Pub Date : 2025-09-24DOI: 10.1016/j.bpc.2025.107532
Laila Zaatouf, Thierry Drujon, Astrid Walrant, Emmanuelle Sachon, Dror E. Warschawski
Staphylococcus aureus (S. aureus) is a Gram-positive pathogenic bacterium and a major cause of nosocomial infections. Between 20 % and 50 % of S. aureus strains are resistant to a wide range of antibiotics. DMS-DA6-NH2 (DA6) is a novel antimicrobial peptide (AMP) that exhibits high efficacy against various bacterial strains, particularly S. aureus, by disrupting its membrane through an as-yet-unknown mechanism. We employed in vivo2H solid state Nuclear Magnetic Resonance (NMR) to investigate the mode of action of AMPs on deuterated bacteria. This technique provides insights into membrane order and its changes with increasing AMP concentration. Our results enabled us to compare the mechanism of DA6 with those of AMPs with established modes of action. We found that DA6 induces pore formation in the membrane of S. aureus. This protocol serves as a template for determining the mechanisms of action of other peptides, an essential step for developing and patenting such drugs for the treatment of human diseases.
{"title":"Antimicrobial peptide mechanism of action on S. aureus membranes determined by in vivo solid-state NMR","authors":"Laila Zaatouf, Thierry Drujon, Astrid Walrant, Emmanuelle Sachon, Dror E. Warschawski","doi":"10.1016/j.bpc.2025.107532","DOIUrl":"10.1016/j.bpc.2025.107532","url":null,"abstract":"<div><div><em>Staphylococcus aureus (S. aureus)</em> is a Gram-positive pathogenic bacterium and a major cause of nosocomial infections. Between 20 % and 50 % of <em>S. aureus</em> strains are resistant to a wide range of antibiotics. DMS-DA6-NH<sub>2</sub> (DA6) is a novel antimicrobial peptide (AMP) that exhibits high efficacy against various bacterial strains, particularly <em>S. aureus</em>, by disrupting its membrane through an as-yet-unknown mechanism. We employed <em>in vivo</em> <sup>2</sup>H solid state Nuclear Magnetic Resonance (NMR) to investigate the mode of action of AMPs on deuterated bacteria. This technique provides insights into membrane order and its changes with increasing AMP concentration. Our results enabled us to compare the mechanism of DA6 with those of AMPs with established modes of action. We found that DA6 induces pore formation in the membrane of <em>S. aureus.</em> This protocol serves as a template for determining the mechanisms of action of other peptides, an essential step for developing and patenting such drugs for the treatment of human diseases.</div></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"328 ","pages":"Article 107532"},"PeriodicalIF":2.2,"publicationDate":"2025-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145155943","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 : 2025-09-22DOI: 10.1016/j.bpc.2025.107530
Yuval Ben-Abu
Recent work by Ben Abu and Wolfson introduces the concept of ‘energetic memory’ in ion channels, providing a mechanistic framework for ultrasound neuromodulation. This discussion examines how K2P (two-pore domain potassium) channels serve as primary mediators of mechanosensitive memory due to their small size (0.5 μm radius), constitutive activity, and critical physiological roles. In contrast, larger Kv channels (5 μm) show intermediate sensitivity while Na+ channels (50 μm) remain largely unaffected, creating size-dependent responses. Nanoindentor experiments demonstrate sustained membrane hyperpolarization following mechanical compression, validating the theoretical predictions. The energetic memory model explains ultrasound therapy's clinical efficacy through preferential K2P channel compression, energy system adaptation, and prolonged recovery phases. This framework enables rational optimization of therapeutic protocols and extends to other mechanically-based interventions, fundamentally expanding our understanding of neural plasticity beyond traditional electrical mechanisms.
Ben Abu和Wolfson最近的工作介绍了离子通道中“能量记忆”的概念，为超声神经调节提供了一个机制框架。本文探讨了K2P（双孔结构域钾）通道如何由于其小尺寸（0.5 μm半径）、本构活性和关键的生理作用而成为机械敏感记忆的主要介质。相比之下，较大的Kv通道（5 μm）表现出中等灵敏度，而Na+通道（50 μm）基本不受影响，产生尺寸相关的响应。纳米压痕实验证明了机械压缩后膜的持续超极化，验证了理论预测。能量记忆模型通过优先压缩K2P通道、能量系统适应和延长恢复期来解释超声治疗的临床疗效。该框架能够合理优化治疗方案，并扩展到其他基于机械的干预措施，从根本上扩展了我们对传统电机制之外的神经可塑性的理解。
{"title":"K2P channels and ultrasound neuromodulation: A mechanosensitive memory perspective","authors":"Yuval Ben-Abu","doi":"10.1016/j.bpc.2025.107530","DOIUrl":"10.1016/j.bpc.2025.107530","url":null,"abstract":"<div><div>Recent work by Ben Abu and Wolfson introduces the concept of ‘energetic memory’ in ion channels, providing a mechanistic framework for ultrasound neuromodulation. This discussion examines how K2P (two-pore domain potassium) channels serve as primary mediators of mechanosensitive memory due to their small size (0.5 μm radius), constitutive activity, and critical physiological roles. In contrast, larger Kv channels (5 μm) show intermediate sensitivity while Na<sup>+</sup> channels (50 μm) remain largely unaffected, creating size-dependent responses. Nanoindentor experiments demonstrate sustained membrane hyperpolarization following mechanical compression, validating the theoretical predictions. The energetic memory model explains ultrasound therapy's clinical efficacy through preferential K2P channel compression, energy system adaptation, and prolonged recovery phases. This framework enables rational optimization of therapeutic protocols and extends to other mechanically-based interventions, fundamentally expanding our understanding of neural plasticity beyond traditional electrical mechanisms.</div></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"328 ","pages":"Article 107530"},"PeriodicalIF":2.2,"publicationDate":"2025-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145155941","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 : 2025-09-22DOI: 10.1016/j.bpc.2025.107529
Jing Zhang, Qiang Ma, Honghui Wang, Bin Chen, Yan Li, Yingmin Liao
The rubber antioxidant, N-(1,3-dimethylbutyl)-N′-phenyl-p-phenylenediamine (6-PPD), as an emerging pollutant, is receiving more and more attention recently. This study investigated the intermolecular interactions of 6-PPD with two key biological macromolecules, human serum albumin (HSA) and alpha-glucosidase (AG), to understand the transport and toxic effects of 6-PPD. Using multiple spectroscopic methods and molecular docking technology, the results demonstrated that 6-PPD could bind to both HSA and AG, thereby inducing fluorescence quenching and conformational changes in both proteins. The binding constants were determined to be (5.93 ± 0.20) × 105 and (3.17 ± 0.15) × 104 L mol−1 respectively for HSA-6-PPD and AG-6-PPD systems at 298 K, revealing strong binding affinities. Molecular docking identified specific binding sites and non-covalent interactions of the two systems. MD and Energy decomposition analysis revealed the dynamics conformational changes of the complexes and identified van der Waals and electrostatic interactions as primary binding drivers for both systems, while polar solvation energy impeded complex formation. TYR161, ILE142, and TYR138 dominated HSA-6-PPD stabilization, whereas AG-6-PPD was driven by hydrophobic interactions with TRP1369 and VAL1373, with ARG1377 incurring substantial desolvation penalties. Synchronous fluorescence and circular dichroism spectroscopy indicated that 6-PPD binding did not disrupt the microenvironment of Tyr and Trp residues in HSA and AG, while induced structural alterations in HSA and AG that could affect their physiological function. In-vitro tests showed that 6-PPD inhibited AG activity in a dose-dependent manner, with an IC50 of 8.22 ± 0.44 μmol L−1. ADMET and PASS online tools was used to predict physicochemical properties and multiorgan toxicity. This work provided insights into the transport and molecular toxicity of 6-PPD, highlighting the adverse biological effects associated with this common rubber additive.
{"title":"Molecular insights into the transport and toxicity of 6-PPD: Interactions with human serum albumin and alpha-glucosidase","authors":"Jing Zhang, Qiang Ma, Honghui Wang, Bin Chen, Yan Li, Yingmin Liao","doi":"10.1016/j.bpc.2025.107529","DOIUrl":"10.1016/j.bpc.2025.107529","url":null,"abstract":"<div><div>The rubber antioxidant, <em>N</em>-(1,3-dimethylbutyl)-<em>N</em>′-phenyl-<em>p</em>-phenylenediamine (6-PPD), as an emerging pollutant, is receiving more and more attention recently. This study investigated the intermolecular interactions of 6-PPD with two key biological macromolecules, human serum albumin (HSA) and alpha-glucosidase (AG), to understand the transport and toxic effects of 6-PPD. Using multiple spectroscopic methods and molecular docking technology, the results demonstrated that 6-PPD could bind to both HSA and AG, thereby inducing fluorescence quenching and conformational changes in both proteins. The binding constants were determined to be (5.93 ± 0.20) × 10<sup>5</sup> and (3.17 ± 0.15) × 10<sup>4</sup> L mol<sup>−1</sup> respectively for HSA-6-PPD and AG-6-PPD systems at 298 K, revealing strong binding affinities. Molecular docking identified specific binding sites and non-covalent interactions of the two systems. MD and Energy decomposition analysis revealed the dynamics conformational changes of the complexes and identified van der Waals and electrostatic interactions as primary binding drivers for both systems, while polar solvation energy impeded complex formation. TYR161, ILE142, and TYR138 dominated HSA-6-PPD stabilization, whereas AG-6-PPD was driven by hydrophobic interactions with TRP1369 and VAL1373, with ARG1377 incurring substantial desolvation penalties. Synchronous fluorescence and circular dichroism spectroscopy indicated that 6-PPD binding did not disrupt the microenvironment of Tyr and Trp residues in HSA and AG, while induced structural alterations in HSA and AG that could affect their physiological function. <em>In-vitro</em> tests showed that 6-PPD inhibited AG activity in a dose-dependent manner, with an IC<sub>50</sub> of 8.22 ± 0.44 μmol L<sup>−1</sup>. ADMET and PASS online tools was used to predict physicochemical properties and multiorgan toxicity. This work provided insights into the transport and molecular toxicity of 6-PPD, highlighting the adverse biological effects associated with this common rubber additive.</div></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"328 ","pages":"Article 107529"},"PeriodicalIF":2.2,"publicationDate":"2025-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145155942","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 : 2025-09-10DOI: 10.1016/j.bpc.2025.107526
Tooba Khalid , Hafiz Abdul Rafey , Adnan Amin , Muhammad Kamran , Muhammad Kazim Zargaham , Samir Anis Ross , Shah-Iram Niaz
Diabetes and the related comorbidities have been associated with elevated levels of advanced glycation end products (AGEs). The biochemical process of advanced glycation, is believed to be playing a pivotal role in the development of complications. Since there exists a great deal of promise for natural products offering antidiabetic potential, we studied advanced glycation inhibition and anti-diabetic profile of Phytolacca latbenia (Moq). on fractions and the sorted compounds based on the QSAR and molecular docking analysis. The top two bioactive compounds; Kaempferol and Esculentoside G, were further evaluated for the MD simulation studies at 150 ns run, compared with the standard. Among the tested compounds, Kaempferol presented significant binding energies in MM-GBSA (−48.63 Kcal/mol) and MD simulation studies (73 %) with transcriptional regulator 4F5S. Molecular docking studies revealed that kaempferol formed three hydrogen bonds with Val342, Ser343 and Ser453, along with Pi-Pi stacking and Pi-cation interactions with Trp213 and Arg217 residues of the 4F5S protein. Kaempferol also displayed significant α-glucosidase inhibition (IC50 0.042 ± 2.31 μg/ml) compared to the acarbose (IC50 0.036 ± 0.31 μg/ml). Almost all of the selected compounds demonstrated adherence to the safety requirements established by ADMET investigation. Liquid–liquid partitioning of the crude methanolic extract with solvents of increasing polarity yielded five solvent fractions;the ethyl acetate fraction (ETOA) obtained by liquid–liquid partitioning of the crude extract with ethyl acetate and water proclaimed substantial results in both the non-oxidative (61 %) and oxidative (58 %) antiglycation assays for thiol group estimation. The ethylacetae fraction (ETOA) demonstrated comparatively strong antioxidant activity, with an IC₅₀ value of 13.25 ± 0.69 μg/ml as determined by the DPPH assay. In α-glucosidase assay, Aqueous fraction demonstrated a considerable inhibition with IC50 value of 0.108 ± 0.32 μg /ml compared to the standard (IC50 0.083 ± 0.43 μg/ml). The safety assessment revealed a slight decline in HeLa cell viability, dropping from 82 % at a 2.5 % concentration to 69 % at a 10 % concentration over 24 h, relative to the control.Therefore, Phytolacca latbenia (Moq). and its phytocompounds tested inhibit α-glucosidase and Advanced glycation end product-the process that underlie diabetic complications and may therefore holds great promise as therapeutic agent, with no toxicity concern,against diabetes and related comorbidities.
{"title":"In silico and in vitro characterization of Phytolacca latbenia (Moq.): QSAR, phytochemical, and toxicological insights into antiglycation and antidiabetic potential","authors":"Tooba Khalid , Hafiz Abdul Rafey , Adnan Amin , Muhammad Kamran , Muhammad Kazim Zargaham , Samir Anis Ross , Shah-Iram Niaz","doi":"10.1016/j.bpc.2025.107526","DOIUrl":"10.1016/j.bpc.2025.107526","url":null,"abstract":"<div><div>Diabetes and the related comorbidities have been associated with elevated levels of advanced glycation end products (AGEs). The biochemical process of advanced glycation, is believed to be playing a pivotal role in the development of complications. Since there exists a great deal of promise for natural products offering antidiabetic potential, we studied advanced glycation inhibition and anti-diabetic profile of <em>Phytolacca latbenia (Moq)</em>. on fractions and the sorted compounds based on the QSAR and molecular docking analysis. The top two bioactive compounds; Kaempferol and Esculentoside G, were further evaluated for the MD simulation studies at 150 ns run, compared with the standard. Among the tested compounds, Kaempferol presented significant binding energies in MM-GBSA (−48.63 Kcal/mol) and MD simulation studies (73 %) with transcriptional regulator 4F5S. Molecular docking studies revealed that kaempferol formed three hydrogen bonds with Val342, Ser343 and Ser453, along with Pi-Pi stacking and Pi-cation interactions with Trp213 and Arg217 residues of the 4F5S protein. Kaempferol also displayed significant α-glucosidase inhibition (IC<sub>50</sub> 0.042 ± 2.31 μg/ml) compared to the acarbose (IC<sub>50</sub> 0.036 ± 0.31 μg/ml). Almost all of the selected compounds demonstrated adherence to the safety requirements established by ADMET investigation. Liquid–liquid partitioning of the crude methanolic extract with solvents of increasing polarity yielded five solvent fractions;the ethyl acetate fraction (ETOA) obtained by liquid–liquid partitioning of the crude extract with ethyl acetate and water proclaimed substantial results in both the non-oxidative (61 %) and oxidative (58 %) antiglycation assays for thiol group estimation. The ethylacetae fraction (ETOA) demonstrated comparatively strong antioxidant activity, with an IC₅₀ value of 13.25 ± 0.69 μg/ml as determined by the DPPH assay. In α-glucosidase assay, Aqueous fraction demonstrated a considerable inhibition with IC<sub>50</sub> value of 0.108 ± 0.32 μg /ml compared to the standard (IC<sub>50</sub> 0.083 ± 0.43 μg/ml). The safety assessment revealed a slight decline in HeLa cell viability, dropping from 82 % at a 2.5 % concentration to 69 % at a 10 % concentration over 24 h, relative to the control.Therefore, <em>Phytolacca latbenia (Moq)</em>. and its phytocompounds tested inhibit α-glucosidase and Advanced glycation end product-the process that underlie diabetic complications and may therefore holds great promise as therapeutic agent, with no toxicity concern,against diabetes and related comorbidities.</div></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"328 ","pages":"Article 107526"},"PeriodicalIF":2.2,"publicationDate":"2025-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145097050","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}
Silver nanoparticles (AgNPs) synthesized through green chemistry approaches offer a sustainable alternative to conventional methods, with potential applications in various biological fields. In this study, we report the synthesis of AgNPs using terpenoids derived from Ipomoea hederifolia L. (Convolvulaceae). The AgNPs (AgNPs-T) were characterized using UV–Vis spectroscopy, which revealed a surface plasmon resonance (SPR) peak at 452 nm, confirming successful synthesis. Fourier-transform infrared spectroscopy (FTIR) analysis identified functional groups such as hydroxyl and carbonyl that facilitated the reduction of silver ions and acted as stabilizing agents. Transmission electron microscopy (TEM) showed that the AgNPs-T were spherical in shape, with sizes ranging from 4 to 20 nm, and were well-dispersed due to the presence of capping agents from the plant extract. The biological activities of AgNPs-T were evaluated, showcasing potent antibacterial activity against several human pathogenic bacteria. Additionally, AgNPs-T exhibited significant antibiofilm and anti-quorum sensing activities, disrupting biofilm formation and inhibiting bacterial communication. The nanoparticles also demonstrated strong antioxidant properties by scavenging DPPH radicals in a dose-dependent manner. Moreover, cytotoxicity studies using the MTT assay revealed that AgNPs-T exerted dose-dependent anticancer effects against breast cancer (MCF-7) cells. These findings suggest that Ipomoea hederifolia-derived AgNPs possess multifunctional biological activities, making them promising candidates for applications in antimicrobial, antioxidant, and anticancer therapies.
{"title":"Sustainable synthesis and functional profiling of Ipomoea hederifolia-derived terpenoids-assisted silver nanoparticles: Mechanistic insights into anticancer, antioxidant, antibiofilm, and anti-quorum sensing activities","authors":"Khushboo Makwana , Reem Binsuwaidan , Mohd Adnan , Nawaf Alshammari , Mitesh Patel","doi":"10.1016/j.bpc.2025.107524","DOIUrl":"10.1016/j.bpc.2025.107524","url":null,"abstract":"<div><div>Silver nanoparticles (AgNPs) synthesized through green chemistry approaches offer a sustainable alternative to conventional methods, with potential applications in various biological fields. In this study, we report the synthesis of AgNPs using terpenoids derived from <em>Ipomoea hederifolia</em> L. (Convolvulaceae). The AgNPs (AgNPs-T) were characterized using UV–Vis spectroscopy, which revealed a surface plasmon resonance (SPR) peak at 452 nm, confirming successful synthesis. Fourier-transform infrared spectroscopy (FTIR) analysis identified functional groups such as hydroxyl and carbonyl that facilitated the reduction of silver ions and acted as stabilizing agents. Transmission electron microscopy (TEM) showed that the AgNPs-T were spherical in shape, with sizes ranging from 4 to 20 nm, and were well-dispersed due to the presence of capping agents from the plant extract. The biological activities of AgNPs-T were evaluated, showcasing potent antibacterial activity against several human pathogenic bacteria. Additionally, AgNPs-T exhibited significant antibiofilm and anti-quorum sensing activities, disrupting biofilm formation and inhibiting bacterial communication. The nanoparticles also demonstrated strong antioxidant properties by scavenging DPPH radicals in a dose-dependent manner. Moreover, cytotoxicity studies using the MTT assay revealed that AgNPs-T exerted dose-dependent anticancer effects against breast cancer (MCF-7) cells. These findings suggest that <em>Ipomoea hederifolia</em>-derived AgNPs possess multifunctional biological activities, making them promising candidates for applications in antimicrobial, antioxidant, and anticancer therapies.</div></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"328 ","pages":"Article 107524"},"PeriodicalIF":2.2,"publicationDate":"2025-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145019315","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 : 2025-09-04DOI: 10.1016/j.bpc.2025.107525
Milad Amiri , Mohammad Javad Masroor , S. Shirin Shahangian , Reza H. Sajedi , Bijan Ranjbar
A comprehensive understanding of the molecular mechanism underlying the Liquid-Liquid Phase Separation (LLPS) pathway of LCD-TDP43 remains a challenge in the context of its neuropathogenesis. The primary driving force behind the TDP-43 LLPS is the interplay of hydrophobic interactions reinforced by aromatic residues. This study presents a novel, convenient, sensitive, and probe-free approach using excitation-emission matrix (EEM) fluorescence to monitor the microenvironment of aromatic residues and π-π stacking interactions during different stages of the LLPS pathway. Protein local structuring and the alterations in the positions of aromatic residues, individually and collectively, were detected by this life-time 3D fingerprinting. A new intermediate state with a unique α-sheet structure in the liquid droplet state and other transient species up to amyloid fibrils was discovered by CD and FTIR analyses. This structure with an inherent tendency for transition to β-amyloids, has not previously been reported in the context of LCD-TDP43 nor other LLPS-prone proteins. Mapping of hydrophobic clustering during phase separation revealed a continuous increase, accompanied by different surrounding polarities. The formation of distinct protein species within the LLPS pathway (from monomer to fibril), along with the amyloidogenic nature of TDP-43 fibrillation, was also confirmed by AFM analysis and ThT assay. To conclude, the 3D fluorescence method introduced in this study provides an effective and straightforward approach to critical valuable insights into the key π-π interactions in the LLPS-dependent aggregation pathway of LCD-containing IDPs. The novel identification of the α-sheet non-fibrilar intermediates may provide a new perspective for elucidating the aggregation mechanism of these proteins.
{"title":"Mapping the structural changes of LCD-TDP43 during the liquid-liquid phase separation by different spectroscopic platforms","authors":"Milad Amiri , Mohammad Javad Masroor , S. Shirin Shahangian , Reza H. Sajedi , Bijan Ranjbar","doi":"10.1016/j.bpc.2025.107525","DOIUrl":"10.1016/j.bpc.2025.107525","url":null,"abstract":"<div><div>A comprehensive understanding of the molecular mechanism underlying the Liquid-Liquid Phase Separation (LLPS) pathway of LCD-TDP43 remains a challenge in the context of its neuropathogenesis. The primary driving force behind the TDP-43 LLPS is the interplay of hydrophobic interactions reinforced by aromatic residues. This study presents a novel, convenient, sensitive, and probe-free approach using excitation-emission matrix (EEM) fluorescence to monitor the microenvironment of aromatic residues and π-π stacking interactions during different stages of the LLPS pathway. Protein local structuring and the alterations in the positions of aromatic residues, individually and collectively, were detected by this life-time 3D fingerprinting. A new intermediate state with a unique α-sheet structure in the liquid droplet state and other transient species up to amyloid fibrils was discovered by CD and FTIR analyses. This structure with an inherent tendency for transition to β-amyloids, has not previously been reported in the context of LCD-TDP43 nor other LLPS-prone proteins. Mapping of hydrophobic clustering during phase separation revealed a continuous increase, accompanied by different surrounding polarities. The formation of distinct protein species within the LLPS pathway (from monomer to fibril), along with the amyloidogenic nature of TDP-43 fibrillation, was also confirmed by AFM analysis and ThT assay. To conclude, the 3D fluorescence method introduced in this study provides an effective and straightforward approach to critical valuable insights into the key π-π interactions in the LLPS-dependent aggregation pathway of LCD-containing IDPs. The novel identification of the α-sheet non-fibrilar intermediates may provide a new perspective for elucidating the aggregation mechanism of these proteins.</div></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"328 ","pages":"Article 107525"},"PeriodicalIF":2.2,"publicationDate":"2025-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145007648","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}
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}
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