaction of magnetic beads with cancer cells in a laser trap formed on a slide containing a depression 16.5 mm in diameter and 0.78 mm of maximum depth. This phenomenon includes the apparent formation and expansion of a dark bubble that attracts and incinerates surrounding matter when it explodes, which leads to a plasma emitting intense radiation that has the appearance of a star on a microscopic scale. We have observed the star-like phenomenon for more than 4 years, and the intensity depends on the laser’s power. Measuring the laser power of the dark bubble shows the entrapment of electromagnetic energy as it expands.</p></div>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2024-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140048465","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}
Pub Date : 2024-02-28DOI: 10.1007/s00249-024-01702-2
Ion Munteanu, Elena Starodub, Sergiu Bazgan, Marina Turcan, Tatiana Paslari, Diana Podoleanu, Nicolae A. Enaki
A new method for repackaging optical metamaterials formed from quartz spheres (fibers) of various diameters is proposed for ultraviolet C disinfection of infected liquids by pathogens (viruses and bacteria). The main idea of the new equipment is connected with the rotation of a contaminated fluid by screw channels within a metamaterial matrix prepared from UVC fibers/spherical optics, to improve the decontamination efficiency. In demonstration of the viability of this approach, dynamic and static inactivation of Baker's yeast via Ultraviolet C radiation regimes are used in this paper to show the efficacy of decontamination within the screw channels.
为对受病原体(病毒和细菌)感染的液体进行紫外线 C 消毒,提出了一种对由不同直径的石英球(纤维)形成的光学超材料进行重新包装的新方法。这种新设备的主要理念是通过由紫外线纤维/球形光学器件制备的超材料矩阵内的螺旋通道旋转受污染的液体,以提高去污效率。为了证明这种方法的可行性,本文利用紫外线 C 辐射对贝克酵母进行动态和静态灭活,以显示螺旋通道内的去污效果。
{"title":"Ultraviolet C intensity dependence of decontamination efficiency for pathogens as function of repacked metamaterials with screw channels","authors":"Ion Munteanu, Elena Starodub, Sergiu Bazgan, Marina Turcan, Tatiana Paslari, Diana Podoleanu, Nicolae A. Enaki","doi":"10.1007/s00249-024-01702-2","DOIUrl":"10.1007/s00249-024-01702-2","url":null,"abstract":"<div><p>A new method for repackaging optical metamaterials formed from quartz spheres (fibers) of various diameters is proposed for ultraviolet C disinfection of infected liquids by pathogens (viruses and bacteria). The main idea of the new equipment is connected with the rotation of a contaminated fluid by screw channels within a metamaterial matrix prepared from UVC fibers/spherical optics, to improve the decontamination efficiency. In demonstration of the viability of this approach, dynamic and static inactivation of Baker's yeast via Ultraviolet C radiation regimes are used in this paper to show the efficacy of decontamination within the screw channels.</p></div>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2024-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139988968","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}
Pub Date : 2024-02-08DOI: 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
Sedimentation velocity analytical ultracentrifugation (SV-AUC) has long been an important method for characterization of antibody therapeutics. Recently, SV-AUC has experienced a wave of new interest and usage from the gene and cell therapy industry, where SV-AUC has proven itself to be the “gold standard” analytical approach for determining capsid loading ratios for adeno-associated virus (AAV) and other viral vectors. While other more common approaches have existed in the realm of cGMP-compliant techniques for years, SV-AUC has long been used strictly for characterization, but not for release testing. This manuscript describes the challenges faced in bringing SV-AUC to a cGMP environment and describes a new program, “BASIS”, which allows for 21 CFR Part 11-compliant data handling and data analysis using the well-known and frequently cited SEDFIT analysis software.
{"title":"BASIS: BioAnalysis SEDFIT integrated software for cGMP analysis of SV-AUC data","authors":"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","doi":"10.1007/s00249-024-01700-4","DOIUrl":"10.1007/s00249-024-01700-4","url":null,"abstract":"<div><p>Sedimentation velocity analytical ultracentrifugation (SV-AUC) has long been an important method for characterization of antibody therapeutics. Recently, SV-AUC has experienced a wave of new interest and usage from the gene and cell therapy industry, where SV-AUC has proven itself to be the “gold standard” analytical approach for determining capsid loading ratios for adeno-associated virus (AAV) and other viral vectors. While other more common approaches have existed in the realm of cGMP-compliant techniques for years, SV-AUC has long been used strictly for characterization, but not for release testing. This manuscript describes the challenges faced in bringing SV-AUC to a cGMP environment and describes a new program, “BASIS”, which allows for 21 CFR Part 11-compliant data handling and data analysis using the well-known and frequently cited SEDFIT analysis software.</p></div>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2024-02-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139701512","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}
Pub Date : 2024-01-24DOI: 10.1007/s00249-023-01699-0
Samira Jalilvand, Hamze Mousavi
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.
色散曲线和状态密度用于分析 DNA 和 RNA 片段的振动特性。分析采用了谐波哈密顿和格林函数技术。研究了 DNA 和 RNA 的两种构型(有限构型和循环构型),并将其与无限构型进行了比较。DNA 分子采用了三种模型,包括鱼骨模型、ldder 模型和鱼骨阶梯模型,而 RNA 分子则采用了半鱼骨模型。为了增强 DNA 和 RNA 模拟的真实感,每个无限系统内的单元格以及有限和循环情况下的长度都被逐渐放大。子点之间的连接采用线性弹簧建模,垂直弹簧的刚度在 DNA 和 RNA 模型的整个长度上呈现随机变化。较短的 DNA 和 RNA 片段在其状态密度中会出现更多的峰值,从而导致分散曲线中出现更多的条带。这表明,随着这些片段中构建模块数量的增加,它们的曲线类似于无限系统的曲线。这些发现对研究类似宏观系统的振动特性具有实际意义。
{"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":null,"pages":null},"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}
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.
{"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":null,"pages":null},"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}
Pub Date : 2024-01-13DOI: 10.1007/s00249-023-01696-3
Liana L. Tevonyan, Artemy D. Beniaminov, Dmitry N. Kaluzhny
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.
摘要 由富含鸟嘌呤的 DNA 区域形成的 G-四重链(G4)结构具有多种独特的光学特性,包括紫外吸收和圆二色光谱。一些 G4 DNA 具有本征紫外荧光,但其来源至今尚未完全清楚。在这项工作中,我们研究了 TMPyP4 和亚甲蓝对由两个 d(G3T)4 序列形成的二聚 G4 DNA 结构本征荧光的影响。我们证明,虽然 G4 DNA 的构象及其二聚体结构保持不变,但配体的结合会导致本征荧光淬灭。配体的结合位点是通过鸟嘌呤的光诱导氧化和结合等值线分析得出的。我们讨论了 DNA 配体复合物如何影响 G4 DNA 的本征荧光。
{"title":"Quenching of G4-DNA intrinsic fluorescence by ligands","authors":"Liana L. Tevonyan, Artemy D. Beniaminov, 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(G<sub>3</sub>T)<sub>4</sub> 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":null,"pages":null},"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}
Pub Date : 2024-01-12DOI: 10.1007/s00249-023-01698-1
Giovanny Angiolillo, Fernanda Abreu, Daniel Acosta-Avalos
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.
磁动细菌是一种微生物,能在细胞内产生成链的磁性纳米粒子,赋予细菌身体磁矩,使其能够顺着地磁场线游动。磁动细菌在环境样本中通常表现出两种游动极性:寻南极性(SS)和寻北极性(NS),其特点是细菌分别与磁场线平行或反平行游动。据观察,在存在不均匀磁场的情况下,NS趋磁细菌可将其游动极性转变为 SS 极性,反之亦然。本研究分析了在磁体存在的情况下从分离的 SS 球菌中获得的 NS 球菌种群。目的是研究两种球菌种群在游动特性和磁矩方面的差异。为此,研究人员记录了球菌的游动轨迹,并计算了速度以及速度与外加磁场之间的夹角。此外,还获得了 SS 和 NS 球菌的显微照片,并测量了它们的磁小体,分析了它们的长度、宽度、长宽比和磁矩,最终获得了每种球菌的磁矩。结果表明,相对于 SS 球菌,NS 球菌具有以下特性:速度更高,细菌磁矩分布更窄,速度与外加磁场之间的角度分布更分散,磁场敏感性更低。这些差异不能用磁小体链磁极性的简单变化来解释,而可能与趋磁细菌中存在活跃的磁感应过程有关。
{"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":null,"pages":null},"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}
Pub Date : 2024-01-03DOI: 10.1007/s00249-023-01697-2
Chinta M. Aryal, Jianjun Pan
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-sn-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-sn-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.
{"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":null,"pages":null},"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}