Pub Date : 2025-12-04DOI: 10.1016/j.bbagen.2025.130894
Marina Hembecker , Diogo Henrique Kita , Azam Rashidian , Luis C. Vesga , Bruna Estelita Ruginsk , Arnold R. Romero Bohórquez , Stelia Carolina Mendez-Sanchez , Vinicius Goncalves Maltarollo , Fabiane Gomes de Moraes Rego , Geraldo Picheth , Antti Poso , Katalin Goda , Suresh V. Ambudkar , Vivian Rotuno Moure , Thales Kronenberger , Glaucio Valdameri
Cancer treatment is challenged by the emergence of multidrug resistance (MDR). MDR is often caused by the overexpression of certain ABC transporters, such as P-glycoprotein (P-gp, ABCB1) in the plasma membrane of tumor cells and tumor stem cells. Inhibition of ABC transporter-mediated efflux of anticancer drugs might be a plausible approach to overcome MDR. Here, we studied the interaction of 16 tetrahydroquinoline/4,5-dihydroisoxazole derivatives (A1 - D4) with human P-gp to identify and characterize new P-gp inhibitors. We found that compounds C1 and D1 inhibited the P-gp-mediated efflux of rhodamine 123 (R123), with IC50 values of 41.5 and 6.6 μM, respectively. Both compounds showed low cytotoxicity on NIH3T3 and NIH3T3-ABCB1 cells over a broad concentration range. Interestingly, C1 and D1 increased the ATPase activity of P-gp at sub-micromolar concentrations, showing EC50 values of 0.17 and 0.62 μM, respectively. However, thermal inactivation and UIC2 reactivity assays supported that, similar to potent P-gp inhibitors, C1 and D1 can hinder the dimerization of the nucleotide binding domains (NBDs), when applied at higher concentrations (≥10 μM). In addition, docking studies showed that D1 preferentially interacts with the central substrate binding cavity of P-gp. Finally, D1 chemosensitized drug-resistant KB-V1 cells overexpressing P-gp. In view of our previous findings that C1 and D1 also inhibit ABCG2 and MRP1, they can be considered as novel pan-ABC transporter inhibitors offering potential for treating chemotherapy-resistant tumors.
{"title":"Tetrahydroquinoline/4,5-dihydroisoxazoline derivatives counteract multidrug resistance in cancer cells by inhibiting P-glycoprotein (ABCB1)-mediated transport","authors":"Marina Hembecker , Diogo Henrique Kita , Azam Rashidian , Luis C. Vesga , Bruna Estelita Ruginsk , Arnold R. Romero Bohórquez , Stelia Carolina Mendez-Sanchez , Vinicius Goncalves Maltarollo , Fabiane Gomes de Moraes Rego , Geraldo Picheth , Antti Poso , Katalin Goda , Suresh V. Ambudkar , Vivian Rotuno Moure , Thales Kronenberger , Glaucio Valdameri","doi":"10.1016/j.bbagen.2025.130894","DOIUrl":"10.1016/j.bbagen.2025.130894","url":null,"abstract":"<div><div>Cancer treatment is challenged by the emergence of multidrug resistance (MDR). MDR is often caused by the overexpression of certain ABC transporters, such as P-glycoprotein (P-gp, ABCB1) in the plasma membrane of tumor cells and tumor stem cells. Inhibition of ABC transporter-mediated efflux of anticancer drugs might be a plausible approach to overcome MDR. Here, we studied the interaction of 16 tetrahydroquinoline/4,5-dihydroisoxazole derivatives (<strong>A1</strong> - <strong>D4</strong>) with human P-gp to identify and characterize new P-gp inhibitors. We found that compounds <strong>C1</strong> and <strong>D1</strong> inhibited the P-gp-mediated efflux of rhodamine 123 (R123), with IC<sub>50</sub> values of 41.5 and 6.6 μM, respectively. Both compounds showed low cytotoxicity on NIH3T3 and NIH3T3-<em>ABCB1</em> cells over a broad concentration range. Interestingly, <strong>C1</strong> and <strong>D1</strong> increased the ATPase activity of P-gp at sub-micromolar concentrations, showing EC<sub>50</sub> values of 0.17 and 0.62 μM, respectively. However, thermal inactivation and UIC2 reactivity assays supported that, similar to potent P-gp inhibitors, <strong>C1</strong> and <strong>D1</strong> can hinder the dimerization of the nucleotide binding domains (NBDs), when applied at higher concentrations (≥10 μM). In addition, docking studies showed that <strong>D1</strong> preferentially interacts with the central substrate binding cavity of P-gp. Finally, <strong>D1</strong> chemosensitized drug-resistant KB-V1 cells overexpressing P-gp. In view of our previous findings that <strong>C1</strong> and <strong>D1</strong> also inhibit ABCG2 and MRP1, they can be considered as novel pan-ABC transporter inhibitors offering potential for treating chemotherapy-resistant tumors.</div></div>","PeriodicalId":8800,"journal":{"name":"Biochimica et biophysica acta. General subjects","volume":"1870 2","pages":"Article 130894"},"PeriodicalIF":2.2,"publicationDate":"2025-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145696023","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 : 2025-12-04DOI: 10.1016/j.bbagen.2025.130893
Ahmed M. Abu-Dief , Samar B. Mohamed , Mehran Feizi-Dehnayebi , Inam Omar , Manara A. Ayoub , Maher Fathalla , Mahmoud Abd El Aleem Ali Ali El-Remaily
In this study, novel bioactive metal complexes of Cu (II), Co (II), and Ni (II) were synthesized using a guanidine-based ligand, 1,3-benzoxazole-2-yl-guanidine (L). The resulting coordination compounds [Cu(L)(CH₃COO)₂(H₂O)]·2H₂O, [Co(L)(NO₃)₂(H₂O)]·3H₂O, and [Ni(L)(NO₃)₂(H₂O)]·H₂O were comprehensively characterized using a range of physicochemical and spectroscopic techniques, including UV–visible spectrophotometry, FT-IR spectroscopy, elemental analysis, molar conductance, MS analysis, TGA, and magnetic measurements. The collected data support the formation of octahedral geometries around the metal centers, highlighting the ligand's flexible coordination behavior. Density functional theory (DFT) calculations were employed to optimize the molecular structures and support the experimental findings. Solution characterization established stoichiometric relationships, equilibrium constants, and pH-dependent properties, indicating their robustness in aqueous environments. The biological potential of the synthesized compounds was further evaluated through in vitro cytotoxicity assays (MTT) against HepG2 (liver), MCF-7 (breast), and HCT-116 (colon) cancer cell lines. Among the tested compounds, the Cu (II)-L complex exhibited the most pronounced antiproliferative activity, particularly against MCF-7 cells. Antioxidant capacity, assessed via DPPH radical scavenging assay, confirmed the strong free-radical neutralizing potential of the metal chelates. Antimicrobial investigations demonstrated broad-spectrum activity against various pathogenic strains, including S. marcescens, M. luteus, E. coli, C. albicans, A. flavus, and F. oxysporum. Notably, the copper complex exhibited significant antibacterial activity against M. luteus and potent antifungal effects against F.oxysporum. These effects highlight the therapeutic promise of guanidine-derived metal chelates as multifunctional agents with potential applications in anticancer, antioxidant, and antimicrobial therapies.
{"title":"Development of benzoxazole-2-yl-guanidine based Cu (II), Co (II), and Ni (II) complexes: Structural features, physicochemical aspects underpinning their pharmaceutical potential supported with theoretical approaches","authors":"Ahmed M. Abu-Dief , Samar B. Mohamed , Mehran Feizi-Dehnayebi , Inam Omar , Manara A. Ayoub , Maher Fathalla , Mahmoud Abd El Aleem Ali Ali El-Remaily","doi":"10.1016/j.bbagen.2025.130893","DOIUrl":"10.1016/j.bbagen.2025.130893","url":null,"abstract":"<div><div>In this study, novel bioactive metal complexes of Cu (II), Co (II), and Ni (II) were synthesized using a guanidine-based ligand, 1,3-benzoxazole-2-yl-guanidine (L). The resulting coordination compounds [Cu(L)(CH₃COO)₂(H₂O)]·2H₂O, [Co(L)(NO₃)₂(H₂O)]·3H₂O, and [Ni(L)(NO₃)₂(H₂O)]·H₂O were comprehensively characterized using a range of physicochemical and spectroscopic techniques, including UV–visible spectrophotometry, FT-IR spectroscopy, elemental analysis, molar conductance, MS analysis, TGA, and magnetic measurements. The collected data support the formation of octahedral geometries around the metal centers, highlighting the ligand's flexible coordination behavior. Density functional theory (DFT) calculations were employed to optimize the molecular structures and support the experimental findings. Solution characterization established stoichiometric relationships, equilibrium constants, and pH-dependent properties, indicating their robustness in aqueous environments. The biological potential of the synthesized compounds was further evaluated through in vitro cytotoxicity assays (MTT) against HepG2 (liver), MCF-7 (breast), and HCT-116 (colon) cancer cell lines. Among the tested compounds, the Cu (II)-L complex exhibited the most pronounced antiproliferative activity, particularly against MCF-7 cells. Antioxidant capacity, assessed via DPPH radical scavenging assay, confirmed the strong free-radical neutralizing potential of the metal chelates. Antimicrobial investigations demonstrated broad-spectrum activity against various pathogenic strains, including <em>S. marcescens</em>, <em>M. luteus</em>, <em>E. coli</em>, <em>C. albicans, A. flavus</em>, and <em>F. oxysporum</em>. Notably, the copper complex exhibited significant antibacterial activity against <em>M. luteus</em> and potent antifungal effects against <em>F.oxysporum</em>. These effects highlight the therapeutic promise of guanidine-derived metal chelates as multifunctional agents with potential applications in anticancer, antioxidant, and antimicrobial therapies.</div></div>","PeriodicalId":8800,"journal":{"name":"Biochimica et biophysica acta. General subjects","volume":"1870 2","pages":"Article 130893"},"PeriodicalIF":2.2,"publicationDate":"2025-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145686563","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 : 2025-11-27DOI: 10.1016/j.bbagen.2025.130891
Takashi Miyano, Haruka Hasegawa, Toshihiro Sera
Hyperglycemia is a well-recognized cause of osteoblast dysfunction. Recent evidence, however, indicates that elevated extracellular osmolarity associated with hyperglycemia may independently impair osteogenic differentiation. However, the mechanisms underlying these effects remain poorly understood. In this study, we examined how osmotic stress influences osteoblast differentiation, with a focus on actin cytoskeletal remodeling and subcellular localization of the Yes-associated protein (YAP), a mechanosensitive transcriptional coactivator involved in osteogenesis. Using MC3T3-E1 pre-osteoblasts, we found that osteogenic induction enhanced cell proliferation, migration, nuclear deformation, and nuclear translocation of YAP, accompanied by upregulated expression of genes encoding osteogenic markers. In contrast, treatment with either glucose or mannitol, used to isolate the osmotic component of hyperglycemia, preserved nuclear morphology, decreased nuclear localization of YAP, and led to perinuclear actin accumulation, as confirmed by radial profile analysis of actin distribution. These effects were accompanied by downregulation of target genes of YAP and reduction in alkaline phosphatase (ALP)-positive cells. Similar effects observed following treatments with both glucose and mannitol suggest that the impairment arises primarily from osmotic stress rather than from glucose-specific metabolic signaling. Notably, pharmacological inhibition of Rho-associated kinase using Y-27632 attenuated perinuclear actin accumulation, restored nuclear translocation of YAP, and rescued the expression of YAP-dependent osteogenic genes under osmotic conditions. Y-27632 also increased the number of ALP-positive cells after treatment with both glucose and mannitol. These findings underscore cytoskeletal remodeling as a central regulator of YAP activity and osteogenesis under osmotic stress, and propose potential therapeutic targets for skeletal fragility in diabetes.
{"title":"Osmotic stress suppresses osteogenic differentiation by inhibiting nuclear translocation of YAP via perinuclear actin accumulation","authors":"Takashi Miyano, Haruka Hasegawa, Toshihiro Sera","doi":"10.1016/j.bbagen.2025.130891","DOIUrl":"10.1016/j.bbagen.2025.130891","url":null,"abstract":"<div><div>Hyperglycemia is a well-recognized cause of osteoblast dysfunction. Recent evidence, however, indicates that elevated extracellular osmolarity associated with hyperglycemia may independently impair osteogenic differentiation. However, the mechanisms underlying these effects remain poorly understood. In this study, we examined how osmotic stress influences osteoblast differentiation, with a focus on actin cytoskeletal remodeling and subcellular localization of the Yes-associated protein (YAP), a mechanosensitive transcriptional coactivator involved in osteogenesis. Using MC3T3-E1 pre-osteoblasts, we found that osteogenic induction enhanced cell proliferation, migration, nuclear deformation, and nuclear translocation of YAP, accompanied by upregulated expression of genes encoding osteogenic markers. In contrast, treatment with either glucose or mannitol, used to isolate the osmotic component of hyperglycemia, preserved nuclear morphology, decreased nuclear localization of YAP, and led to perinuclear actin accumulation, as confirmed by radial profile analysis of actin distribution. These effects were accompanied by downregulation of target genes of YAP and reduction in alkaline phosphatase (ALP)-positive cells. Similar effects observed following treatments with both glucose and mannitol suggest that the impairment arises primarily from osmotic stress rather than from glucose-specific metabolic signaling. Notably, pharmacological inhibition of Rho-associated kinase using Y-27632 attenuated perinuclear actin accumulation, restored nuclear translocation of YAP, and rescued the expression of YAP-dependent osteogenic genes under osmotic conditions. Y-27632 also increased the number of ALP-positive cells after treatment with both glucose and mannitol. These findings underscore cytoskeletal remodeling as a central regulator of YAP activity and osteogenesis under osmotic stress, and propose potential therapeutic targets for skeletal fragility in diabetes.</div></div>","PeriodicalId":8800,"journal":{"name":"Biochimica et biophysica acta. General subjects","volume":"1870 2","pages":"Article 130891"},"PeriodicalIF":2.2,"publicationDate":"2025-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145628462","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}
Ursolic acid (UA) has emerged as a promising bioactive compound with potential therapeutic effects, particularly in the upregulation of SIRT6, an important protein involved in various cellular processes, including longevity, stress response, and metabolism. Despite the growing interest in UA and its beneficial biological activities, the precise mechanisms governing its interaction with SIRT6 remain inadequately elucidated. This study aims to conduct a comprehensive investigation into the binding affinity of UA to SIRT6, as well as its effects on the protein's stability, kinetics, and structural characteristics.
Molecular dynamics simulations using Schrodinger software analyzed parameters such as radius of gyration, RMSD, RMSF, and binding energy. The SIRT6 gene was cloned into the pET28a vector, expressed in Escherichia coli, and purified via affinity chromatography. Kinetic parameters (Km, Vmax, and Kcat) were assessed using fluorescence enzyme assays, while structural modifications were examined via fluorescence spectroscopy, FTIR, and UV–visible spectrophotometry.
UA significantly enhances SIRT6 stability, reducing its radius of gyration and lowering binding energy from −25.38 to −47.93 kcal/mol. Kinetic analysis revealed a decrease in Km (13 to 10), an increase in Vmax (5013.42 to 9421.48 μM/min), and a rise in Kcat (15.03/s to 281.01/s), improving the Kcat/Km ratio. Structural assessments confirmed UA-induced modifications, increasing alpha-helix content (8.5 % to 26.2 %) and elevating the folding ratio from 0.066 to 14.8. However, it decreased aggregation index from 402.38 to 81.25. This integrative study elucidates UA's molecular influence on SIRT6, underscoring its potential therapeutic relevance across various signaling pathways.
{"title":"Ursolic acid activates SIRT6 by enhancing enzyme-substrate interactions and promoting protein structural rearrangement","authors":"Zohreh Tabatabaian Nimavard , Nuredin Bakhtiari , Fereshteh Taghavi , Sako Mirzaie , Farangis Ataei , Hamid-Reza Khaledi","doi":"10.1016/j.bbagen.2025.130890","DOIUrl":"10.1016/j.bbagen.2025.130890","url":null,"abstract":"<div><div>Ursolic acid (UA) has emerged as a promising bioactive compound with potential therapeutic effects, particularly in the upregulation of SIRT6, an important protein involved in various cellular processes, including longevity, stress response, and metabolism. Despite the growing interest in UA and its beneficial biological activities, the precise mechanisms governing its interaction with SIRT6 remain inadequately elucidated. This study aims to conduct a comprehensive investigation into the binding affinity of UA to SIRT6, as well as its effects on the protein's stability, kinetics, and structural characteristics.</div><div>Molecular dynamics simulations using Schrodinger software analyzed parameters such as radius of gyration, RMSD, RMSF, and binding energy. The SIRT6 gene was cloned into the pET28a vector, expressed in <em>Escherichia coli</em>, and purified via affinity chromatography. Kinetic parameters (Km, Vmax, and Kcat) were assessed using fluorescence enzyme assays, while structural modifications were examined via fluorescence spectroscopy, FTIR, and UV–visible spectrophotometry.</div><div>UA significantly enhances SIRT6 stability, reducing its radius of gyration and lowering binding energy from −25.38 to −47.93 kcal/mol. Kinetic analysis revealed a decrease in Km (13 to 10), an increase in Vmax (5013.42 to 9421.48 μM/min), and a rise in Kcat (15.03/s to 281.01/s), improving the Kcat/Km ratio. Structural assessments confirmed UA-induced modifications, increasing alpha-helix content (8.5 % to 26.2 %) and elevating the folding ratio from 0.066 to 14.8. However, it decreased aggregation index from 402.38 to 81.25. This integrative study elucidates UA's molecular influence on SIRT6, underscoring its potential therapeutic relevance across various signaling pathways.</div></div>","PeriodicalId":8800,"journal":{"name":"Biochimica et biophysica acta. General subjects","volume":"1870 2","pages":"Article 130890"},"PeriodicalIF":2.2,"publicationDate":"2025-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145623196","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}
Cavin family proteins alter the invasiveness of tumor cells. However, research on the pathogenesis of Cavins in tumors is lacking. To address this knowledge-gap, we conducted a systematic analysis about the mechanism of action of Cavins in cancer. We evaluated the diagnostic value of Cavin-3 and its potential as a new therapeutic target for lung squamous cell carcinoma (LUSC). Bioinformatic analysis showed that Cavin-3 can inhibit LUSC tumor cells by regulating the expression of EREG and IL1A, thereby activating the MAPK pathway to promote the release of tumor necrosis factor (TNF) and other inflammatory factors. Moreover, in vitro experiments have shown that Cavin-3 may promote the expression of inflammatory factors by regulating the MAPK signaling pathway, thereby killing tumor cells and inhibiting tumor proliferation.
{"title":"Cavin-3 promotes TNF expression via the MAPK signaling pathway in lung squamous cell carcinoma","authors":"Xiaoyan Xu , Yonghong Nie , Jiatuo Xu , Rilei Jiang","doi":"10.1016/j.bbagen.2025.130892","DOIUrl":"10.1016/j.bbagen.2025.130892","url":null,"abstract":"<div><div>Cavin family proteins alter the invasiveness of tumor cells. However, research on the pathogenesis of Cavins in tumors is lacking. To address this knowledge-gap, we conducted a systematic analysis about the mechanism of action of Cavins in cancer. We evaluated the diagnostic value of Cavin-3 and its potential as a new therapeutic target for lung squamous cell carcinoma (LUSC). Bioinformatic analysis showed that Cavin-3 can inhibit LUSC tumor cells by regulating the expression of EREG and IL1A, thereby activating the MAPK pathway to promote the release of tumor necrosis factor (TNF) and other inflammatory factors. Moreover, in vitro experiments have shown that Cavin-3 may promote the expression of inflammatory factors by regulating the MAPK signaling pathway, thereby killing tumor cells and inhibiting tumor proliferation.</div></div>","PeriodicalId":8800,"journal":{"name":"Biochimica et biophysica acta. General subjects","volume":"1870 2","pages":"Article 130892"},"PeriodicalIF":2.2,"publicationDate":"2025-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145628483","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}
Chromatin structure and its plasticity are central to gene regulation and DNA-associated processes, yet their nanoscale architecture and dynamic assembly remain elusive. Here, we propose a novel in situ approach—combining hypotonic treatment with high-drop spreading—to obtain native, naked chromosomes and visualize chromatin fine structure using atomic force microscopy (AFM). This strategy enables minimally invasive observation of chromatin under near-physiological conditions. We reveal that chromatin is composed of ∼10 nm DNA–histone particles as its fundamental units. Strikingly, these particles exhibit remarkable structural plasticity, dynamically assembling into heterogeneous nucleosome-beaded chains through stacking and partial melting. This challenges the classical “beads-on-a-string” model by demonstrating that chromatin is neither uniform nor static, but structurally versatile at the nanoscale. In addition, we investigated how histone acetylation and ATP modulate chromatin plasticity. Our findings highlight the coexistence of core particle stability and spatial-temporal variability, providing a revised molecular framework for chromatin's functional adaptability. These insights offer a fresh perspective on how chromatin structural diversity underpins its complex regulatory capacity.
{"title":"Decoding chromatin nanoscale plasticity in situ: Insights from native AFM imaging","authors":"Hongfeng Cui, Yu Zhang, Tianyu Chen, Mengzhu Guo, Qi Wen, Jiawei Peng, Yifei Yang, Xian Hao","doi":"10.1016/j.bbagen.2025.130887","DOIUrl":"10.1016/j.bbagen.2025.130887","url":null,"abstract":"<div><div>Chromatin structure and its plasticity are central to gene regulation and DNA-associated processes, yet their nanoscale architecture and dynamic assembly remain elusive. Here, we propose a novel <em>in situ</em> approach—combining hypotonic treatment with high-drop spreading—to obtain native, naked chromosomes and visualize chromatin fine structure using atomic force microscopy (AFM). This strategy enables minimally invasive observation of chromatin under near-physiological conditions. We reveal that chromatin is composed of ∼10 nm DNA–histone particles as its fundamental units. Strikingly, these particles exhibit remarkable structural plasticity, dynamically assembling into heterogeneous nucleosome-beaded chains through stacking and partial melting. This challenges the classical “beads-on-a-string” model by demonstrating that chromatin is neither uniform nor static, but structurally versatile at the nanoscale. In addition, we investigated how histone acetylation and ATP modulate chromatin plasticity. Our findings highlight the coexistence of core particle stability and spatial-temporal variability, providing a revised molecular framework for chromatin's functional adaptability. These insights offer a fresh perspective on how chromatin structural diversity underpins its complex regulatory capacity.</div></div>","PeriodicalId":8800,"journal":{"name":"Biochimica et biophysica acta. General subjects","volume":"1870 1","pages":"Article 130887"},"PeriodicalIF":2.2,"publicationDate":"2025-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145562483","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}
In this study we expressed, purified and demonstrated the protein liquid-liquid phase separation (LLPS) formation by the receptor binding domain (RBD) of coronavirus spike protein in vitro.
Our molecular dynamics simulations revealed multiple structurally disordered regions lacking secondary structural elements within RBD that exhibited high structural flexibility with deviations as high as 6 Å over 500 ns in support of our in vitro findings.
Additionally these disordered regions overlap with epitopes potentially altering their architecture.
Based on these results we conclude that the structural disorderedness of RBD causes LLPS formation in vitro and may potentially challenge the COVID-19 vaccine efficacy.
{"title":"Receptor binding domain of SARS CoV2 spike protein exhibits in vitro liquid-liquid phase separation due to structural disorderedness that may challenge the vaccine-generated antibody binding","authors":"Manikanta Sodasani , Abhinav V.K.S. Grandhi , Niharikha Mukala , Jahnavi Chintalapati , Madhuri Vissapragada , Madhumita Aggunna , Ravikiran S. Yedidi","doi":"10.1016/j.bbagen.2025.130889","DOIUrl":"10.1016/j.bbagen.2025.130889","url":null,"abstract":"<div><div>In this study we expressed, purified and demonstrated the protein liquid-liquid phase separation (LLPS) formation by the receptor binding domain (RBD) of coronavirus spike protein <em>in vitro</em>.</div><div>Our molecular dynamics simulations revealed multiple structurally disordered regions lacking secondary structural elements within RBD that exhibited high structural flexibility with deviations as high as 6 Å over 500 ns in support of our <em>in vitro</em> findings.</div><div>Additionally these disordered regions overlap with epitopes potentially altering their architecture.</div><div>Based on these results we conclude that the structural disorderedness of RBD causes LLPS formation <em>in vitro</em> and may potentially challenge the COVID-19 vaccine efficacy.</div></div>","PeriodicalId":8800,"journal":{"name":"Biochimica et biophysica acta. General subjects","volume":"1870 1","pages":"Article 130889"},"PeriodicalIF":2.2,"publicationDate":"2025-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145572886","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 : 2025-11-19DOI: 10.1016/j.bbagen.2025.130888
Tanaya Chatterjee, Debasmita Sinha
Background
The modern era has witnessed the vast applications of nanoparticles (NPs) ranging from drug delivery to biomedical usages. Herein we report for the first time the effect of gold nanoparticles (AuNPs) of different sizes and shapes on a stress response protein σB from Staphylococcus aureus, the pathogen causing infection. Among the three conserved domains of σB, we focused on Domain 3 which binds to an anti-sigma factor RsbW of S. aureus.
Methods
We explored the interaction of recombinant σB3 (rσB3) with three types of AuNPs; spherical with 10 nm (AuNS10) and 100 nm (AuNS100) diameter and rod shaped (AuNR10). Structural modulations of rσB3 by AuNPs were studied using different biophysical techniques. Native-PAGE was run for rσB3-cRsbW binding assay using AuNR10.
Results
Isothermal titration calorimetry revealed exothermic and endothermic heat changes for rσB3-AuNSs and rσB3-AuNR, respectively. Far-UV CD of rσB3 showed loss of α-helical content with AuNR10 using higher molar ratios of 1:5 and 1:10. Binding to 4,4′-dianilino-1,1′-binaphthyl-5,5′-disulfonic acid (bis-ANS) indicated enhanced fluorescence intensity for rσB3-AuNR10 conjugate, implying unfolding of rσB3 thereby exposing hydrophobic regions. Binding assay of rσB3 with cRsbW displayed impaired protein-protein interaction using rσB3-AuNR10 molar ratio of 1:10. The efficacy of AuNR10 was also observed for the biofilm inhibition by S. aureus.
Conclusions
We show how the size and shape of AuNPs modulate the structure/function of rσB3 of S. aureus.
General significance
Because of the involvement of rσB3 in S. aureus pathogenesis, the structural/functional modulation by AuNR10 could be of therapeutic relevance for nanoparticle-based antibacterial strategies.
{"title":"The effect of gold nanoparticle size and shape on the structure and activity of Domain 3 of an alternative sigma factor of Staphylococcus aureus","authors":"Tanaya Chatterjee, Debasmita Sinha","doi":"10.1016/j.bbagen.2025.130888","DOIUrl":"10.1016/j.bbagen.2025.130888","url":null,"abstract":"<div><h3>Background</h3><div>The modern era has witnessed the vast applications of nanoparticles (NPs) ranging from drug delivery to biomedical usages. Herein we report for the first time the effect of gold nanoparticles (AuNPs) of different sizes and shapes on a stress response protein <em>σ</em><sup><em>B</em></sup> from <em>Staphylococcus aureus,</em> the pathogen causing infection. Among the three conserved domains of <em>σ</em><sup><em>B</em></sup>, we focused on Domain 3 which binds to an anti-sigma factor RsbW of <em>S. aureus</em>.</div></div><div><h3>Methods</h3><div>We explored the interaction of recombinant <em>σ</em><sup><em>B3</em></sup> (r<em>σ</em><sup><em>B3</em></sup>) with three types of AuNPs; spherical with 10 nm (AuNS10) and 100 nm (AuNS100) diameter and rod shaped (AuNR10). Structural modulations of r<em>σ</em><sup><em>B3</em></sup> by AuNPs <em>were</em> studied using different biophysical techniques. Native-PAGE was run for r<em>σ</em><sup><em>B3</em></sup>-cRsbW binding assay using AuNR10.</div></div><div><h3>Results</h3><div>Isothermal titration calorimetry revealed exothermic and endothermic heat changes for r<em>σ</em><sup><em>B3</em></sup>-AuNSs and r<em>σ</em><sup><em>B3</em></sup>-AuNR, respectively. Far-UV CD of r<em>σ</em><sup><em>B3</em></sup> showed loss of α-helical content with AuNR10 using higher molar ratios of 1:5 and 1:10. Binding to 4,4′-dianilino-1,1′-binaphthyl-5,5′-disulfonic acid (bis-ANS) indicated enhanced fluorescence intensity for r<em>σ</em><sup><em>B3</em></sup>-AuNR10 conjugate, implying unfolding of r<em>σ</em><sup><em>B3</em></sup> thereby exposing hydrophobic regions. Binding assay of r<em>σ</em><sup><em>B3</em></sup> with cRsbW displayed impaired protein-protein interaction using r<em>σ</em><sup><em>B3</em></sup>-AuNR10 molar ratio of 1:10. The efficacy of AuNR10 was also observed for the biofilm inhibition by <em>S. aureus.</em></div></div><div><h3>Conclusions</h3><div>We show how the size and shape of AuNPs modulate the structure/function of r<em>σ</em><sup><em>B3</em></sup> of <em>S. aureus</em>.</div></div><div><h3>General significance</h3><div>Because of the involvement of r<em>σ</em><sup><em>B3</em></sup> in <em>S. aureus</em> pathogenesis, the structural/functional modulation by AuNR10 could be of therapeutic relevance for nanoparticle-based antibacterial strategies.</div></div>","PeriodicalId":8800,"journal":{"name":"Biochimica et biophysica acta. General subjects","volume":"1870 1","pages":"Article 130888"},"PeriodicalIF":2.2,"publicationDate":"2025-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145562553","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 : 2025-11-12DOI: 10.1016/j.bbagen.2025.130886
Yulia V. Bertsova, Marina V. Serebryakova, Alexander A. Baykov, Alexander V. Bogachev
Bacteria coping with oxygen deficiency can switch to alternative terminal electron acceptors, which can be normal metabolic intermediates or products of dedicated coupled reactions. In the latter case, the genes for the respective terminal reductase and coupling enzyme are expected to cluster in the genome. Here, we determined the roles of two uncharacterized periplasmic proteins encoded by the swoo_3912–swoo_3913 gene cluster in the facultatively anaerobic marine bacterium Shewanella woodyi. We confirmed the current database annotation of the former protein as “urocanate reductase” but identified the latter protein as a histidine betaine trimethylammonia-lyase (HBTL). HBTL converts histidine betaine into urocanate and trimethylamine and is remarkably specific for histidine betaine as substrate. HBTL requires Mg2+ for activity and undergoes slow reversible inactivation at low Mg2+ concentrations. HBTL activity was not evident in S. woodyi cells grown aerobically but was induced in cells grown anaerobically. Both histidine betaine and urocanate supported anaerobic S. woodyi growth and, hence, respiration. Similar gene clusters are found in many anaerobic bacteria, suggesting a wide occurrence of the anaerobic respiration pathway discovered in this work in the bacterial world.
{"title":"Histidine betaine trimethylammonia-lyase, enzyme coupled with terminal urocanate reductase in Shewanella woodyi grown anaerobically","authors":"Yulia V. Bertsova, Marina V. Serebryakova, Alexander A. Baykov, Alexander V. Bogachev","doi":"10.1016/j.bbagen.2025.130886","DOIUrl":"10.1016/j.bbagen.2025.130886","url":null,"abstract":"<div><div>Bacteria coping with oxygen deficiency can switch to alternative terminal electron acceptors, which can be normal metabolic intermediates or products of dedicated coupled reactions. In the latter case, the genes for the respective terminal reductase and coupling enzyme are expected to cluster in the genome. Here, we determined the roles of two uncharacterized periplasmic proteins encoded by the <em>swoo_3912</em>–<em>swoo_3913</em> gene cluster in the facultatively anaerobic marine bacterium <em>Shewanella woodyi</em>. We confirmed the current database annotation of the former protein as “urocanate reductase” but identified the latter protein as a histidine betaine trimethylammonia-lyase (HBTL). HBTL converts histidine betaine into urocanate and trimethylamine and is remarkably specific for histidine betaine as substrate. HBTL requires Mg<sup>2+</sup> for activity and undergoes slow reversible inactivation at low Mg<sup>2+</sup> concentrations. HBTL activity was not evident in <em>S. woodyi</em> cells grown aerobically but was induced in cells grown anaerobically. Both histidine betaine and urocanate supported anaerobic <em>S. woodyi</em> growth and, hence, respiration. Similar gene clusters are found in many anaerobic bacteria, suggesting a wide occurrence of the anaerobic respiration pathway discovered in this work in the bacterial world.</div></div>","PeriodicalId":8800,"journal":{"name":"Biochimica et biophysica acta. General subjects","volume":"1870 1","pages":"Article 130886"},"PeriodicalIF":2.2,"publicationDate":"2025-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145522421","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 : 2025-11-11DOI: 10.1016/j.bbagen.2025.130885
Neha Attal , Trenton A. Pritt , Melissa Stair , Tony E. Reeves , Iain H. McKillop
Background
Early alcohol-dependent liver disease (ALD) is characterized by increased hepatic fat storage (hepatosteatosis). Fatty acid binding protein 4 (FABP4), a protein not normally expressed in liver, becomes highly expressed in ALD. This study developed a hepatocyte-specific FABP4 mouse knockout (HS-Fabp4−/−) to study liver responses to alcohol.
Methods
An HS-Fabp4−/− mouse was created using a Cre/loxP embryonic stem cell approach. Male and female HS-Fabp4−/− and wildtype (WT; C57Bl/6) mice were maintained on ethanol-drinking water (EtOH-DW) for 4-weeks. Liver damage, triglyceride content and pathology were assessed. Hepatic FABP1–9 mRNA and FABP4 and FABP5 protein were measured. Human hepatoma cell proliferation in response to exogenous FABP4 or FABP5 was analyzed.
Results
Hepatocyte-specific FABP4 deletion was confirmed in HS-Fabp4−/− mice. No gross phenotypic differences were observed between HS-Fabp4−/− and WT. Maintenance on EtOH-DW resulted in microsteatosis, increased hepatic triglycerides, and elevated aspartate and alanine transaminases, with no differences detected between pair-matched HS-Fabp4−/− and WT mice. Hepatic FABP1–9 mRNA analysis revealed increased FABP4 and FABP5 mRNA expression in WT mice, and elevated FABP5 mRNA in HS-Fabp4−/− mice in response to EtOH-DW, effects that were mirrored in serum FABP4/5 protein. Exposure of hepatoma cells to FABP4 or FABP5 revealed FABP4, but not FABP5, stimulated cell proliferation.
Conclusions
Hepatocyte-specific FABP4 deletion does not alter hepatic fat accumulation in response to EtOH feeding. Hepatic FABP4 protein produced in response to EtOH is released from hepatocytes and exogenous FABP4 promotes hepatoma cell proliferation in vitro, an effect not observed for FABP5.
{"title":"Hepatic response to ethanol feeding in a hepatocyte-specific fatty acid binding protein-4 knock out mouse model","authors":"Neha Attal , Trenton A. Pritt , Melissa Stair , Tony E. Reeves , Iain H. McKillop","doi":"10.1016/j.bbagen.2025.130885","DOIUrl":"10.1016/j.bbagen.2025.130885","url":null,"abstract":"<div><h3>Background</h3><div>Early alcohol-dependent liver disease (ALD) is characterized by increased hepatic fat storage (hepatosteatosis). Fatty acid binding protein 4 (FABP4), a protein not normally expressed in liver, becomes highly expressed in ALD. This study developed a hepatocyte-specific FABP4 mouse knockout (HS-<em>Fabp4</em><sup>−/−</sup>) to study liver responses to alcohol.</div></div><div><h3>Methods</h3><div>An HS-<em>Fabp4</em><sup>−/−</sup> mouse was created using a Cre/loxP embryonic stem cell approach. Male and female HS-<em>Fabp4</em><sup>−/−</sup> and wildtype (WT; C57Bl/6) mice were maintained on ethanol-drinking water (EtOH-DW) for 4-weeks. Liver damage, triglyceride content and pathology were assessed. Hepatic FABP1–9 mRNA and FABP4 and FABP5 protein were measured. Human hepatoma cell proliferation in response to exogenous FABP4 or FABP5 was analyzed.</div></div><div><h3>Results</h3><div>Hepatocyte-specific FABP4 deletion was confirmed in HS-<em>Fabp4</em><sup>−/−</sup> mice. No gross phenotypic differences were observed between HS-<em>Fabp4</em><sup>−/−</sup> and WT. Maintenance on EtOH-DW resulted in microsteatosis, increased hepatic triglycerides, and elevated aspartate and alanine transaminases, with no differences detected between pair-matched HS-<em>Fabp4</em><sup>−/−</sup> and WT mice. Hepatic FABP1–9 mRNA analysis revealed increased FABP4 and FABP5 mRNA expression in WT mice, and elevated FABP5 mRNA in HS-<em>Fabp4</em><sup>−/−</sup> mice in response to EtOH-DW, effects that were mirrored in serum FABP4/5 protein. Exposure of hepatoma cells to FABP4 or FABP5 revealed FABP4, but not FABP5, stimulated cell proliferation.</div></div><div><h3>Conclusions</h3><div>Hepatocyte-specific FABP4 deletion does not alter hepatic fat accumulation in response to EtOH feeding. Hepatic FABP4 protein produced in response to EtOH is released from hepatocytes and exogenous FABP4 promotes hepatoma cell proliferation <em>in vitro</em>, an effect not observed for FABP5.</div></div>","PeriodicalId":8800,"journal":{"name":"Biochimica et biophysica acta. General subjects","volume":"1870 1","pages":"Article 130885"},"PeriodicalIF":2.2,"publicationDate":"2025-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145511575","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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