Biophysical chemistry最新文献

{"title":"Salvianolic acid B prevents the amyloid transformation of A53T mutant of α-synuclein.","authors":"Almas Akhtar, Payal Singh, Nikita Admane, Abhinav Grover","doi":"10.1016/j.bpc.2024.107379","DOIUrl":"https://doi.org/10.1016/j.bpc.2024.107379","url":null,"abstract":"<p><p>Parkinson's disease (PD) is a neurodegenerative disorder involving the progressive loss of dopaminergic neurons in the substantia nigra pars compacta triggered by the accumulation of amyloid aggregates of α-synuclein protein. This study investigates the potential of Salvianolic Acid B (SalB), a water-soluble polyphenol derived from Salvia miltiorrhiza Bunge, in modulating the aggregation of the A53T mutant of α-synuclein (A53T Syn). This mutation is associated with rapid aggregation and a higher rate of protofibril formation in early-onset familial PD. Computational and experimental approaches demonstrated Sal-B effectively prevents the amyloid fibrillation of A53T Syn by interacting with the N-terminal region and NAC domain. Sal-B particularly associates with the KTKEGV motif and NACore segment of A53T Syn by hydrophobic and hydrogen bonding interactions. Replica exchange molecular dynamics (REMD) simulations indicated that Sal-B reduces intramolecular hydrogen bonding and structural transitions into β-sheet rich conformations, thereby lowering the aggregation propensity of A53T Syn. Systematic analysis conducted using biophysical techniques and high-end microscopy has demonstrated significant inhibition in the amyloid transformation of A53T Syn corroborated by a 92 % decrease in ThT maxima at 100 μM Sal-B concentration and microscopic techniques validated the absence of mature fibrillar amyloids. DLS data revealed heterogeneous particle sizes, supporting the formation of smaller unstructured aggregates. These findings underscore Sal-B as a promising therapeutic candidate for PD and related synucleinopathies, warranting further investigation in cellular and animal models to advance potential treatments and early intervention strategies.</p>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"318 ","pages":"107379"},"PeriodicalIF":3.3,"publicationDate":"2024-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142852302","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bilirubin: Photophysical and photochemical properties, phototherapy, analytical methods of measurement. A short review.","authors":"Alexander S Tatikolov, Pavel G Pronkin, Ina G Panova","doi":"10.1016/j.bpc.2024.107378","DOIUrl":"https://doi.org/10.1016/j.bpc.2024.107378","url":null,"abstract":"<p><p>Bilirubin, a yellow bile pigment, plays an important role in the body, being a potent antioxidant and having anti-inflammatory, immunomodulatory, cytoprotective, and neuroprotective functions. This makes bilirubin promising as a therapeutic and diagnostic agent in biomedicine. However, excess bilirubin is toxic and should be removed from the body. Bilirubin exhibits photochemical activity, which has been the subject of numerous studies up to now. Such studies are relevant because the bilirubin photochemistry provides the basis for bilirubin removing in phototherapy of neonatal jaundice (neonatal hyperbilirubinemia) and for some therapeutic applications. Furthermore, it can model several elementary processes of molecular photonics. In particular, the bilirubin molecule is capable of ultrafast Z-E photoisomerization and contains two almost identical dipyrromethenone chromophores capable of exciton coupling. The present review considers the data on the photophysical and photochemical properties of bilirubin and ultrafast routes of its phototransformations, as well as its photochemical reactions in phototherapy of neonatal hyperbilirubinemia and the ways to decrease the possible adverse effects of the phototherapy. The main analytical methods of bilirubin measurement in biological systems are also viewed.</p>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"318 ","pages":"107378"},"PeriodicalIF":3.3,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142845805","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Self-assembling of coiled-coil peptides into virus-like particles: Basic principles, properties, design, and applications with special focus on vaccine design and delivery.","authors":"Kisalay Jha, Puja Jaishwal, Thakur Prasad Yadav, Satarudra Prakash Singh","doi":"10.1016/j.bpc.2024.107375","DOIUrl":"https://doi.org/10.1016/j.bpc.2024.107375","url":null,"abstract":"<p><p>Self-assembling peptide nanoparticles (SAPN) based delivery systems, including virus-like particles (VLP), have shown great potential for becoming prominent in next-generation vaccine and drug development. The VLP can mimic properties of natural viral capsid in terms of size (20-200 nm), geometry (i.e., icosahedral structures), and the ability to generate a robust immune response (with multivalent epitopes) through activation of innate and/or adaptive immune signals. In this regard, coiled-coil (CC) domains are suitable building blocks for designing VLP because of their programmable interaction specificity, affinity, and well-established sequence-to-structure relationships. Generally, two CC domains with different oligomeric states (trimer and pentamer) are fused to form a monomeric protein through a short, flexible spacer sequence. By using combinations of symmetry axes (2-, 3- and 5- folds) that are unique to the geometry of the desired protein cage, it is possible, in principle, to assemble well-defined protein cages like VLP. In this review, we have discussed the crystallographic rules and the basic principles involved in the design of CC-based VLP. It also explored the functions of numerous noncovalent interactions in generating stable VLP structures, which play a crucial role in improving the properties of vaccine immunogenicity, drug delivery, and 3D cell culturing.</p>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"318 ","pages":"107375"},"PeriodicalIF":3.3,"publicationDate":"2024-12-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142823863","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Development of immobilized peroxidase on amino-functionalized magnetic MgFe₂O₄ nanoparticles for antioxidant activity and decolorization.","authors":"Keziban Atacan, Nuray Güy, Alican Bahadir Semerci, Mahmut Özacar","doi":"10.1016/j.bpc.2024.107366","DOIUrl":"https://doi.org/10.1016/j.bpc.2024.107366","url":null,"abstract":"<p><p>This investigation aims to immobilize peroxidase onto 3-aminopropyltriethoxysilane (APTES)-functionalized MgFe₂O₄ magnetic nanoparticles to increase enzyme stability, efficiency, and recyclability. The synthesized samples were analyzed using X-ray diffraction, Fourier transform infrared spectroscopy, Thermogravimetric analysis, Vibrating sample magnetometer, and Scanning electron microscopy. The free and immobilized peroxidase were examined against different pH and temperatures as well as storage time and reuse. The immobilized peroxidase maintained 52 % of its initial activity after 10 consecutive measurements thanks to easy magnetic separation. In addition, antioxidant activity was increased by immobilizing the peroxidase to the MgFe₂O₄ magnetic nanoparticles. Congo red dye removal for peroxidase immobilized MgFe₂O₄-APTES was found to be 98.6 % for 240 min. Also, it showed approximately two times more dye decolorization efficiency compared to MgFe₂O₄ and APTES modified MgFe₂O₄. Finally, the immobilized peroxidase was studied by a decolorization study of congo red. So, we believe that the immobilized peroxidase on magnetic nanoparticles reported in this study may be utilized in diverse biotechnology, industrial, and environmental practices.</p>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"318 ","pages":"107366"},"PeriodicalIF":3.3,"publicationDate":"2024-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142790682","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Fifty-hertz magnetic fields induce DNA damage through activating mPTP associated mitochondrial permeability transition in senescent human fetal lung fibroblasts.","authors":"Chuan Sun, Sanying Wang, Jing Zhang, Xuqiang Zhou, Tianjun Zhu, Genxiang Mao","doi":"10.1016/j.bpc.2024.107367","DOIUrl":"https://doi.org/10.1016/j.bpc.2024.107367","url":null,"abstract":"<p><p>With the rapid development and using of electromagnetic technology, artificial electromagnetic fields (EMFs) have become an emerging environmental factor in our daily life. Extremely-low-frequency (ELF) magnetic fields (MFs), generally generated by power lines and various electric equipment, is one of the most common EMFs in the environment which were concerned for the potential impact on human health. Base on limited evidence, ELF-MFs have been classified as possible carcinogen to human by International Agency for Research on Cancer (IARC), but the mechanisms have not been fully elucidated. Senescent cells are a group of special cells, characterized by cell cycle arrest, senescence-associated secretory phenotype (SASP), accumulation of macromolecular damage, and metabolic disturbance, play important role in fetal development, tissue aging, and even carcinogenesis. Thus, EMFs may promote carcinogenesis by affecting senescent cells, however, there are few studies. In this study, we found that exposure to 50 Hz MFs at 1.0 mT for 24 h could induce significant DNA damage in senescent but not non-senescent human fetal lung fibroblast suggested that senescent cells are more sensitive to 50 Hz MFs on DNA damage, and further results revealed that reactive oxygen species (ROS) generation mediated by mitochondrial permeability transition pore (mPTP) activation play critical role in this process. Our results indicated that cellular senescence can lead to cell sensitivity to the DNA damage effect of 50 Hz MFs, however, whether this play important role in mediating the carcinogenesis of EMFs await further study.</p>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"318 ","pages":"107367"},"PeriodicalIF":3.3,"publicationDate":"2024-12-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142790612","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Trp residues near peptide termini enhance the membranolytic activity of cationic amphipathic α-helices.","authors":"Erik Strandberg, Patrick Horten, David Bentz, Parvesh Wadhwani, Jochen Bürck, Anne S Ulrich","doi":"10.1016/j.bpc.2024.107365","DOIUrl":"https://doi.org/10.1016/j.bpc.2024.107365","url":null,"abstract":"<p><p>KIA peptides were designed as a series of cationic antimicrobial agents of different lengths, based on the repetitive motif [KIAGKIA]. As amphiphilic helices, they tend to bind initially to the surface of lipid membranes. Depending on the conditions, they are proposed to flip, insert and form toroidal pores, such that the peptides are aligned in a transmembrane orientation. Tryptophan residues are often found near the ends of transmembrane helices, anchoring them to the amphiphilic bilayer interfaces. Hence, we introduced Trp residues near one or both termini of KIA peptides with lengths of 14-24 amino acids. Our hypothesis was that if Trp residues can stabilize the transmembrane orientation, then these KIA peptides will exhibit an increased propensity to form pores, with increased membranolytic activity. Using solid-state ¹⁵N NMR, we found that peptides with Trp near the ends are indeed more likely to be flipped into a transmembrane orientation, especially short peptides. Short KIA peptides also exhibited higher antimicrobial activity when modified with Trp, while longer peptides showed similar activities with and without Trp. The hemolytic activity of KIA peptides of all lengths was higher with Trp near the ends. Vesicle leakage was also increased (sometimes more than 10-fold) for the Trp-mutants, especially in thicker membranes. Higher functionality of amphiphilic helices may thus be achieved in general by exploiting the anchoring effect of Trp. These results demonstrate that the incorporation of Trp increases membranolytic activities (vesicle leakage, hemolysis and antimicrobial activity), in a way compatible with a transmembrane pore model of peptide activity.</p>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"318 ","pages":"107365"},"PeriodicalIF":3.3,"publicationDate":"2024-12-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142806077","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The swelling behaviour of hair studied through the structural change of keratin protein during the permanent waving treatment.","authors":"Takayuki Togashi, Maako Tabata, Akimasa Mochizuki, Jiro Tanaka, Kaori Wada, Yoshio Muroga, Hiroki Ikake","doi":"10.1016/j.bpc.2024.107364","DOIUrl":"https://doi.org/10.1016/j.bpc.2024.107364","url":null,"abstract":"<p><p>Filament of human hair is formed from α-keratin protein and its physical property is predominantly dominated by the structure of microfibril (also known as intermediate filaments (IF)). It is known that human hair is swollen by permanent waving (pw) treatment which consists of the reducing process and following oxidizing process, but a detail in the swelling behaviour remains still unclarified. The present work was devoted to the analysis of the swelling behaviour of hair through the structural change of IF during pw treatment, where 1.0 mol/L ammonium thioglycolate solution (pH 9.25) was employed as reducing reagent. The structure of IF was represented in terms of its microstructure, which is given by α-helix content in keratin chain, and its macrostructure, which is given by alignment of IF along human hair axis, and the structures were studied by SAXS and CP/MAS ¹³C NMR and others. It is shown that the microstructure and macrostructure of IF simultaneously start to change at an initial stage of the pw treatment without any induction period and both structures are sufficiently swollen at that stage. Furthermore, it is shown that the microstructure and macrostructure of IF is partly destructed by reducing treatment, but the destructed structures are considerably restored by following oxidizing treatment.</p>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"318 ","pages":"107364"},"PeriodicalIF":3.3,"publicationDate":"2024-11-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142790948","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"ROC-guided virtual screening, molecular dynamics simulation, and bioactivity validation assessment Z195914464 as a 3CL Mpro inhibitor","authors":"Xiongpiao Wei ,&nbsp;Min Li ,&nbsp;Yuanbiao Tu ,&nbsp;Linxiao Wang","doi":"10.1016/j.bpc.2024.107357","DOIUrl":"10.1016/j.bpc.2024.107357","url":null,"abstract":"<div><div>Discovering novel class anti-SARS-CoV-2 compounds with novel backbones is essential for preventing and controlling SARS-CoV-2 transmission, which poses a substantial threat to the health and social sustainable development of the global population because of its high pathogenicity and high transmissibility. Although the potential mutation of SARS-CoV-2 might diminish the therapeutic efficacy of drugs, 3CL Mpro is the target highly conservative in contrast with other targets. It is an essential enzyme for coronavirus replication. Based on this, this study utilized the drug discovery strategy of Knime molecular filtering framework, ROC-guided virtual screening, clustering analysis, binding mode analysis, and activity evaluation approaches to identify compound <strong>Z195914464</strong> (IC₅₀: 7.19 μM) is a novel class inhibitor of anti-SARS-CoV-2 against the 3CL Mpro target. In addition, based on molecular dynamics simulations and MMPBSA analyses, discovered that compound <strong>Z195914464</strong> can interact with more key residues and lower bonding energies, which explains why it exhibited more activity than the other three compounds. In summary, this study developed a method for the rapid and accurate discovery of active compounds and can also be applied in the discovery of active compounds in other targets.</div></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"317 ","pages":"Article 107357"},"PeriodicalIF":3.3,"publicationDate":"2024-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142746584","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cholesterol modulates the interaction of sodium salt with negatively charged phospholipid membrane","authors":"Kalyan Kumar Banerjee,&nbsp;Pabitra Maity,&nbsp;Surajit Das,&nbsp;Sanat Karmakar","doi":"10.1016/j.bpc.2024.107354","DOIUrl":"10.1016/j.bpc.2024.107354","url":null,"abstract":"<div><div>We present a systematic study on how alkali metal salts, like NaCl and NaI, affect negatively charged phospholipid vesicles using a range of experimental methods. Our goal was to find out how chain saturation and cholesterol affect the interaction between the ions and the membrane. An isothermal titration calorimetry study on large unilamellar vesicles made from dimyristoyl phosphatidylcholine (DMPC) revealed that Na⁺ shows higher binding affinity to the gel phase at 15 °C compared to the fluid phase at 30 °C. Further, cations also show stronger affinity to the membrane in the fluid composed of saturated lipids than that of unsaturated lipids. The binding affinity of Na + with anionic vesicles prepared from a mixture of DMPC and DMPG was found to decrease significantly with increasing cholesterol as well as salt concentrations, as revealed by the zeta potential study. Besides the binding constant, the Gouy Chapman theory based on the electrostatic double layer shows that cholesterol reduces the surface charge density without altering the significant area per molecule. Further, the effect of counterions was investigated using fluorescence spectroscopy of an environment-sensitive lipophilic dye, nile red. Although cholesterol alters the emission properties of nile red significantly, there is no significant change in the presence of ions. This result suggests that anions do not bind significantly to anionic vesicles. The main striking feature of the ion-membrane interaction in the presence of cholesterol is that membranes with saturated lipids exhibit a completely opposite trend from membranes with unsaturated lipids.</div></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"317 ","pages":"Article 107354"},"PeriodicalIF":3.3,"publicationDate":"2024-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142695132","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Multispectral analysis and molecular docking of a zinc (II) complex interaction with bovine serum albumin and studies on antibacterial properties, and catecholase mimicry of the complex","authors":"Mohd Tameem ,&nbsp;Mohd Amir ,&nbsp;Mohd Muslim ,&nbsp;Ruby Ahmed ,&nbsp;Mo Ahamad Khan ,&nbsp;Musheer Ahmad ,&nbsp;Farman Ali ,&nbsp;Saleem Javed","doi":"10.1016/j.bpc.2024.107355","DOIUrl":"10.1016/j.bpc.2024.107355","url":null,"abstract":"<div><div>This paper presents the synthesis process of a ligand known as 2-(naphthalene-1-yl)-1H-phenanthro[9,10-d]imidazole (NIP) and its metal complex with zinc (II), denoted as FA-128. The structural validation of FA-128 is accomplished through single-crystal X-ray diffraction (XRD). To explore the biological implications, FA-128's interaction with BSA is investigated. This exploration involves fluorescence and UV–vis absorption spectrometry techniques. The outcomes reveal the formation of robust complexes, as FA-128 significantly quenches the inherent fluorescence of BSA. Various aspects are examined, including binding constants, the count of binding sites, thermodynamic parameters, and energy transfer mechanisms. Evident alterations in BSA conformation are detected using synchronous fluorescence and circular dichroism (CD) spectrum techniques. The study proceeds to molecular docking, elucidating binding sites in the FA-128-BSA interaction. Biochemical reactions between metal complexes and proteins often trigger diverse conformational changes in protein structures. This understanding provides crucial insights into the impacts, mechanisms, and systemic transportation of numerous drugs within the body. FA-128 demonstrated superior antibacterial activity against <em>Staphylococcus aureus</em> (ZOI: 10.50 ± 0.50 mm, MIC: 100 μg/mL) and <em>Klebsiella pneumoniae</em> (ZOI: 13.0 ± 0.25 mm, MIC: 50 μg/mL). In addition, FA-128 has been evaluated as a catalytic system in the oxidation of 3,5-di-tert-butylcatechol (3,5DTBC) in a methanol solvent. FA-128 displays good catecholase-like activity with a significant turnover number (k_cat) of 7.56 × 10² h⁻¹, a Michaelis-Menten constant (K_M) of 8.14 × 10⁻⁴ M, and a maximum reaction rate (V_max) of 2.45 × 10⁻⁵ M s⁻¹ under aerobic conditions.</div></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"317 ","pages":"Article 107355"},"PeriodicalIF":3.3,"publicationDate":"2024-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142695145","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}