Journal of cellular biochemistry最新文献

{"title":"The Effect of Protein Tagging on Aggregation and Phase Separation","authors":"Harunobu Saito,&nbsp;Kenji Sugase","doi":"10.1002/jcb.70096","DOIUrl":"10.1002/jcb.70096","url":null,"abstract":"<p>Protein tags are widely used for purification, solubilization, detection, and imaging, yet they can substantially alter protein self-assembly. This interference is particularly significant for intrinsically disordered proteins and low-complexity domains, whose aggregation and phase separation are mediated by weak multivalent interactions that are easily disrupted by exogenous elements. In this review, we examine how affinity tags, solubility tags, fluorescent proteins, and chemical labels influence aggregation, amyloid formation, and liquid-liquid phase separation (LLPS). We first classify recurring perturbation mechanisms into six primary categories: solubility enhancement, artificial multivalency, electrostatic interactions, local effects, metal coordination, and positional dependence. Crucially, these non-exclusive mechanisms often operate simultaneously within a single construct. We then review representative case studies across pathogenic amyloids, RNA-binding proteins, viral inclusions, functional amyloids, yeast prions, and membrane proteins. These examples demonstrate that tags alter assembly kinetics, phase boundaries, material properties, fibril morphology, oligomeric states, and observed phenotypes, rather than merely serving as neutral tools for detection. In some systems, tags suppress intrinsic assembly; in others, they promote non-native condensation or stabilize alternative aggregate states. Finally, we discuss practical experimental strategies to distinguish intrinsic protein behavior from construct-dependent effects, emphasizing matched comparisons, orthogonal validation, and the careful interpretation of measurements based on tag cleavage or fluorescence. Collectively, the evidence indicates that protein tags should be treated as experimental variables that shape assembly states rather than as inert technical additions.</p>","PeriodicalId":15219,"journal":{"name":"Journal of cellular biochemistry","volume":"127 6","pages":""},"PeriodicalIF":3.0,"publicationDate":"2026-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcb.70096","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148251631","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":"Intrinsic Disorder Status in Human Proteins Interacting With SARS-CoV-2 Proteins: Insights From Five Years of Translational Research","authors":"Muhamed Adilović,&nbsp;Betul Akcesme,&nbsp;Altijana Hromić-Jahjefendić,&nbsp;Vladimir N. Uversky","doi":"10.1002/jcb.70098","DOIUrl":"10.1002/jcb.70098","url":null,"abstract":"<div>\u0000 \u0000 <p>SARS-CoV-2 infection is driven by extensive interactions between viral proteins and host cellular factors, yet the structural properties of host proteins within these interaction networks remain incompletely understood. Intrinsically disordered proteins and regions are key contributors to protein–protein interaction networks due to their conformational flexibility and associated with it multifunctionality, binding promiscuity, and regulatory versatility. In this study, we performed a systematic, proteome-wide analysis of intrinsic disorder in human proteins interacting with SARS-CoV-2 by integrating five experimentally validated interaction datasets comprising 2055 unique host proteins. Using disorder prediction, structural confidence assessment, functional and domain annotation, protein–protein interaction network analysis, phase-separation propensity estimation, and independent validation with the D²P² platform on a selected set of proteins, we characterized the structural organization of the SARS-CoV-2 human interactome. Our results reveal a balanced distribution of ordered and disordered host proteins, distinct functional and domain signatures across disorder classes, consistent inverse relationships between disorder and structural confidence, and increased network connectivity and phase-separation propensity among highly disordered interactors. These findings indicate that SARS-CoV-2 exploits structural diversity within the host proteome rather than preferentially targeting a single disorder class and highlight intrinsic disorder as a key contributor to interaction plasticity and network organization at the systems level.</p></div>","PeriodicalId":15219,"journal":{"name":"Journal of cellular biochemistry","volume":"127 6","pages":""},"PeriodicalIF":3.0,"publicationDate":"2026-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148251666","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":"TRIM32 Alleviates the Inflammation in Spinal Cord Injury Progression Through Inducing the Ubiquitination Degradation of TLR4","authors":"Xiaolin Liu,&nbsp;Shoubo Chen,&nbsp;Jinnan Shi,&nbsp;Jiaxing Liu,&nbsp;Jinxing Shi,&nbsp;Wenhua Wu","doi":"10.1002/jcb.70097","DOIUrl":"https://doi.org/10.1002/jcb.70097","url":null,"abstract":"<div>\u0000 \u0000 <p>Inflammatory response induced cell apoptosis plays a crucial role in the pathological process of secondary injury in spinal cord injury (SCI), and targeted reduction of secondary inflammatory response can effectively promote neuronal recovery after SCI. TRIM32, an E3 ubiquitin ligase, has been shown to modulate inflammation by influencing ubiquitination modifications. In this study, we sought to investigate the function of TRIM32 in the progression of SCI. LPS treated PC12 cells and SD rats were utilized to establish the SCI model. HE staining and BBB score was conducted to analyze the SCI development of rats. The inflammatory factor contents were detected using ELISA kits. Cell growth was analyzed by CCK-8 and flow cytometry assays. Western blot was performed to detect ubiquitination levels and protein levels. In addition, CO-IP assay was carried out to analyze the relationship between TRIM32 and TLR4. TRIM32's ubiquitination modification of TLR4 is achieved through K48 linkage. TRIM32 was down-regulated in the LPS treated PC12 cells and SCI rats. Overexpression of TRIM32 decreased the IL-1β, IL-6, and TNF-α contents in vivo and in vitro. Additionally, TRIM32 overexpression increased the ubiquitination levels of TLR4, which further decreased the protein stability and expression of TLR4. TRIM32's ubiquitination modification of TLR4 is achieved through K48 linkage. Furthermore, the overexpression of TLR4 counteracted the influence of TRIM32 on cell viability, the rate of apoptosis, and the levels of IL-1β, IL-6, and TNF-α in PC12 cells subjected to LPS treatment. In rats with SCI, the upregulation of TRIM32 alleviated damage to spinal cord tissues and enhanced the BBB scoring. This study demonstrated that TRIM32 overexpression inhibited the inflammation in SCI progression through inducing the ubiquitination degradation of TLR4. TRIM32 might be an intriguing host therapeutic target for the treatment of SCI.</p>\u0000 </div>","PeriodicalId":15219,"journal":{"name":"Journal of cellular biochemistry","volume":"127 6","pages":""},"PeriodicalIF":2.8,"publicationDate":"2026-06-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148194138","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":"Bedaquiline Binding at the Leading Site of Mycobacterium tuberculosis ATP Synthase Induces Distinct Structural and Dynamic Changes","authors":"Pragya Anand,&nbsp;Yusuf Akhter","doi":"10.1002/jcb.70095","DOIUrl":"10.1002/jcb.70095","url":null,"abstract":"&lt;div&gt;\u0000 \u0000 &lt;p&gt;ATP synthase (ATPase) is a crucial molecular motor in &lt;i&gt;Mycobacterium tuberculosis&lt;/i&gt; (&lt;i&gt;Mtb&lt;/i&gt;), essential for energy production and oxygen-dependent pathogenesis. The enzyme consists of two distinct rotors: a membrane-embedded Fₒ unit and a cytosolic catalytic F&lt;sub&gt;1&lt;/sub&gt; unit, along with a stator, a central stalk, and a heterodimeric peripheral stalk (PS). As the F&lt;sub&gt;0&lt;/sub&gt; region hosts critical drug-binding pockets, it has gained significant interest. This study focuses on local structural dynamics at the leading site in the presence of bedaquiline (BDQ). All-atom molecular dynamics simulations were performed using GROMACS in a heterogeneous bilayer composed of phosphoinositol, phosphoethanolamine, phosphoglycerol, and cardiolipin (PI: PE: PG: CL) in a 32:42:4:50 ratio. The results revealed key interactions of BDQ with cL&lt;sup&gt;59&lt;/sup&gt;, cF&lt;sup&gt;65&lt;/sup&gt;, cE&lt;sup&gt;61&lt;/sup&gt;, cA&lt;sup&gt;62&lt;/sup&gt;, cI&lt;sup&gt;55&lt;/sup&gt;, cI&lt;sup&gt;66&lt;/sup&gt;, cG&lt;sup&gt;58&lt;/sup&gt;, aI&lt;sup&gt;215&lt;/sup&gt;, and aF&lt;sup&gt;219&lt;/sup&gt; at the a/c interface, consistent with energetically favored binding conformation. Quantitative lipid contact analysis revealed higher CL interactions with BDQ at leading site together with interfacial water molecules, whereas protein-lipid contacts based on only lipid headgroup (P-atoms) analysis remained independent of lipid abundance in the system. RMSD and RMSF revealed BDQ-induced fluctuations in the outer helix of subunit-c, while subunit-a remained comparatively more stable during the simulation. Distance analysis further indicated that the ligand remains confined within the binding region despite local flexibility. We further identified putative non-collinear proton channels, which showed no significant global perturbation upon BDQ binding. Residues aG&lt;sup&gt;195&lt;/sup&gt;, aN&lt;sup&gt;105&lt;/sup&gt;, aD&lt;sup&gt;220&lt;/sup&gt;, aN&lt;sup&gt;190&lt;/sup&gt;, aQ&lt;sup&gt;227&lt;/sup&gt;, cE&lt;sup&gt;61&lt;/sup&gt; (inlet side), cE&lt;sup&gt;61&lt;/sup&gt; (outlet side), aE&lt;sup&gt;176&lt;/sup&gt;, aE&lt;sup&gt;175&lt;/sup&gt;, aA&lt;sup&gt;178&lt;/sup&gt;, aK&lt;sup&gt;179&lt;/sup&gt;, aS&lt;sup&gt;182&lt;/sup&gt;, aY&lt;sup&gt;238&lt;/sup&gt;, aQ&lt;sup&gt;110&lt;/sup&gt;, aF&lt;sup&gt;192&lt;/sup&gt;, aL&lt;sup&gt;122&lt;/sup&gt; form the two half channels in &lt;i&gt;Mtb&lt;/i&gt;. The pooled water-count analysis for channels showed similar hydration levels in all simulated systems. We hypothesize that selective targeting of the leading pocket by newer drugs, in the presence of CL lipids, can modulate the proton inlet channel. The heterogeneous bilayer supports the structural and functional integrity of the membrane and ATPase complex. A CL-enriched membrane environment may provide a useful framework for investigating membrane-associated effects of BDQ and its analogs. Chain-wise analysis showed synchronous movement of the PS subunits and twisting of the δ-binding region, which may be perturbed in the presence of the F&lt;sub&gt;1&lt;/sub&gt; unit. The dynamics also revealed subunit-bδ involvement with the subunit-a at the leading pocket, a less studied PS and stator function. Identifying residue-specific interactions between ","PeriodicalId":15219,"journal":{"name":"Journal of cellular biochemistry","volume":"127 5","pages":""},"PeriodicalIF":2.8,"publicationDate":"2026-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148101377","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":"Agrin Ablation in Osteoblasts Compromises Long Bone Structure and Osteoblastic Differentiation of Mesenchymal Stem Cells","authors":"Gabriela Camarneiro Siqueira,&nbsp;Maria Paula Oliveira Gomes,&nbsp;Letícia Faustino Adolpho,&nbsp;Aline Ying Ying Wang,&nbsp;Fabiola Singaretti Olveira,&nbsp;Adriana Luisa Gonçalves Almeida,&nbsp;Roger Rodrigo Fernandes,&nbsp;Ana Paula Macedo,&nbsp;Ana Paula Ramos,&nbsp;Adalberto Luiz Rosa,&nbsp;Marcio Mateus Beloti","doi":"10.1002/jcb.70094","DOIUrl":"10.1002/jcb.70094","url":null,"abstract":"<p>Agrin is an important factor in maintaining skeletal architecture. However, the role of osteoblast-expressed agrin in bone tissue remains unexplored. Thus, we hypothesized that agrin-deficient osteoblasts negatively affect bone tissue homeostasis by disrupting osteoblastic differentiation of mesenchymal stem cells (MSCs). To investigate this hypothesis, mice with deletion of agrin in Runx2-expressing osteoblasts were generated using Runx2-Cre mice. Microtomographic analyses revealed that agrin ablation in osteoblasts resulted in deleterious effects on the cortical bone of the femurs, leading to a tendency towards reduced bone stiffness, as indicated by the three-point bending test. This negative impact of agrin-deficient osteoblasts on bone tissue may be partially attributed to the reduced osteoblastic differentiation of MSCs derived from these mice, as evidenced by lower expression of osteoblastic marker genes and alkaline phosphatase activity. This disruption in osteoblastic differentiation is directly linked to agrin-deficient osteoblasts, as demonstrated by diminished gene expression of agrin and its receptors in MSCs collected from these animals. Our findings highlight the role of osteoblast-secreted agrin in maintaining long bone structure, mainly by promoting MSC differentiation into osteoblasts. The findings indicate that agrin could be an effective therapeutic target for treating bone loss-related conditions, such as osteoporosis and aging.</p>","PeriodicalId":15219,"journal":{"name":"Journal of cellular biochemistry","volume":"127 5","pages":""},"PeriodicalIF":2.8,"publicationDate":"2026-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcb.70094","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148054642","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":"","authors":"","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":15219,"journal":{"name":"Journal of cellular biochemistry","volume":"127 5","pages":""},"PeriodicalIF":2.8,"publicationDate":"2026-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148061759","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":"","authors":"","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":15219,"journal":{"name":"Journal of cellular biochemistry","volume":"127 5","pages":""},"PeriodicalIF":2.8,"publicationDate":"2026-05-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148073833","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":"","authors":"","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":15219,"journal":{"name":"Journal of cellular biochemistry","volume":"127 5","pages":""},"PeriodicalIF":2.8,"publicationDate":"2026-05-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148073834","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":"The Leptin Renaissance: Orchestrating the Next Endocrine Paradigm.","authors":"Muhammad Junaid, Hu Zeming, Yabin Zhu","doi":"10.1002/jcb.70091","DOIUrl":"10.1002/jcb.70091","url":null,"abstract":"<p><p>Leptin, a hormone historically recognized for regulating appetite and energy homeostasis, is increasingly appreciated as a central mediator of immune function, metabolic integration, and tissue-specific signaling. Despite decades of research, leptin resistance limits the efficacy of conventional therapies, such as hormone replacement, in treating obesity and related disorders. Emerging evidence demonstrates that leptin interacts bidirectionally with the gut microbiome, influencing systemic metabolism and immune responses. Advances in multi-omics profiling, synthetic biology, and tissue-targeted therapeutics provide unprecedented opportunities to overcome these barriers. Here, we present a perspective emphasizing integrative strategies that combine precision medicine, immune modulation, engineered leptin analogs, and microbiome-targeted interventions. Leveraging these innovations could redefine leptin-based therapies, enabling system-level restoration of metabolic and immune homeostasis. Understanding leptin as a pleiotropic, multi-system hormone positions it at the forefront of the next endocrine paradigm.</p>","PeriodicalId":15219,"journal":{"name":"Journal of cellular biochemistry","volume":"127 5","pages":"e70091"},"PeriodicalIF":3.0,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147972815","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":"Correction to \"Resveratrol Pretreatment Enhanced Homing of SDF-1α-preconditioned Bone Marrow-Derived Mesenchymal Stem Cells in a Rat Model of Liver Cirrhosis\".","authors":"","doi":"10.1002/jcb.70092","DOIUrl":"https://doi.org/10.1002/jcb.70092","url":null,"abstract":"","PeriodicalId":15219,"journal":{"name":"Journal of cellular biochemistry","volume":"127 5","pages":"e70092"},"PeriodicalIF":2.8,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147868610","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}