Bovine Serum Albumin (BSA) is a globular, water-soluble protein widely used as a model system due to its stability, binding capacity, and structural similarity to human serum albumin (HSA). Cold atmospheric plasma (CAP) has emerged as a versatile tool for biomolecule modification, sterilization, food preservation, and wound healing. This study explores the effects of CAP on glycated BSA, focusing on structural and self-assembly processes. SEM analysis reveals that CAP induces distinct protein self-assemblies depending on treatment duration. Thioflavin assays show increased fluorescence intensity in CAP-treated glycated BSA compared to native and glycated BSA, indicating an enhancement in β-sheet content and self-assembly. These findings offer valuable insights into CAP's role in modulating protein structures, with implications for biomaterials, disease mechanisms, and protein engineering.
{"title":"Exploring impact of cold atmospheric plasma directed self-assembly of glycated bovine serum albumin","authors":"Ashim Jyoti Bharati , Daphishisha Phawa , Priojeet Daimary , Monalisa Patra , Kamatchi Sankaranarayanan","doi":"10.1016/j.bpc.2025.107516","DOIUrl":"10.1016/j.bpc.2025.107516","url":null,"abstract":"<div><div>Bovine Serum Albumin (BSA) is a globular, water-soluble protein widely used as a model system due to its stability, binding capacity, and structural similarity to human serum albumin (HSA). Cold atmospheric plasma (CAP) has emerged as a versatile tool for biomolecule modification, sterilization, food preservation, and wound healing. This study explores the effects of CAP on glycated BSA, focusing on structural and self-assembly processes. SEM analysis reveals that CAP induces distinct protein self-assemblies depending on treatment duration. Thioflavin assays show increased fluorescence intensity in CAP-treated glycated BSA compared to native and glycated BSA, indicating an enhancement in β-sheet content and self-assembly. These findings offer valuable insights into CAP's role in modulating protein structures, with implications for biomaterials, disease mechanisms, and protein engineering.</div></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"327 ","pages":"Article 107516"},"PeriodicalIF":2.2,"publicationDate":"2025-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144895305","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}
Pub Date : 2025-08-21DOI: 10.1016/j.bpc.2025.107513
Julia B. Ejarque , Anna C.F. Couto , Thábata Matos , Evandro L. Duarte , M. Teresa Lamy , Julio H.K. Rozenfeld
{"title":"Corrigendum to “Effect of disialoganglioside GD3 on the subgel, gel and fluid phases of cationic DODAB vesicles” [biophysical chemistry 326 (2025) 107503]","authors":"Julia B. Ejarque , Anna C.F. Couto , Thábata Matos , Evandro L. Duarte , M. Teresa Lamy , Julio H.K. Rozenfeld","doi":"10.1016/j.bpc.2025.107513","DOIUrl":"10.1016/j.bpc.2025.107513","url":null,"abstract":"","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"327 ","pages":"Article 107513"},"PeriodicalIF":2.2,"publicationDate":"2025-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144941603","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}
The study of the interaction between small molecules and biological macromolecules is a critical area of research with significant implications across various scientific fields. Larotrectinib, a tropomyosin kinase inhibitor, is used to treat patients with solid tumors harboring neurotrophic tyrosine receptor kinase (NTRK) gene fusions. In this investigation, the interaction between larotrectinib and calf thymus DNA (ctDNA) was thoroughly examined using a combination of techniques, including UV–Vis spectrophotometry, spectrofluorimetry, viscosity measurements, ionic strength variation, thermodynamic analysis, molecular dynamics simulations, and docking studies. The results demonstrated a strong binding interaction between larotrectinib and ctDNA, with the drug primarily binding to the minor groove of ctDNA. This binding mode was established through competitive binding assays using ethidium bromide and rhodamine B, as well as UV–Vis spectroscopy and viscosity analysis. The binding constant (Kb) at 298 K, determined using the Benesi-Hildebrand equation, was found to be 4.4 × 105 M−1, pointing out a high binding affinity between larotrectinib and ctDNA. Thermodynamic analysis revealed that the interaction is driven mainly by hydrophobic forces and hydrogen bonding, as evidenced by the calculated enthalpy (ΔH0) and entropy (ΔS0) changes. Molecular docking studies further supported these findings, showing that larotrectinib binds preferentially to the AT-rich regions of the B-DNA minor groove. This was validated by molecular dynamics studies, which provided additional confirmation of the binding mechanism. Overall, these findings provide valuable understanding into the molecular interactions and pharmacological mechanisms of larotrectinib, contributing to a deeper insight of its role as a potent anticancer agent.
{"title":"Unraveling the molecular interaction of Larotrectinib with calf thymus DNA: A comprehensive study using multi-spectroscopic, thermodynamic, and computational techniques","authors":"Manal A. Alossaimi , Taibah Aldakhil , Heba Elmansi , Fathalla Belal , Galal Magdy","doi":"10.1016/j.bpc.2025.107512","DOIUrl":"10.1016/j.bpc.2025.107512","url":null,"abstract":"<div><div>The study of the interaction between small molecules and biological macromolecules is a critical area of research with significant implications across various scientific fields. Larotrectinib, a tropomyosin kinase inhibitor, is used to treat patients with solid tumors harboring neurotrophic tyrosine receptor kinase (NTRK) gene fusions. In this investigation, the interaction between larotrectinib and calf thymus DNA (ctDNA) was thoroughly examined using a combination of techniques, including UV–Vis spectrophotometry, spectrofluorimetry, viscosity measurements, ionic strength variation, thermodynamic analysis, molecular dynamics simulations, and docking studies. The results demonstrated a strong binding interaction between larotrectinib and ctDNA, with the drug primarily binding to the minor groove of ctDNA. This binding mode was established through competitive binding assays using ethidium bromide and rhodamine B, as well as UV–Vis spectroscopy and viscosity analysis. The binding constant (K<sub>b</sub>) at 298 K, determined using the Benesi-Hildebrand equation, was found to be 4.4 × 10<sup>5</sup> M<sup>−1</sup>, pointing out a high binding affinity between larotrectinib and ctDNA. Thermodynamic analysis revealed that the interaction is driven mainly by hydrophobic forces and hydrogen bonding, as evidenced by the calculated enthalpy (ΔH<sup>0</sup>) and entropy (ΔS<sup>0</sup>) changes. Molecular docking studies further supported these findings, showing that larotrectinib binds preferentially to the AT-rich regions of the B-DNA minor groove. This was validated by molecular dynamics studies, which provided additional confirmation of the binding mechanism. Overall, these findings provide valuable understanding into the molecular interactions and pharmacological mechanisms of larotrectinib, contributing to a deeper insight of its role as a potent anticancer agent.</div></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"327 ","pages":"Article 107512"},"PeriodicalIF":2.2,"publicationDate":"2025-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144829400","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}
Pub Date : 2025-08-08DOI: 10.1016/j.bpc.2025.107505
Francisco Melo , Nicolás Flores , Igor Navarrete , Leonardo Caballero , Alberto Cornejo
Tau's spread and internalization are related to disease progression in Alzheimer's disease and tauopathies. Tau internalization plays a critical role in the spreading. The cells involved in brain surveillance involved in the clearance of aggregates include parenchymal-border macrophages (microglia), perivascular macrophages, and meningeal and choroid plexus macrophages. However, in events such as strokes, or tau amyloids can breach the blood-brain barrier (BBB). Facilitating the dissemination of aggregates. Thus, we evaluated whether the tau aggregates have effect over a semi-permeable layer such as DOPC. Nano-indentation showed that tau monomers of full length and tau 4R (microtubule binding domain) interact differently with DOPC, and the amyloids increase the Fp (critical force) but not disrupt the DOPC. Then, to analyze the effect of aggregates on N2a cells, we incubated tau aggregates for 24 h; resulting in the decrease of axon-like structures compromising the cell integrity. Afterwards, cultured tau aggregates with raw 264.7 cells (mouse macrophages) showed that the 4R microtubule-binding domain co-localize with Rab5 and Lamp1, suggesting a key role to lysosomes in the clearance of tau aggregates.
{"title":"Internalization of external tau aggregates co-localize with early endocytic markers and lysosomes","authors":"Francisco Melo , Nicolás Flores , Igor Navarrete , Leonardo Caballero , Alberto Cornejo","doi":"10.1016/j.bpc.2025.107505","DOIUrl":"10.1016/j.bpc.2025.107505","url":null,"abstract":"<div><div>Tau's spread and internalization are related to disease progression in Alzheimer's disease and tauopathies. Tau internalization plays a critical role in the spreading. The cells involved in brain surveillance involved in the clearance of aggregates include parenchymal-border macrophages (microglia), perivascular macrophages, and meningeal and choroid plexus macrophages. However, in events such as strokes, or tau amyloids can breach the blood-brain barrier (BBB). Facilitating the dissemination of aggregates. Thus, we evaluated whether the tau aggregates have effect over a semi-permeable layer such as DOPC. Nano-indentation showed that tau monomers of full length and tau 4R (microtubule binding domain) interact differently with DOPC, and the amyloids increase the Fp (critical force) but not disrupt the DOPC. Then, to analyze the effect of aggregates on N2a cells, we incubated tau aggregates for 24 h; resulting in the decrease of axon-like structures compromising the cell integrity. Afterwards, cultured tau aggregates with raw 264.7 cells (mouse macrophages) showed that the 4R microtubule-binding domain co-localize with Rab5 and Lamp1, suggesting a key role to lysosomes in the clearance of tau aggregates.</div></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"327 ","pages":"Article 107505"},"PeriodicalIF":2.2,"publicationDate":"2025-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144829663","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}
Pub Date : 2025-08-04DOI: 10.1016/j.bpc.2025.107503
Julia B. Ejarque , Anna C.F. Couto , Thábata Matos , Evandro L. Duarte , M. Teresa Lamy , Julio H.K. Rozenfeld
GD3 is a disialoganglioside overexpressed in several types of cancer cells. The synthetic cationic lipid DODAB has been successfully employed as a vaccine adjuvant, and would be suitable to enhance GD3 immunogenicity. Here, mixed dispersions of GD3 and DODAB were characterized by Differential Scanning Calorimetry (DSC) and Electron Paramagnetic Resonance (EPR) spectroscopy. GD3 is miscible with DODAB, and decreases the DODAB gel-fluid transition cooperativity. GD3 does not affect the temperature hysteresis between gel-fluid and fluid-gel transitions. GD3 does not affect the formation of a subgel phase in DODAB bilayers cooled below 15 °C. GD3 decreases the acyl chain packing of the DODAB subgel phase, which could explain the broad and shallow exothermic event between 5 °C and 20 °C that appears on thermograms of mixed dispersions. These results might contribute to the development of novel GD3-based cancer immunotherapies, including at the low temperatures involved in cold chain stability.
{"title":"Effect of disialoganglioside GD3 on the subgel, gel and fluid phases of cationic DODAB vesicles","authors":"Julia B. Ejarque , Anna C.F. Couto , Thábata Matos , Evandro L. Duarte , M. Teresa Lamy , Julio H.K. Rozenfeld","doi":"10.1016/j.bpc.2025.107503","DOIUrl":"10.1016/j.bpc.2025.107503","url":null,"abstract":"<div><div>GD3 is a disialoganglioside overexpressed in several types of cancer cells. The synthetic cationic lipid DODAB has been successfully employed as a vaccine adjuvant, and would be suitable to enhance GD3 immunogenicity. Here, mixed dispersions of GD3 and DODAB were characterized by Differential Scanning Calorimetry (DSC) and Electron Paramagnetic Resonance (EPR) spectroscopy. GD3 is miscible with DODAB, and decreases the DODAB gel-fluid transition cooperativity. GD3 does not affect the temperature hysteresis between gel-fluid and fluid-gel transitions. GD3 does not affect the formation of a subgel phase in DODAB bilayers cooled below 15 °C. GD3 decreases the acyl chain packing of the DODAB subgel phase, which could explain the broad and shallow exothermic event between 5 °C and 20 °C that appears on thermograms of mixed dispersions. These results might contribute to the development of novel GD3-based cancer immunotherapies, including at the low temperatures involved in cold chain stability.</div></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"326 ","pages":"Article 107503"},"PeriodicalIF":2.2,"publicationDate":"2025-08-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144766874","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}
Numerous pathological conditions, collectively termed amyloidosis, are associated with the aggregation of misfolded proteins under stressed physiochemical conditions. Natural compounds capable of modulating protein aggregation or disassembling preformed fibrils hold promise as potential therapeutic candidates for treating aggregation-related diseases. In this study, we aim to examine the binding interaction and effectiveness of Lobeline (Lob), a piperidine alkaloid, in preventing the formation of acid-denatured Lysozyme (Lyz) amyloid using various spectroscopic, cheminformatics and imaging techniques. Steady-state and time-resolved fluorescence measurements confirm a direct interaction between Lyz and Lob with a binding constant of ∼106 M−1 with a 1:1 binding stoichiometry. The association has been found to be spontaneous and is driven by entropy involving non-electrostatic interactions. Molecular Docking shows that Lob stabilizes Lyz by hydrophobic and hydrophilic interactions. The anti-amyloid properties of Lob in Lyz amyloid fibrils are assessed through a range of in vitro techniques, including turbidity measurement, dynamic light scattering (DLS), Thioflavin T (ThT) fluorescence, Circular Dichroism studies and Field Emission Scanning Electron Microscopy (FESEM) imaging. These studies demonstrate that Lob halts the fibrillation of acid-treated Lyz at the nucleation stage by providing alternative pathways for hydrogen bonding and other weak interactions with key amino acid residues necessary for the formation of oligomers and fibrils.
{"title":"Molecular mechanisms of Lobeline-mediated inhibition of lysozyme amyloidogenesis: A synergistic approach using biophysical and cheminformatics techniques","authors":"Vibeizonuo Rupreo , Ria Saha , Jhimli Bhattacharyya , Rajib Kumar Mitra","doi":"10.1016/j.bpc.2025.107502","DOIUrl":"10.1016/j.bpc.2025.107502","url":null,"abstract":"<div><div>Numerous pathological conditions, collectively termed amyloidosis, are associated with the aggregation of misfolded proteins under stressed physiochemical conditions. Natural compounds capable of modulating protein aggregation or disassembling preformed fibrils hold promise as potential therapeutic candidates for treating aggregation-related diseases. In this study, we aim to examine the binding interaction and effectiveness of Lobeline (Lob), a piperidine alkaloid, in preventing the formation of acid-denatured Lysozyme (Lyz) amyloid using various spectroscopic, cheminformatics and imaging techniques. Steady-state and time-resolved fluorescence measurements confirm a direct interaction between Lyz and Lob with a binding constant of ∼10<sup>6</sup> M<sup>−1</sup> with a 1:1 binding stoichiometry. The association has been found to be spontaneous and is driven by entropy involving non-electrostatic interactions. Molecular Docking shows that Lob stabilizes Lyz by hydrophobic and hydrophilic interactions. The anti-amyloid properties of Lob in Lyz amyloid fibrils are assessed through a range of in vitro techniques, including turbidity measurement, dynamic light scattering (DLS), Thioflavin T (ThT) fluorescence, Circular Dichroism studies and Field Emission Scanning Electron Microscopy (FESEM) imaging. These studies demonstrate that Lob halts the fibrillation of acid-treated Lyz at the nucleation stage by providing alternative pathways for hydrogen bonding and other weak interactions with key amino acid residues necessary for the formation of oligomers and fibrils.</div></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"326 ","pages":"Article 107502"},"PeriodicalIF":2.2,"publicationDate":"2025-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144750822","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}
Pub Date : 2025-07-16DOI: 10.1016/j.bpc.2025.107493
Huzaifa Yasir Khan , Yassir Hasan Khan , Md Nadir Hassan , Azeem Ahmad , Rizwan Hasan Khan , Farukh Arjmand
Amyloid fibrillation is a key feature in the pathogenesis of various protein misfolding diseases. This process is driven by both primary and secondary nucleation mechanisms. Many small molecules are known to modulate protein aggregation, with certain anticancer drugs demonstrating the ability to interfere with amyloid formation. In lieu of above rationale, with the aim to repurpose anticancer drugs for other therapeutic remedies, we investigated the potential of an ionic anticancer chemotherapeutic drug candidate, namely aquachlorobis(DACH)copper(II) flufenamate complex; [{Cu(DACH)2(H2O)Cl}.(fluf)] for the inhibition of amyloid formation in Human lysozyme protein. Utilizing various biophysical techniques, viz., distinctive dye binding assays, confocal microscopy, and dynamic light scattering experiments, the potency of Cu(II) complex to inhibit human lysozyme fibrillation was studied. Our findings demonstrated that Cu(II) complex significantly disrupted amyloid fibrillation by targeting and inhibiting both primary and secondary nucleation pathways. The results indicated the high effectiveness of Cu(II) complex in preventing Human Lysozyme fibrillation, making it a promising candidate for addressing amyloidosis and paving a way for repurposing anticancer drug scaffolds as anti-AD agents.
{"title":"Inhibition of nucleation and disruption of amyloid fibrillation in human lysozyme aggregation by a potent Cu(II) flufenamate chemotherapeutic drug candidate","authors":"Huzaifa Yasir Khan , Yassir Hasan Khan , Md Nadir Hassan , Azeem Ahmad , Rizwan Hasan Khan , Farukh Arjmand","doi":"10.1016/j.bpc.2025.107493","DOIUrl":"10.1016/j.bpc.2025.107493","url":null,"abstract":"<div><div>Amyloid fibrillation is a key feature in the pathogenesis of various protein misfolding diseases. This process is driven by both primary and secondary nucleation mechanisms. Many small molecules are known to modulate protein aggregation, with certain anticancer drugs demonstrating the ability to interfere with amyloid formation. In lieu of above rationale, with the aim to repurpose anticancer drugs for other therapeutic remedies, we investigated the potential of an ionic anticancer chemotherapeutic drug candidate, namely aquachlorobis(DACH)copper(II) flufenamate complex; [{Cu(DACH)<sub>2</sub>(H<sub>2</sub>O)Cl}.(fluf)] for the inhibition of amyloid formation in Human lysozyme protein. Utilizing various biophysical techniques, <em>viz.</em>, distinctive dye binding assays, confocal microscopy, and dynamic light scattering experiments, the potency of Cu(II) complex to inhibit human lysozyme fibrillation was studied. Our findings demonstrated that Cu(II) complex significantly disrupted amyloid fibrillation by targeting and inhibiting both primary and secondary nucleation pathways. The results indicated the high effectiveness of Cu(II) complex in preventing Human Lysozyme fibrillation, making it a promising candidate for addressing amyloidosis and paving a way for repurposing anticancer drug scaffolds as anti-AD agents.</div></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"326 ","pages":"Article 107493"},"PeriodicalIF":3.3,"publicationDate":"2025-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144672260","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}
Pub Date : 2025-07-10DOI: 10.1016/j.bpc.2025.107492
Hidetaka Torigoe, Sumire Nakayama
Many biomolecules are crowded in vivo environments. Metal ion–nucleic acid interactions are important in vivo molecular crowding conditions for structure formation and biological activity of nucleic acids. Although metal ion–nucleic acid interactions have been investigated in detail under diluted conditions, studies examining the molecular crowding effect on metal ion–nucleic acid interactions are limited. Hg2+ specifically binds to T–T mismatched duplex DNA to form T–Hg–T base pair under diluted conditions. Here, we examined the binding under molecular crowding conditions. To the best of our knowledge, no previous studies reported the metal-mediated base-pair formation under molecular crowding conditions. UV melting showed that the specific stabilization of only the T–T mismatched duplex by Hg2+ addition was maintained under molecular crowding conditions. CD spectra showed that no significant structural change of the T–T mismatched duplex by Hg2+ addition was preserved under molecular crowding conditions. Isothermal titration calorimetric analyses showed that the 1:1 M ratio for the specific binding of Hg2+ to T–T was maintained under molecular crowding conditions. However, the magnitudes of the negative ∆H and the positive ∆S were significantly larger and smaller, respectively, than those under diluted conditions, which may lead to the smaller magnitudes of Ka and ∆G. Smaller number of released water molecules upon the binding under molecular crowding conditions may result in these results. The present findings may be useful for developing efficient metal-mediated base-pair formation, leading to progress in their efficient applications in various fields including nanotechnology.
{"title":"Molecular crowding effect on specific binding of Hg2+ to T–T mismatched base pair in duplex DNA","authors":"Hidetaka Torigoe, Sumire Nakayama","doi":"10.1016/j.bpc.2025.107492","DOIUrl":"10.1016/j.bpc.2025.107492","url":null,"abstract":"<div><div>Many biomolecules are crowded in vivo environments. Metal ion–nucleic acid interactions are important in vivo molecular crowding conditions for structure formation and biological activity of nucleic acids. Although metal ion–nucleic acid interactions have been investigated in detail under diluted conditions, studies examining the molecular crowding effect on metal ion–nucleic acid interactions are limited. Hg<sup>2+</sup> specifically binds to T–T mismatched duplex DNA to form T–Hg–T base pair under diluted conditions. Here, we examined the binding under molecular crowding conditions. To the best of our knowledge, no previous studies reported the metal-mediated base-pair formation under molecular crowding conditions. UV melting showed that the specific stabilization of only the T–T mismatched duplex by Hg<sup>2+</sup> addition was maintained under molecular crowding conditions. CD spectra showed that no significant structural change of the T–T mismatched duplex by Hg<sup>2+</sup> addition was preserved under molecular crowding conditions. Isothermal titration calorimetric analyses showed that the 1:1 M ratio for the specific binding of Hg<sup>2+</sup> to T<em>–</em>T was maintained under molecular crowding conditions. However, the magnitudes of the negative ∆<em>H</em> and the positive ∆<em>S</em> were significantly larger and smaller, respectively, than those under diluted conditions, which may lead to the smaller magnitudes of <em>K</em><sub>a</sub> and ∆<em>G</em>. Smaller number of released water molecules upon the binding under molecular crowding conditions may result in these results. The present findings may be useful for developing efficient metal-mediated base-pair formation, leading to progress in their efficient applications in various fields including nanotechnology.</div></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"326 ","pages":"Article 107492"},"PeriodicalIF":3.3,"publicationDate":"2025-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144623810","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}
Pub Date : 2025-07-09DOI: 10.1016/j.bpc.2025.107490
Shreyada N. Save , Soumya S. Sahoo , Kalyani Ananthamohan , Saleem Yousf , Pratishtha Singh , Osama Aazmi , Jeetender Chugh , Shilpy Sharma
The development of insulin resistance (IR) in the skeletal muscle has been identified as one of the hallmarks of Type 2 diabetes mellitus (T2DM). Studies have shown that palmitic acid (PA), a saturated free fatty acid (FFA), can contribute to the development of IR in various insulin-responsive tissues via the induction of oxidative stress and mitochondrial dysfunction. The specific molecular mechanisms and metabolic changes that lead to IR development are not completely defined, and a better understanding of these mechanisms is needed. Our study aims to identify metabolites linked with the development of IR in skeletal muscles using PA and map the major metabolic pathways involved. Rat-derived L6 myotubes were exposed to PA to establish IR. Cellular and biochemical experiments were performed, and the metabolic perturbations associated with the induction of oxidative stress and IR were identified using 1H NMR-based metabolomics. PA exposure was associated with a loss of cellular viability due to lipid accumulation in the myotubes. This was associated with an induction of oxidative stress, loss of function, and reduced mitochondrial membrane potential. The metabolic fingerprint linked with the development of oxidative stress and IR in skeletal muscles was identified, wherein significant perturbations in the levels of methanol, dimethylamine, serine, lysine, proline, glycerol, and alanine (p < 0.05) were observed. The dysregulated metabolites and pathways identified in this study can be proposed as biomarkers for detecting palmitate-induced oxidative stress and development of IR in the skeletal myotubes – phenotypes associated with T2DM and related metabolic disorders.
{"title":"Mapping the metabolic perturbations associated with palmitate-induced oxidative stress and development of insulin resistance in skeletal muscle cells","authors":"Shreyada N. Save , Soumya S. Sahoo , Kalyani Ananthamohan , Saleem Yousf , Pratishtha Singh , Osama Aazmi , Jeetender Chugh , Shilpy Sharma","doi":"10.1016/j.bpc.2025.107490","DOIUrl":"10.1016/j.bpc.2025.107490","url":null,"abstract":"<div><div>The development of insulin resistance (IR) in the skeletal muscle has been identified as one of the hallmarks of Type 2 diabetes mellitus (T2DM). Studies have shown that palmitic acid (PA), a saturated free fatty acid (FFA), can contribute to the development of IR in various insulin-responsive tissues via the induction of oxidative stress and mitochondrial dysfunction. The specific molecular mechanisms and metabolic changes that lead to IR development are not completely defined, and a better understanding of these mechanisms is needed. Our study aims to identify metabolites linked with the development of IR in skeletal muscles using PA and map the major metabolic pathways involved. Rat-derived L6 myotubes were exposed to PA to establish IR. Cellular and biochemical experiments were performed, and the metabolic perturbations associated with the induction of oxidative stress and IR were identified using <sup>1</sup>H NMR-based metabolomics. PA exposure was associated with a loss of cellular viability due to lipid accumulation in the myotubes. This was associated with an induction of oxidative stress, loss of function, and reduced mitochondrial membrane potential. The metabolic fingerprint linked with the development of oxidative stress and IR in skeletal muscles was identified, wherein significant perturbations in the levels of methanol, dimethylamine, serine, lysine, proline, glycerol, and alanine (<em>p</em> < 0.05) were observed. The dysregulated metabolites and pathways identified in this study can be proposed as biomarkers for detecting palmitate-induced oxidative stress and development of IR in the skeletal myotubes – phenotypes associated with T2DM and related metabolic disorders.</div></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"326 ","pages":"Article 107490"},"PeriodicalIF":3.3,"publicationDate":"2025-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144654622","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}
Pub Date : 2025-07-09DOI: 10.1016/j.bpc.2025.107489
Michael Overduin , Gestél C. Kuyler , Mansoore Esmaili , Catharine A. Trieber , Claudia Acevedo-Morantes , Alexander P. Orazietti , Rustem Shaykhutdinov , Rakesh K. Bhat , Tomisin Omotoso , Sabiha Tajammul , Mohammad Rahim , Sophie Zinn-Justin , Russell E. Bishop , R. Scott Prosser , Holger Wille , Bert Klumperman
Copolymers formed by non-alternating distributions of styrene and maleic acid monomers directly solubilize intact membranes into ∼10 nm discs. However, these copolymers are inherently polydisperse in terms of polymer structure, difficult to detect, prone to precipitation with divalent cations, and have limited working pH ranges due to their charges. The exposed polar sidechain of nanodisc-forming amphipathic copolymers provides a handle for integrating critical chemical features for facile solubilization, purification, detection, and resolution of diverse membrane protein complexes, including 7-transmembrane G-Protein-Coupled Receptor (GPCR) and beta-barrel proteins directly from cellular material. Here, we report that when derivatized with amine oxide (AO) moieties, alternating and intrinsically fluorescent derivatives of poly(styrene-alt-maleic anhydride) (SMAnh) spontaneously convert biological membranes into nanodiscs with diameters of 15–30 nm that can be resolved by dynamic light scattering and electron microscopy. Compared to non-alternating poly(styrene-co-maleic acid) (SMA), their fluorescence signals allow monitoring under diverse solution conditions, whether free or lipid bilayer-bound. These copolymers are useful in a broad pH range, are tolerant of high levels of divalent cations (>200 mM CaCl2) and are designed to reduce undesirable nonspecific interactions. The resulting nanodiscs can accommodate the PagP palmitoyltransferase expressed in Escherichia coli outer membranes and the human adenosine A2A receptor expressed into Pichia pastoris membranes, resulting in readily purified proteins that are less likely to be perturbed by polymer charge or hydrophobicity.
苯乙烯和马来酸单体的非交替分布形成的共聚物直接将完整的膜溶解成约10 nm的圆盘。然而，就聚合物结构而言，这些共聚物本质上是多分散的，难以检测，容易与二价阳离子沉淀，并且由于它们的电荷而具有有限的工作pH范围。暴露的纳米盘状两亲共聚物的极性侧链为多种膜蛋白复合物（包括7-跨膜g蛋白偶联受体（GPCR）和直接来自细胞材料的β -桶蛋白）的快速溶解、纯化、检测和分离提供了关键的化学特性。在这里，我们报道了当与氧化胺（AO）部分衍生时，聚苯乙烯-马来酸酐（SMAnh）的交替和本质荧光衍生物自发地将生物膜转化为直径为15-30 nm的纳米片，可以通过动态光散射和电子显微镜分辨。与非交变聚苯乙烯-共马来酸（SMA）相比，它们的荧光信号可以在不同的溶液条件下进行监测，无论是游离的还是脂质双分子层结合的。这些共聚物适用于较宽的pH范围，可耐受高水平的二价阳离子（200 mM CaCl2），并可减少不良的非特异性相互作用。由此产生的纳米圆盘可以容纳大肠杆菌外膜中表达的PagP棕榈酰转移酶和毕赤酵母膜中表达的人腺苷A2A受体，从而产生易于纯化的蛋白质，这些蛋白质不太可能受到聚合物电荷或疏水性的干扰。
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