Archives of biochemistry and biophysics最新文献

{"title":"Eriodictyol 5-O-methyl ether inhibits prostate cancer progression through targeting STAT3 signaling and inducing apoptosis and paraptosis","authors":"Min Hee Yang ,&nbsp;Ninh The Son ,&nbsp;Jairo Kenupp Bastos ,&nbsp;Nguyen Dinh Luyen ,&nbsp;Nguyen Ngoc Linh ,&nbsp;Kwang Seok Ahn","doi":"10.1016/j.abb.2025.110331","DOIUrl":"10.1016/j.abb.2025.110331","url":null,"abstract":"<div><div>Prostate cancer ranks as one of the most prevalent cancers among men and is a major cause of cancer-related mortality globally This study aims to elucidate the molecular mechanisms underlying the anti-cancer effects of eriodictyol 5-<em>O</em>-methyl ether (ERIO) on prostate cancer cells, focusing on its impact on STAT3 signaling, apoptosis, and paraptosis. ERIO exhibited significant cytotoxicity against DU145, PC-3, and LNCaP cells. It suppressed constitutive and IL-6-induced STAT3 activation by inhibiting the phosphorylation of JAK1, JAK2, and Src kinases. ERIO upregulated SHP-2 expression, leading to the dephosphorylation of STAT3. ERIO induced apoptosis, evidenced by increased caspase-3 and PARP cleavage, and paraptosis, characterized by increased ROS production, decreased mitochondrial membrane potential, and ER stress. The antioxidant NAC reversed the effects of ERIO, highlighting the importance of oxidative stress in its anti-cancer activity. ERIO effectively inhibited prostate cancer cell growth by targeting STAT3 signaling and inducing both apoptosis and paraptosis. These findings suggest that ERIO has significant therapeutic potential for prostate cancer treatment and warrant further investigation in <em>in vivo</em> and clinical studies.</div></div>","PeriodicalId":8174,"journal":{"name":"Archives of biochemistry and biophysics","volume":"766 ","pages":"Article 110331"},"PeriodicalIF":3.8,"publicationDate":"2025-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143381460","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":"Annealing synchronizes the TOM complex with Tom7 in a new orientation","authors":"Liuyan Yang ,&nbsp;Mingdong Liu ,&nbsp;Lei Qi ,&nbsp;Yunhui Liu ,&nbsp;Xubo Lin ,&nbsp;Yu-Zhong Zhang ,&nbsp;Qing-Tao Shen","doi":"10.1016/j.abb.2025.110329","DOIUrl":"10.1016/j.abb.2025.110329","url":null,"abstract":"<div><div>Annealing is an ideal approach to synchronizing soluble proteins into their minimum-energy states via tandem heating and cooling treatments. Like soluble proteins, many membrane proteins also suffer intrinsic structural flexibility, the major obstacle to high-resolution structural determination. How to apply annealing onto membrane proteins remains unexplored. Here, we utilized the translocase of the outer mitochondrial membrane (TOM) as the model and investigated the ideal annealing conditions for membrane proteins. After structural determination via cryo-electron microscopy, we indicated that fast cooling the heated TOM complex to 0 °C can significantly improve the local resolution compared with the unannealed one. Structural analyses showed that annealing renders the TOM complex into a new conformation with its Tom7 α1 helix from a reclining position on the membrane surface to a lying orientation, accompanied by the loop between β6 and β7 in Tom40, flipping outward from the Tom40 β-barrel, ideal for preprotein translocation. In all, our results demonstrate the role of annealing in synchronizing membrane proteins and unveil unidentified conformations of the TOM complex.</div></div>","PeriodicalId":8174,"journal":{"name":"Archives of biochemistry and biophysics","volume":"766 ","pages":"Article 110329"},"PeriodicalIF":3.8,"publicationDate":"2025-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143381455","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":"PPIA enhances cell growth and metastasis through CD147 in oral cancer","authors":"En-Chi Liao ,&nbsp;Ching-Hsuan Law ,&nbsp;Hsin-Yi Chen ,&nbsp;Yu-Shan Wei ,&nbsp;Yi-Ting Tsai ,&nbsp;Li-Hsun Lin ,&nbsp;Meng-Wei Lin ,&nbsp;Yi- Shiuan Wang ,&nbsp;Hsiu-Chuan Chou ,&nbsp;Hong-Lin Chan","doi":"10.1016/j.abb.2025.110328","DOIUrl":"10.1016/j.abb.2025.110328","url":null,"abstract":"<div><div>Oral cancer is a malignant tumor, and the associated death rate has significantly increased over the past few decades. Secreted fractions are involved in various physiological processes, and their analysis has become a promising approach for discovering diagnostic and prognostic biomarkers for cancer detection and monitoring metastasis. Therefore, the discovery of potential prognostic, diagnostic, and therapeutic biomarkers for oral cancer metastasis is beneficial for developing effective strategies in oral cancer therapy. In this study, we used secretomic analysis to identify the secreted proteins involved in oral cancer. One of the identified proteins, peptidylprolyl isomerase A (PPIA), was selected for further investigation. We used RNA interference to investigate the effect of PPIA secretion on invasion and migration of OC3–I5 cells. Our results showed that reducing the expression and secretion of PPIA significantly decreased invasion and migration of OC3–I5 cells. Next, we used recombinant PPIA to investigate its direct effect on OC3 cell metastasis. The results revealed that proliferation, migration, and invasion of OC3 cells were significantly increased by treatment with the recombinant PPIA. Immunohistochemical analyses revealed higher PPIA expression in tumor tissues compared to normal tissues. Concisely, PPIA activated the ERK1/2 and p38 MAPK signaling pathways and enhanced cell proliferation and metastasis through CD147. In summary, PPIA may prove to be a novel target for oral cancer therapy as well as a prognostic marker.</div></div>","PeriodicalId":8174,"journal":{"name":"Archives of biochemistry and biophysics","volume":"765 ","pages":"Article 110328"},"PeriodicalIF":3.8,"publicationDate":"2025-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143360548","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":"A relative metabolic flux analysis model of glucose anaplerosis","authors":"Heesoo Jeong ,&nbsp;Nathaniel M. Vacanti","doi":"10.1016/j.abb.2025.110330","DOIUrl":"10.1016/j.abb.2025.110330","url":null,"abstract":"<div><div>Glucose provides substrate for the predominant anaplerotic pathway which involves the activity of pyruvate carboxylase (PC). PC-mediated anaplerosis has been extensively studied as a metabolic regulator in glycolytic cells during tumorigenesis and metastasis. Herein, inaccuracies in established methods to measure relative intracellular flux through PC are highlighted and a compartmentalized condensed metabolic network (CCMN) is used to resolve the total malate pool into relative contributions from PC and other sources by metabolic flux analysis (MFA) with [U–¹³C₆]glucose tracing. Performance of the CCMN method is evaluated in breast cancer cell lines that are exposed to small molecules targeting metabolism. Across conditions and cell lines, the CCMN approach yields results nearest to an accepted gold-standard methodology, using [3–¹³C]glucose, or even exposes the gold standard's limitations. The CCMN method does not require a separate experiment with a much more costly and generally less informative metabolic tracer, such as [3–¹³C]glucose, and in some cases, may outperform its application.</div></div>","PeriodicalId":8174,"journal":{"name":"Archives of biochemistry and biophysics","volume":"768 ","pages":"Article 110330"},"PeriodicalIF":3.8,"publicationDate":"2025-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143373757","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":"Production of the recombinant human riboflavin transporters SLC52A1, 3 and functional assay in proteoliposomes","authors":"Lara Console ,&nbsp;Maria Tolomeo ,&nbsp;Luciana Travo ,&nbsp;Deborah Giudice ,&nbsp;Alessia Nisco ,&nbsp;Maria Barile ,&nbsp;Cesare Indiveri","doi":"10.1016/j.abb.2025.110327","DOIUrl":"10.1016/j.abb.2025.110327","url":null,"abstract":"<div><div>Riboflavin, the FMN and FAD precursor, is a crucial vitamin in cell metabolism. Its adsorption and tissue distribution are mediated by tree membrane transporters namely RFVT1-3. Mutations of their genes are associated with Riboflavin Transporter Deficiency. Moreover, derangements of the level of these transporters have been found in several human cancers. To obtain a suitable experimental tool for studying the function of the single proteins, for testing the effect of pathological mutations and for validating predicted ligands as candidate drugs, we have set up a proteoliposome system harbouring the functional RFVT1 or RFVT3. RFVT proteins have been produced in <em>E. coli</em> and purified to the homogeneity by affinity chromatography. The purified proteins show an apparent molecular mass of 45.6 or 48.4 kDa, which are very close to the theoretical mass of RFVT1 or RFVT3, respectively. The purified transporters have been reconstituted into proteoliposomes using a methodology previously pointed out for RFVT2. The transport of riboflavin shows cooperative kinetics with K_0.5 values of 0.86 or 1.13 μM and Hill coefficients of 1.19 or 1.3 for RFVT1 or RFVT3, respectively. The K_0.5 data of both the transporters are similar the Km reported in intact cell studies. The transporters are inhibited by the riboflavin analogues FMN and lumiflavin in agreement with the molecular docking simulations.</div></div>","PeriodicalId":8174,"journal":{"name":"Archives of biochemistry and biophysics","volume":"766 ","pages":"Article 110327"},"PeriodicalIF":3.8,"publicationDate":"2025-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143363423","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Flavin adenine dinucleotide (FAD) as a non-canonical RNA cap: Mechanisms, functions, and emerging insights","authors":"Pablo Gonzalez-Jabalera,&nbsp;Andres Jäschke","doi":"10.1016/j.abb.2025.110326","DOIUrl":"10.1016/j.abb.2025.110326","url":null,"abstract":"<div><div>Flavin adenine dinucleotide (FAD), a versatile metabolic cofactor, is emerging as an important non-canonical RNA cap across various life domains. This review explores FAD's dual role as a coenzyme and an RNA modifier, focusing on its incorporation as a 5′ cap structure during transcription initiation and its subsequent implications for RNA metabolism and cellular functions. A comprehensive view of the mechanisms underlying FAD capping and decapping is presented, highlighting key enzymes that play a role in these processes. FAD-capped RNA is shown to play critical roles in viral replication, as demonstrated in the Hepatitis C virus, where FAD capping supports cellular immune evasion. Analytical techniques, including mass spectrometry and innovative sequencing methodologies, have advanced our understanding of the flavin cap, enabling its identification and quantification in different biological systems. This review underscores the significance of FAD-RNA capping as a novel regulatory mechanism, proposes innovative methodologies for its study, and emphasizes its potential therapeutic applications in viral and cellular biology.</div></div>","PeriodicalId":8174,"journal":{"name":"Archives of biochemistry and biophysics","volume":"766 ","pages":"Article 110326"},"PeriodicalIF":3.8,"publicationDate":"2025-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143373442","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Molecular characterization of the E2 conjugating enzyme LinfUbc13 in Leishmania infantum","authors":"Eduardo Vagner Rodrigues da Silva ,&nbsp;Caroline Torres ,&nbsp;Hariel Nemamiah Escolarique Ribeiro ,&nbsp;Camila Rolemberg Santana Travaglini Berti de Correia ,&nbsp;Taissa de Oliveira de Castro ,&nbsp;Giovanna da Costa Mancin ,&nbsp;Mayla Gabriela Zanchetta Venancio ,&nbsp;Munira Muhammad Abdel Baqui ,&nbsp;Felipe Roberti Teixeira ,&nbsp;Marcelo Damário Gomes","doi":"10.1016/j.abb.2024.110272","DOIUrl":"10.1016/j.abb.2024.110272","url":null,"abstract":"<div><div>UBC13 is an orthologue of <em>Homo sapiens</em> ubiquitin-conjugation E2 enzymes described in <em>Leishmania mexicana</em>, a null mutant lacking this gene cannot be produced, suggesting essential functions in this parasite. <em>Leishmania infantum</em> is an etiological agent of visceral leishmaniasis, the most severe type of disease that is potentially fatal if untreated. The ubiquitination process has been targeted for leishmanicidal compounds, indicating its essential function in parasite homeostasis. Therefore, the molecular characterization of the ubiquitination process may provide a better understanding of the molecular and cellular basis of leishmaniasis. Here, we characterized the gene <em>LINF_350017900</em> in <em>Leishmania infantum</em>, which was named <em>LinfUBC13</em>, an E2 orthologue of UBC13 in <em>Leishmania mexicana</em> and the UBE2D family in <em>Homo sapiens</em>, sharing 72–74 % identity with UBE2D1, UBE2D2, and UBE2D3. LinfUbc13 contains conserved catalytic residues, including Cys86 and the HPN motif, which are essential for ubiquitin-conjugating activity. Structural analysis revealed a high similarity between LinfUbc13 and human UBE2D proteins, with a root-mean-square deviation (RMSD) of 0.4 Å, suggesting conserved functions. Recombinant LinfUbc13 was expressed and shown to accept ubiquitin from E1, forming a thioester intermediate. Functional assays demonstrated that LinfUbc13 transfers ubiquitin to p53 through human HDM2 E3 ligase, confirming its role in ubiquitination. Subcellular localization showed that LinfUbc13 was distributed throughout the parasite cytoplasm. These findings highlight the conserved nature of the ubiquitin-proteasome system between <em>Leishmania infantum</em> and <em>Homo sapiens</em>, showing that LinfUbc13 is an E2 enzyme that plays a crucial role in parasitic development.</div></div>","PeriodicalId":8174,"journal":{"name":"Archives of biochemistry and biophysics","volume":"764 ","pages":"Article 110272"},"PeriodicalIF":3.8,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142845690","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":"Retraction notice to “Inhibition of carnitine palmitoyl transferase 1A-induced fatty acid oxidation suppresses cell progression in gastric cancer” [Archiv. Biochem. Biophys. 696 (2020) 108664]","authors":"Liqiang Wang ,&nbsp;Changfeng Li ,&nbsp;Yumei Song ,&nbsp;ZhenKun Yan","doi":"10.1016/j.abb.2024.110264","DOIUrl":"10.1016/j.abb.2024.110264","url":null,"abstract":"","PeriodicalId":8174,"journal":{"name":"Archives of biochemistry and biophysics","volume":"764 ","pages":"Article 110264"},"PeriodicalIF":3.8,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142811703","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":"Therapeutic potential of SMAD7 targeting miRNA in the pathogenesis of diabetic nephropathy","authors":"V. Pooja Rathan,&nbsp;K. Bhuvaneshwari,&nbsp;G. Nideesh Adit,&nbsp;S. Kavyashree,&nbsp;N. Thulasi,&nbsp;A.V.S. Geetha,&nbsp;K.L. Milan,&nbsp;K.M. Ramkumar","doi":"10.1016/j.abb.2024.110265","DOIUrl":"10.1016/j.abb.2024.110265","url":null,"abstract":"<div><div>Diabetic nephropathy (DN) is a common complication of diabetes and a leading cause of end-stage renal disease, characterized by progressive kidney fibrosis and inflammation. The transforming growth factor-beta (TGF-β) signaling pathway plays a crucial role in the pathogenesis of diabetes nephropathy, and SMAD7 is a key negative regulator of this pathway. Recent studies have highlighted the involvement of miRNA in the progression of DN. Computational analysis identified 11 potential miRNAs such as miR-424, miR-195, miR-216a, miR-503, miR-15a-5p, miR-15b-5p, miR-665, miR-520h, miR16-5p, miR-21 and miR-32-5p which are predicted to target 3′UTR of SMAD7 mRNA. This review aims to explore the role of these miRNAs in the progression of DN. Notably, these miRNAs have shown therapeutic potential in mitigating fibrosis and inflammation by modulating SMAD7 expression in DN. Future directions can be to investigate the mechanistic pathways through which these miRNAs exert their effects, as well as optimizing delivery systems for effective clinical application. Targeting miRNAs that modulate SMAD7 expression represents a promising strategy for developing specific and effective therapies for diabetic nephropathy.</div></div>","PeriodicalId":8174,"journal":{"name":"Archives of biochemistry and biophysics","volume":"764 ","pages":"Article 110265"},"PeriodicalIF":3.8,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142817070","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":"Selenoprotein K at the intersection of cellular pathways","authors":"Atinuke Odunsi ,&nbsp;Mariia A. Kapitonova ,&nbsp;George Woodward ,&nbsp;Erfan Rahmani ,&nbsp;Farid Ghelichkhani ,&nbsp;Jun Liu ,&nbsp;Sharon Rozovsky","doi":"10.1016/j.abb.2024.110221","DOIUrl":"10.1016/j.abb.2024.110221","url":null,"abstract":"<div><div>Selenoprotein K (selenok) is linked to the integrated stress response, which helps cells combat stressors and regain normal function. The selenoprotein contains numerous protein interaction hubs and post-translational modification sites and is involved in protein palmitoylation, vesicle trafficking, and the resolution of ER stress. Anchored to the endoplasmic reticulum (ER) membrane, selenok interacts with protein partners to influence their stability, localization, and trafficking, impacting various cellular functions such as calcium homeostasis, cellular migration, phagocytosis, gene expression, and immune response. Consequently, selenok expression level is linked to cancer and neurodegenerative diseases.</div><div>Because it contains the reactive amino acid selenocysteine, selenok is likely to function as an enzyme. However, highly unusual for enzymes, the protein segment containing the selenocysteine lacks a stable secondary or tertiary structure, yet it includes multiple interaction sites for protein partners and post-translational modifications. Currently, the reason(s) for the presence of the rare selenocysteine in selenok is not known. Furthermore, of selenok's numerous interaction sites, only some have been sufficiently characterized, leaving many of selenok's potential protein partners to be discovered. In this review, we explore selenok's role in various cellular pathways and its impact on human health, thereby highlighting the links between its diverse cellular functions.</div></div>","PeriodicalId":8174,"journal":{"name":"Archives of biochemistry and biophysics","volume":"764 ","pages":"Article 110221"},"PeriodicalIF":3.8,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142685777","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}