Journal of Molecular Biology最新文献

{"title":"Beyond Immunity: RIG-I as a Bifunctional Regulator of Cell Fate in Non-Infectious Diseases","authors":"Ou Qiao ,&nbsp;Herui Hao ,&nbsp;Sania Saeed ,&nbsp;Xinyue Wang ,&nbsp;Li Zhang ,&nbsp;Yuru Wang ,&nbsp;Xin Chen ,&nbsp;Fengjiao Bao ,&nbsp;Yingjie Hou ,&nbsp;Xiaohong Duan ,&nbsp;Shuquan Rao ,&nbsp;Ning Li ,&nbsp;Yanhua Gong","doi":"10.1016/j.jmb.2025.169450","DOIUrl":"10.1016/j.jmb.2025.169450","url":null,"abstract":"<div><div>Retinoic acid-inducible gene (RIG-I) is highly regarded for recognizing short-stranded RNA with a triphosphate motif at the 5′ end to participate in the antiviral innate immune response. Recent studies have demonstrated that RIG-I expression remains upregulated during the terminal phase of RNA virus infection, persisting even after interferon production has terminated. Furthermore, studies have demonstrated the up-regulation or activation of RIG-I expression in non-viral disease contexts, implying a potential non-immune role for RIG-I. RIG-I possesses multiple structural domains, including Cards, Helicase, and CTD, which confer functional versatility in response to diverse stimuli. These domains enable RIG-I to participate in various biological processes beyond viral immunity, such as programmed cell death (PCD), tumor immunity, and cell proliferation. This review focuses on the role of RIG-I in regulating PCD, encompassing apoptosis, immunogenic cell death, necroptosis, pyroptosis, and autophagy. We systematically analyze the molecular mechanisms by which RIG-I modulates these PCD pathways and discuss the therapeutic potential of RIG-I-targeting activators and antagonists. These advances provide critical insights for developing novel treatments for diseases linked to RIG-I dysregulation.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"437 24","pages":"Article 169450"},"PeriodicalIF":4.5,"publicationDate":"2025-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145111732","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"iBitter-Stack: A multi-representation ensemble learning model for accurate bitter peptide identification","authors":"Sarfraz Ahmad ,&nbsp;Momina Ahsan ,&nbsp;Muhammad Nabeel Asim ,&nbsp;Andreas Dengel ,&nbsp;Muhammad Imran Malik","doi":"10.1016/j.jmb.2025.169448","DOIUrl":"10.1016/j.jmb.2025.169448","url":null,"abstract":"<div><div>The identification of bitter peptides is crucial in various domains, including food science, drug discovery, and biochemical research. These peptides not only contribute to the undesirable taste of hydrolyzed proteins but also play key roles in physiological and pharmacological processes. However, experimental methods for identifying bitter peptides are time-consuming and expensive. With the rapid expansion of peptide sequence databases in the post-genomic era, the demand for efficient computational approaches to distinguish bitter from non-bitter peptides has become increasingly significant. In this study, we propose a novel stacking-based ensemble learning framework aimed at enhancing the accuracy and reliability of bitter peptide classification. Our method integrates diverse sequence-based feature representations and leverages a broad set of machine learning classifiers. The first stacking layer comprises multiple base classifiers, each trained on distinct feature encoding schemes, while the second layer employs logistic regression to refine predictions using an eight-dimensional probability vector. Extensive evaluations on a carefully curated dataset demonstrate that our model significantly outperforms existing predictive methods, providing a robust and reliable computational tool for bitter peptide identification. Our approach achieves an accuracy of 96.09% and a Matthews Correlation Coefficient (MCC) of 0.9220 on the independent test set, underscoring its effectiveness and generalizability. To facilitate real-time usage and broader accessibility, we have also developed a user-friendly web server based on the proposed method, which is freely accessible at <span>ibitter-stack-webserver.streamlit.app</span>. This tool enables researchers and practitioners to conveniently screen peptide sequences for bitterness in real-time applications.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"437 24","pages":"Article 169448"},"PeriodicalIF":4.5,"publicationDate":"2025-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145102590","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Surface-Tethering Enhances Precision in Measuring Diffusion Within 3D Protein Condensates.","authors":"Emily R Sumrall, Guoming Gao, Shelby Stakenas, Nils G Walter","doi":"10.1016/j.jmb.2025.169447","DOIUrl":"10.1016/j.jmb.2025.169447","url":null,"abstract":"<p><p>Biomolecular condensates, or membraneless organelles, play pivotal roles in cellular organization by compartmentalizing biochemical reactions and regulating diverse processes such as RNA metabolism, signal transduction, and stress response. Super-resolved imaging and single molecule tracking are essential for probing the internal dynamics of these condensates, yet the intrinsic Brownian motion of the entire condensate could interfere with diffusion measurements, confounding the interpretation of molecular mobility. Here we systematically assess and address this challenge with both experiments and simulations, using in vitro reconstituted condensates as simplified models of endogenous cellular assemblies. We show that tethering effectively suppresses the global translational and rotational Brownian motions of the entire condensate, eliminating inherent motion interference while preserving their spherical morphology. Quantitative analysis reveals that untethered condensates systematically overestimate molecular diffusion coefficients and step sizes, particularly for slowly diffusing structured mRNAs, while rapidly diffusing unstructured RNAs are unaffected due to temporal scale separation. Comparative evaluation of tethering strategies demonstrates tunable control over condensate stability and internal dynamics, with implications for optimizing experimental design. Finally, combining with simulations that sweep through the entire physiological parameter space, we provide a practical guideline for judging whether tethering is necessary in an experiment based on condensate size, diffusion type, and diffusion coefficient of the biomolecule of interest. Our findings establish surface tethering as a valuable and robust approach for accurate quantification of intra-condensate molecular dynamics, providing a methodological framework for future studies of membraneless organelles.</p>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":" ","pages":"169447"},"PeriodicalIF":4.5,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145090956","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Biomolecular Condensates; Emerging Themes and Concepts","authors":"Shana Elbaum-Garfinkle ,&nbsp;Richard Kriwacki","doi":"10.1016/j.jmb.2025.169449","DOIUrl":"10.1016/j.jmb.2025.169449","url":null,"abstract":"","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"437 24","pages":"Article 169449"},"PeriodicalIF":4.5,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145090938","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Allostery in Biomolecular Condensates.","authors":"Ruth Nussinov, Clil Regev, Hyunbum Jang","doi":"10.1016/j.jmb.2025.169446","DOIUrl":"10.1016/j.jmb.2025.169446","url":null,"abstract":"<p><p>Allosteric proteins and membrane-less biomolecular condensates are physics-governed pivotal functional components. Allosteric regulation is an inherent physical property of dynamic proteins, and dynamic proteins are allosteric. Thus, in biomolecular condensates (like everywhere else in the cell), allostery is at play, and often missing in condensate descriptions is that the cooperative transitions can involve allosteric effects. The condensate environment can be especially conducive to allostery. Condensed settings can increase the chance of protein interaction and allosteric encounters in function-specific condensates. Specific protein-protein interactions provide the structural framework for signals to transmit cooperatively and dynamically, ultimately modulating cell activity. Their interfaces are commonly enriched in nonpolar (hydrophobic) surface. With abundant functionally specific proteins, and surfaces accommodating multiple hydrophobic patches, interconnected multivalent molecular networks are expected. Lacking hydrophobic cores, disordered proteins' folding-upon-binding scenarios often form strong hydrophobic interfaces, and cooperative (partially disordered) multimers are also common. Repelling water is a major force in condensate formation, albeit not the sole. Here we emphasize dilution as functional and allosteric determinant. Extremely high dilution in rapidly growing proliferating cells can stimulate senescence; lower dilution increases concentration, thus, higher probability of increased proximity and reduced separation, driving protein-protein interactions, and allostery. Is there then effective allostery in condensates? We believe that it depends on the cell state. Under normal physiological conditions, with condensates water content around 40% of total cell mass-yes; over 70% could be too diluted. If too low-it can become function-poor aggregate-like. Effective allostery and signaling require specific interactions, extending from clustered receptors to the cytoskeleton.</p>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":" ","pages":"169446"},"PeriodicalIF":4.5,"publicationDate":"2025-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12453622/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145079259","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"On the Molecular Basis of the Hypersaline Adaptation of Halophilic Proteins.","authors":"Gabriel Ortega-Quintanilla, Oscar Millet","doi":"10.1016/j.jmb.2025.169439","DOIUrl":"10.1016/j.jmb.2025.169439","url":null,"abstract":"<p><p>Halophilic organisms have adapted to survive in environments with extremely high salinity, such as saline lakes. To achieve this, they modify their proteome to withstand salt concentrations that inactivate non-adapted mesophilic proteins. The surfaces of halophilic proteins feature a very characteristic amino acid composition, favoring short, polar, and acidic amino acids-such as aspartate, glutamate, and threonine-while disfavoring bulky, hydrophobic amino acids-such as lysine, methionine, and leucine. In this work, we review our understanding of the molecular basis of haloadaptation. We critically examine the role of electrostatic interactions in stabilizing halophilic proteins, while underlining the importance of other contributions from hydrophobic solvation and preferential ion exclusion. Finally, we describe the mechanistic link by which the halophilic amino acid composition optimizes function in hypersaline environments, balancing the trade-off between stability, solubility, and catalytic function.</p>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":" ","pages":"169439"},"PeriodicalIF":4.5,"publicationDate":"2025-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145068836","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Learning About Protein Stability and Functional Activity From Ancestral Reconstruction.","authors":"Satoshi Akanuma","doi":"10.1016/j.jmb.2025.169435","DOIUrl":"10.1016/j.jmb.2025.169435","url":null,"abstract":"<p><p>Understanding how proteins have evolved to adapt their stability and function to changing temperatures remains a central question in molecular biology. While structural analyses, site-directed mutagenesis, and directed evolution have yielded valuable insights, ancestral sequence reconstruction (ASR) has recently emerged as a powerful tool for addressing the drivers behind protein evolution. Specifically, by enabling the inference and experimental characterization of reconstructed ancient proteins, ASR provides unique perspectives on the molecular mechanisms underlying both thermostability and low-temperature-adaptation. This review outlines the historical development of research on protein temperature adaptation and highlights the role of ASR in advancing the field. Selected case studies illustrate how ASR has uncovered structural and dynamic features associated with extreme thermostability or enhanced activity at low temperatures. Common sources of uncertainty in ASR and how they can be addressed are also discussed. Finally, the broader potential of ASR is described, both for elucidating early evolutionary processes and for guiding the design of enzymes useful for industrial applications.</p>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":" ","pages":"169435"},"PeriodicalIF":4.5,"publicationDate":"2025-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145058226","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Exploring the Role of Structural and Dynamic Complexity in SARS-CoV-2 Nucleocapsid Protein-Heparin Interactions by NMR.","authors":"Tessa Bolognesi, Marco Schiavina, Cristina Ciabini, Michela Parafioriti, Cristina Gardini, Stefano Elli, Marco Guerrini, Roberta Pierattelli, Isabella C Felli","doi":"10.1016/j.jmb.2025.169437","DOIUrl":"10.1016/j.jmb.2025.169437","url":null,"abstract":"<p><p>Among the structural proteins of SARS-CoV-2, the nucleocapsid (N) protein stands out for its pronounced structural heterogeneity and multifunctionality throughout the viral life cycle. Recent studies have demonstrated that the N protein localizes to the surface of infected and neighboring non-infected cells, by interacting with heparan sulfate in the extracellular matrix. The N protein (419 residues) comprises two folded domains (⁴⁴NTD¹⁸⁰ and ²⁴⁹CTD³⁶¹) interspersed with three intrinsically disordered regions (¹IDR1⁴³, ¹⁸¹IDR2²⁴⁸, ³⁶²IDR3⁴¹⁹). The coexistence of ordered and disordered elements raises a key question: how does this structural heterogeneity influence N's interactions with biological partners? Here we employ high-resolution NMR spectroscopy as the primary technique to characterize the interaction of three N protein constructs (⁴⁴NTD¹⁸⁰, ¹NTR²⁴⁸, and ¹N⁴¹⁹) with heparin-based ligands of increasing complexity. NMR provides atomic level information on the structured NTD domain and on the otherwise difficult to investigate flexible regions. Molecular dynamics simulations further probe the interaction between NTD and short heparin oligosaccharides. Our data reveal a clear correlation between ligand size and binding affinity: longer saccharide chains promote stronger binding. Additionally, the inclusion of intrinsically disordered regions in the NTR construct significantly enhances the interaction compared to NTD, highlighting the functional relevance of structural disorder. Finally, the full-length protein exhibits distinct spectral behavior with the investigated heparin-based ligand, potentially reflecting additional binding contributions and altered dynamics arising from its complex structure. These findings underscore the utility of NMR spectroscopy in elucidating the dynamic, multivalent nature of protein-polyanion interactions, particularly in highly flexible proteins with a modular domain organization.</p>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":" ","pages":"169437"},"PeriodicalIF":4.5,"publicationDate":"2025-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145058205","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Decoding the Central Dogma: Quantitative Insights into Transcription and Translation Dynamics in the p53-Mediated DNA Damage Response.","authors":"Joshua François, Ashwini Jambhekar, Galit Lahav","doi":"10.1016/j.jmb.2025.169436","DOIUrl":"10.1016/j.jmb.2025.169436","url":null,"abstract":"<p><p>The central dogma describes the flow of genetic information from DNA to RNA and then to protein, a process regulated at multiple steps with the potential for reverse information flow. DNA damage, caused by external factors like radiation or internal processes, poses a threat to genomic stability and necessitates a robust DNA damage response (DDR). The tumor suppressor protein p53 is a pivotal component of the DDR, orchestrating gene expression to repair DNA, halt the growth of damaged cells or trigger cell death. Here, we discuss various quantitative methods that enabled new insights into p53 regulation of transcription and translation dynamics in response to DNA damage. Imaging techniques, such as live-cell fluorescence microscopy, have enabled the visualization of both p53 and the mRNA and protein levels of its key targets, such as MDM2, a negative regulator of p53; and p21, a key regulator of the cell cycle. Singe-cell live imaging of p53 in response to various DNA damaging agents, and in combination with inhibitors of its key regulators, suggested p53 dynamics as an important mechanism controlling cell fate and enabled the development of quantitative models for the control of p53 levels. Omics approaches complement imaging by offering comprehensive, quantitative insights into mRNA and protein changes following DNA damage. Mathematical models connect p53 dynamics with target gene regulation, revealing complexities in transcription-translation relationships. Integrating these methods can elucidate DDR intricacies at the single-cell level, enhancing our understanding of p53's role in regulating gene expression and cell fate determination.</p>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":" ","pages":"169436"},"PeriodicalIF":4.5,"publicationDate":"2025-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145058202","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cryo-EM Observation of AA Amyloid Fibrils in Mouse Model of Systemic AApoAII Amyloidosis","authors":"Giada Andreotti ,&nbsp;Keichii Higuchi ,&nbsp;Matthias Schmidt ,&nbsp;Marcus Fändrich","doi":"10.1016/j.jmb.2025.169438","DOIUrl":"10.1016/j.jmb.2025.169438","url":null,"abstract":"<div><div>The co-deposition of amyloid fibrils from different precursor proteins is a topic of increasing relevance for protein misfolding diseases. Using cryo-electron microscopy (cryo-EM), we here determined the structures of two serum amyloid A (SAA) protein-derived amyloid fibril morphologies that were extracted from a mouse strain that is primarily known to be associated with apolipoprotein A-II-derived amyloid fibrils. The two fibril morphologies show the same protomer conformation as in previously reported ex vivo amyloid fibrils from SAA protein but a different relative arrangement of fibril protein stacks. These data establish that serum amyloid A-derived amyloid fibrils share the same fibril protein fold in different mouse strains and disease contexts.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"437 24","pages":"Article 169438"},"PeriodicalIF":4.5,"publicationDate":"2025-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145058252","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}