Biophysical chemistry最新文献

{"title":"Thermodynamics and kinetics analysis of lipid-assisted transport of intrinsically disorder proteins.","authors":"Carmelo La Rosa","doi":"10.1016/j.bpc.2025.107504","DOIUrl":"10.1016/j.bpc.2025.107504","url":null,"abstract":"<p><p>Intrinsically disordered proteins (IDPs) are implicated in numerous neurodegenerative diseases, including Alzheimer's, Parkinson's, and type 2 diabetes. Although the amyloid and toxic oligomer hypotheses have provided significant molecular insights into these diseases, they are incomplete in fully explaining the complexity of the observed phenomena. In this study, we propose a new quantitative hypothesis, the lipid-chaperone hypothesis, which postulates a central role for the interaction between IDPs and lipids in the pathogenesis of these diseases. The resulting lipid-protein complex facilitate protein transfer into the cell membrane and the subsequent formation of pores, compromising cellular integrity. To experimentally test this hypothesis, we developed a mathematical model describing the kinetics of pore formation. The model was calibrated using experimental data and allowed us to estimate the kinetic constants and Gibbs free energy associated with the formation of the lipid-protein complex. These results support the hypothesis that the interaction between IDPs and lipids is a crucial event in the pathogenesis of IDP-related diseases and suggest that modulating this interaction could represent a promising therapeutic strategy.</p>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"326 ","pages":"107504"},"PeriodicalIF":2.2,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144803326","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":"Antimicrobial peptide mechanism of action on S. aureus membranes determined by in vivo solid-state NMR","authors":"Laila Zaatouf,&nbsp;Thierry Drujon,&nbsp;Astrid Walrant,&nbsp;Emmanuelle Sachon,&nbsp;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-NH₂ (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> ²H 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}

{"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⁺ 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}

{"title":"Molecular insights into the transport and toxicity of 6-PPD: Interactions with human serum albumin and alpha-glucosidase","authors":"Jing Zhang,&nbsp;Qiang Ma,&nbsp;Honghui Wang,&nbsp;Bin Chen,&nbsp;Yan Li,&nbsp;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) × 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. <em>In-vitro</em> 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.</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}

{"title":"In silico and in vitro characterization of Phytolacca latbenia (Moq.): QSAR, phytochemical, and toxicological insights into antiglycation and antidiabetic potential","authors":"Tooba Khalid ,&nbsp;Hafiz Abdul Rafey ,&nbsp;Adnan Amin ,&nbsp;Muhammad Kamran ,&nbsp;Muhammad Kazim Zargaham ,&nbsp;Samir Anis Ross ,&nbsp;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 (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, <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}

{"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 ,&nbsp;Reem Binsuwaidan ,&nbsp;Mohd Adnan ,&nbsp;Nawaf Alshammari ,&nbsp;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}

{"title":"Mapping the structural changes of LCD-TDP43 during the liquid-liquid phase separation by different spectroscopic platforms","authors":"Milad Amiri ,&nbsp;Mohammad Javad Masroor ,&nbsp;S. Shirin Shahangian ,&nbsp;Reza H. Sajedi ,&nbsp;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}

{"title":"Exploring impact of cold atmospheric plasma directed self-assembly of glycated bovine serum albumin","authors":"Ashim Jyoti Bharati ,&nbsp;Daphishisha Phawa ,&nbsp;Priojeet Daimary ,&nbsp;Monalisa Patra ,&nbsp;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}

{"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 ,&nbsp;Anna C.F. Couto ,&nbsp;Thábata Matos ,&nbsp;Evandro L. Duarte ,&nbsp;M. Teresa Lamy ,&nbsp;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}

{"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 ,&nbsp;Taibah Aldakhil ,&nbsp;Heba Elmansi ,&nbsp;Fathalla Belal ,&nbsp;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_b) 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.</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}