Journal of Molecular Biology最新文献

{"title":"Structural basis of substrate accommodation and thiourea-mediated inhibition of the Mycobacterium tuberculosis dehydratase HadAB.","authors":"Soumya Sarathi Ganguly, Rituparna Saha, Bina Kumari Singh, Soumya De, Amit Kumar Das","doi":"10.1016/j.jmb.2026.170053","DOIUrl":"https://doi.org/10.1016/j.jmb.2026.170053","url":null,"abstract":"<p><p>Mycobacterium tuberculosis relies on the fatty acid synthase II (FAS II) pathway for the biosynthesis of mycolic acids, which are essential components of its lipid-rich cell envelope and major contributors to intrinsic drug resistance. The HadAB dehydratase complex catalyzes a critical dehydration step during early meromycolate chain elongation; however, the structural basis governing substrate accommodation and inhibitor recognition has remained unclear. Here, we report the first substrate-bound crystal structure of M. tuberculosis HadAB in complex with Palmitoyl-CoA at 1.69 Å resolution, revealing the architecture and dynamic remodeling of the acyl housing tunnel. The structure reveals that the tunnel is formed at the HadA-HadB interface, with HadA contributing primarily to substrate accommodation and HadB providing the catalytic machinery. Comparison with the previously determined apo-structure reveals substrate-induced displacement of the α4 hot-dog helix of HadA, resulting in elongation and reshaping of the tunnel to accommodate fatty acyl intermediates. The structure further reveals the positioning of Cys61, at the distal end of the acyl housing tunnel, and Cys105, which mediate covalent inhibition by thiourea-derived compounds. Biochemical analyses demonstrate selective activation of Thioacetazone and SPA0355 by mycobacterial Baeyer-Villiger monooxygenases, EthA and MymA, leading to cysteine-dependent modification and inhibition of HadAB. A cell viability assay against Mycobacterium smegmatis demonstrated promising antimycobacterial activity for SPA0355, similar to Thioacetazone. Furthermore, modelling of HadAB-AcpM provided insights into the interaction between HadAB and its physiological acyl carrier protein AcpM. Together, these findings establish the molecular basis of substrate recognition, tunnel plasticity, and prodrug-mediated inhibition of HadAB, providing a framework for structure-guided development of therapeutics that target mycobacterial lipid biosynthesis.</p>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":" ","pages":"170053"},"PeriodicalIF":4.7,"publicationDate":"2026-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149126221","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":"MutTMP Stab-pred: Predicting Thermodynamic Stability Changes Upon Mutations in α-helical and β-barrel Membrane Proteins.","authors":"P Ramakrishna Reddy, A Kulandaisamy, M Michael Gromiha","doi":"10.1016/j.jmb.2026.170052","DOIUrl":"10.1016/j.jmb.2026.170052","url":null,"abstract":"<p><p>Membrane proteins (TMPs) are integral components of cell membranes that adopt two principal structural folds, transmembrane α-helical proteins (TMHs) and transmembrane β-barrel proteins (TMBs). Mutations in these proteins can substantially alter their native structure, folding, and function, and are often implicated in human diseases. Although several computational approaches have been developed to predict the effects of mutations on protein stability, their performance for TMPs remains limited. To address this problem, we compiled a dataset of 379 membrane protein mutations with experimentally measured stability changes (ΔΔG⁰) from the MPTherm database and developed two machine-learning models for predicting ΔΔG⁰ of TMHs and TMBs using sequence, structure, and energetic features. Our method, MutTMH Stab-pred could predict ΔΔG⁰ of TMHs with a correlation and mean absolute error (MAE) of 0.70 and 0.92 kcal/mol, respectively on the hold-out test set. Further, the MutTMB Stab-pred method could predict ΔΔG⁰ of TMBs with a correlation and MAE of 0.92 and 0.97 kcal/mol, respectively, on the hold-out test set. In leave-one-protein-out and leave-one-homology-cluster-out cross-validation, the MAEs are 1.36 and 1.37 kcal/mol, respectively for MutTMH Stab-pred and 1.31 and 1.35 kcal/mol for MutTMB Stab-pred. Both models are freely available at https://web.iitm.ac.in/bioinfo2/MutTMP%20Stab-pred/. As a large-scale application, we analyzed the stability changes of 33,449 disease-associated and benign missense mutations from the MutDPAL dataset and found that disease-associated mutations were predicted to be destabilizing more frequently than benign mutations. These computational tools provide a valuable resource for understanding mutation-induced stability changes in membrane proteins at a large scale.</p>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":" ","pages":"170052"},"PeriodicalIF":4.7,"publicationDate":"2026-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149102296","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":"RNAdex: graph-based 3D RNA Motif library incorporating non-Watson-Crick interactions.","authors":"Jingyi Li, Jian Wang, Srinivasan Ekambaram, Nikolay V Dokholyan","doi":"10.1016/j.jmb.2026.170047","DOIUrl":"10.1016/j.jmb.2026.170047","url":null,"abstract":"<p><p>The structures of RNA exhibit recurrent patterns, which are defined as motifs. Motifs are crucial for the biological functions of RNA molecules. A 3D RNA motif library includes 3D RNA structures, providing a resource for motif-based 3D RNA structure prediction and design. Existing motif libraries face challenges in systematically extracting and classifying highly complex topologies with crossing interactions and non-Watson-Crick interactions. To overcome this limitation, we built RNAdex, an RNA motif library that stores 3D atomic coordinates and incorporates non-Watson-Crick interactions and crossing interactions from the Protein Data Bank. Leveraging motifs from RNAdex, we developed a measure of motif-content similarity between RNAs and observed that the pairwise similarity scores resemble a power-law distribution. To explore this macroscopic statistical pattern, we present a physics-inspired, hypothesis-generating framework for RNA structural evolution. RNAdex motif graphs were used to compare motif content and formulate testable hypotheses about RNA structural evolution. RNAdex is available athttps://rnadex.dokhlab.org.</p>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":" ","pages":"170047"},"PeriodicalIF":4.7,"publicationDate":"2026-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149102260","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":"Structural Insights into MLKL-Mediated Necroptosis: Emerging Mechanisms.","authors":"Brooke Dreyer, Jianbin Ruan","doi":"10.1016/j.jmb.2026.170030","DOIUrl":"10.1016/j.jmb.2026.170030","url":null,"abstract":"<p><p>Necroptosis is a regulated form of lytic cell death that plays important roles in inflammation, host defense, and disease. Central to this pathway is mixed lineage kinase domain-like (MLKL) protein, the terminal effector responsible for membrane disruption. Upon phosphorylation by receptor-interacting protein kinase 3 (RIPK3), MLKL undergoes conformational changes, oligomerizes, and translocates to cellular membranes. However, despite extensive study the detailed molecular mechanism by which MLKL mediates necroptotic cell death remains incompletely understood. Multiple models have been proposed including pore formation, higher-order or amyloid-like polymerization, and cation channel formation, yet each is supported by limited and often indirect evidence. Notably, high-resolution structures of membrane-associated, active MLKL assemblies are still unresolved, hindering a unified mechanistic understanding. In addition, emerging studies suggest that membrane permeabilization and terminal membrane rupture may be mechanistically distinct processes, potentially involving additional effectors such as SIGLEC12. In this review, we summarize current structural and mechanistic insights into MLKL, including its domain architecture, activation mechanisms, and species-specific divergences. We then evaluate competing models of MLKL-mediated membrane disruption and highlight key challenges and future directions. We emphasize the need to directly visualize the active, oligomeric MLKL assemblies in the membrane-bound state and to integrate structural, biochemical, and cellular approaches for a comprehensive understanding of MLKL-mediated membrane permeabilization. Resolving these questions will be essential for understanding necroptosis and for developing therapeutic strategies targeting MLKL-mediated cell death.</p>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":" ","pages":"170030"},"PeriodicalIF":4.7,"publicationDate":"2026-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149029477","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":"PrimerBac: A Searchable Database of Taxon-specific Primers for Rapid Microbial Identification.","authors":"Yingjian Hou, Shuo Feng, Mao Gu, Zhengxing Song, Yingying Ding, Zitong Wang, Yijia Hou, Jing Li, Xingzhen Lao","doi":"10.1016/j.jmb.2026.170027","DOIUrl":"10.1016/j.jmb.2026.170027","url":null,"abstract":"<p><p>Species-resolved PCR detection of gut microorganisms is challenged by within-species genomic diversity and sequence conservation among related taxa. We developed PrimerBac (https://primerbac.cn), a searchable database that integrates gut-focused reference collection, RefSeq pan-genome analysis, core-orthogroup marker selection, background screening, and assembly-level ePCR evaluation. The reference intestinal resource contains 1762 species, and complete pan-genome analyses were obtained for 1179 species. PrimerBac provides 1,148,644 primer pairs for 991 prokaryotic species and 611,077 pairs for 424 genera. Broad screening of 22,207 RefSeq reference/representative assemblies yielded 68.9% sensitivity. In a non-overlapping temporal panel of 4115 post-construction assemblies, 57 of 65 evaluable targets were detected (87.7% sensitivity; 95% CI, 77.5-93.6%), with 84.0% hit-defined macro precision. PrimerBac therefore provides a searchable and systematically evaluated resource for targeted microbial identification.</p>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":" ","pages":"170027"},"PeriodicalIF":4.7,"publicationDate":"2026-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149015178","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":"ZBP1 Evolution and Antagonism by Large DNA Viruses.","authors":"Mamadou Amadou Diallo, Jonathan Maelfait","doi":"10.1016/j.jmb.2026.170026","DOIUrl":"10.1016/j.jmb.2026.170026","url":null,"abstract":"<p><p>ZBP1 is a nucleic acid receptor that restricts virus infection by activating an inflammatory gene response and by inducing host cell death. Left-handed Z-form nucleic acids accumulating in infected cells activate ZBP1 by binding to its N-terminal Zα domains. Signal transduction relies on the presence of RIP homotypic interaction motifs (RHIMs) that recruit the RIPK1 and RIPK3 signalling kinases to induce NF-κB activation or cell death under the forms of apoptosis or necroptosis. The expression of Zα domain proteins by poxviruses and RHIM-containing proteins by herpesviruses that antagonise ZBP1 may reflect a long-standing evolutionary interaction between ZBP1-mediated immunity and large DNA viruses. Phylogenetic analysis shows that ZBP1 likely emerged during jawed vertebrate speciation with ZBP1 orthologues first appearing in cartilaginous fish. ZBP1 is subsequently lost in entire vertebrate clades, including bony fish, scaled reptiles, birds, marsupials, and rabbits and hares, suggesting reoccurring counterselection of ZBP1-based immunity. Evidence of a ZBP1-like protein in distantly related bivalve molluscs indicates that sensing of Z-form nucleic acids coupled to RHIM-mediated signal transduction has evolved at least twice throughout the animal kingdom. Here, we study the origins, structure and function of ZBP1 and its Zα domains and RHIMs, discuss their respective roles in sensing Z-nucleic acids and signal transduction, and review ZBP1's mutually antagonistic relationship with large DNA viruses.</p>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":" ","pages":"170026"},"PeriodicalIF":4.7,"publicationDate":"2026-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148987514","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":"TISON: A Web Server for Omics-driven Integrative Cancer Modeling & Simulations towards Personalized Medicine.","authors":"Zainab Nasir, Muhammad Umer Sultan, Mahnoor Naseer Gondal, Zain Bin Tanveer, Ammar Arif, Rida Nasir Butt, Abdul Rehman, Hira Anees Awan, Muhammad Faizyab Ali Chaudhary, Zainab Arshad, Waleed Ahmed, Ghulam Mustafa, Salaar Khan, Talha Ahmad Khan, Bibi Amina, Muhammad Farhan Khalid, Risham Hussain, Huma Khawar, Adan Tanveer, Sakina Ali Asghar, Shaoor Ahmad Khan, Sadia Mahmood, Rahma Ijaz, Osama Shiraz Shah, Hadia Hameed, Ammar Khan, Rida Akbar, Mahum Azhar, Susana Alam, Anmol Karim, Sameera Arzoo, Muhammad Farooq Ahmad Butt, Murtaza Taj, Sameer Ahmed, Syed Waqar Nabi, Wim Vanderbauwhede, Emad Ud Din, Fayyaz Ahmed, Aejaz Nasir, Amir Faisal, Usman Majeed, Safee Ullah Chaudhary","doi":"10.1016/j.jmb.2026.170025","DOIUrl":"https://doi.org/10.1016/j.jmb.2026.170025","url":null,"abstract":"<p><p>Next-generation sequencing (NGS) has catalyzed the generation of individualized multi-omics datasets, potentiating precise molecular insights into cancer initiation, progression, and metastasis. The subsequent data analytics have necessitated the development of computational pipelines that couple patient-specific omics with biomolecular network models, enabling personalized simulations for precision oncology. However, to date, no unified webserver supports patient-specific network modeling alongside systematic therapy prioritization and in silico therapeutic evaluation. To address this gap, we present TISON (Theatre for In-silico Systems Oncology; https://tison.lums.edu.pk/), a webserver for in-silico precision oncology. TISON integrates copy-number alterations, exome-derived somatic mutations, and transcriptomic expression data with biomolecular networks to generate patient-specific models. Dynamical analyses of these models help identify attractor states, characterize phenotypic transitions, and quantify oncogenic signaling. TISON further computes patient-specific drug scores and evaluates single and combined regimens on personalized networks to derive therapeutic response indices, including efficacy, cytotoxicity, resistivity, and overall therapeutic response. To demonstrate TISON's translational potential, we evaluated two head and neck squamous cell carcinoma patients from TCGA. Our results show that TISON-prioritized sequential therapies reprogrammed tumor networks from proliferative toward apoptosis-dominant states i.e. reducing propensity for proliferation from ∼0.65-0.88 to <0.15 while increasing apoptosis from ∼0.06-0.32 to >0.85. Next, TISON prioritizes therapeutic regimens by computing a therapeutic response index based on efficacy-cytotoxicity trade-offs. Taken together, these case studies demonstrate TISON as an integrated precision-oncology platform that operationalizes patient multi-omics data to augment clinically interpretable therapy prioritization and decision-support workflows.</p>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":" ","pages":"170025"},"PeriodicalIF":4.7,"publicationDate":"2026-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148981798","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":"NEK7 Accelerates NLRP3 Inflammasome Activation.","authors":"Svenja Wöhrle, Tamara Ćiković, Clara Dufossez, Emilia Neuwirt, Elena Puma, Franziska Kraatz, Anna Kostina, Oliver Gorka, Clemens Kreutz, Christina J Groß, Olaf Groß","doi":"10.1016/j.jmb.2026.169960","DOIUrl":"10.1016/j.jmb.2026.169960","url":null,"abstract":"<p><p>The NLRP3 inflammasome is a major driver of immunopathology, making it a sought-after drug target. In spite of two decades of intense research, its activation mechanism is still poorly understood, impeding inhibitor design. NEK7 was reported to be essential for NLRP3 activation, and several newly identified NLRP3 inhibitors were suggested to act by interfering with their interaction. Here we report that NEK7 accelerates, but is in principle dispensable for NLRP3 activation. The onset of inflammasome activation on the single-cell level was unaltered in the absence of NEK7, yet the rate of cells to undergo inflammasome formation and subsequent pyroptosis was approximately 4-fold reduced. Therefore, therapeutic targeting of the NEK7-NLRP3 interaction might have an incomplete effect, which has to be considered for drug development. We confirmed entrectinib as a NEK7-dependent inhibitor, while other published drug candidates turned out not to rely on its presence. Our results support two possible scenarios for the role of NEK7 in NLRP3 activation: either, NEK7 accelerates one unique pathway of NLRP3 activation, or it is essential for a first, fast pathway, while being dispensable for a second, slower NLRP3 activation pathway.</p>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":" ","pages":"169960"},"PeriodicalIF":4.7,"publicationDate":"2026-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148617860","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":"Bacterial Countermeasures Against Inflammasomes.","authors":"Aadrita Hazra, Bishajit Sarkar, Emma K Carlson, Sivapriya Kailasan Vanaja","doi":"10.1016/j.jmb.2026.169948","DOIUrl":"10.1016/j.jmb.2026.169948","url":null,"abstract":"<p><p>Inflammasomes are vital components of the innate immune system that sense invading pathogens and other danger signals. Upon activation, these cytosolic platforms induce pyroptotic cell death and IL-1 cytokine production. Inflammasome responses provide protection against several bacteria that cause serious diseases. Consequently, bacterial pathogens have evolved strategies to counteract inflammasome responses and establish colonization of the host. This review highlights the sophisticated mechanisms by which bacterial pathogens circumvent inflammasome-mediated antibacterial responses. An in-depth understanding of these inhibitory tactics will pave the way to the development of targeted therapeutic approaches.</p>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":" ","pages":"169948"},"PeriodicalIF":4.7,"publicationDate":"2026-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148468080","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":"Clinical Inflammasome Biomarkers: Progress and Prospects.","authors":"Jared R Coombs, Sabrina S Burgener, Kate Schroder","doi":"10.1016/j.jmb.2026.169941","DOIUrl":"10.1016/j.jmb.2026.169941","url":null,"abstract":"<p><p>Pathological inflammasome signalling fuels low-grade inflammation and drives chronic disease. This underlying subclinical inflammation is notoriously difficult to define and measure at the molecular level. Although inflammasome inhibitors in clinical development hold immense therapeutic potential across a range of disease indications, their progress to market is hampered by a lack of inflammasome-specific biomarkers, posing some barriers to investment and clinical translation. While direct indicators of inflammasome signalling specifically report pathway activity, they are experimental, technically challenging, and their assays remain non-standardised. Meanwhile, routinely measured markers of inflammation (e.g. acute-phase reactants) are the current foundation of clinical trials for anti-inflammatory drug candidates, including trials of inflammasome inhibitors, as they are easily detectable and clinically well-validated. Their relationship to inflammasome signalling, however, is distal and confounded by other inflammatory signalling networks. Novel biomarker strategies are urgently required that faithfully and reproducibly reflect inflammasome signalling in humans. Here, we review the trade-off between inflammasome specificity and feasibility, weighing the opportunities and limitations of both proximal and distal biomarkers of inflammasome signalling.</p>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":" ","pages":"169941"},"PeriodicalIF":4.7,"publicationDate":"2026-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148389701","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}