Journal of Molecular Biology最新文献

{"title":"GTFKAN: A Novel Microbe-drug Association Prediction Model Based on Graph Transformer and Fourier Kolmogorov-Arnold Networks","authors":"Jiacheng Lai,&nbsp;Zhen Zhang,&nbsp;Bin Zeng,&nbsp;Lei Wang","doi":"10.1016/j.jmb.2025.169201","DOIUrl":"10.1016/j.jmb.2025.169201","url":null,"abstract":"<div><div>Microbes have been shown to be closely related to human health. In recent years, lots of computational methods for predicting microbial-drug association have been proposed. In this manuscript, we introduced a novel predictive model, called GTFKAN, to identify potential microbe-drug associations by combining Graph Transformation Networks (GTN) with Fourier Kolmogorov-Arnold Networks (FKAN). In GTFKAN, we would first compute the Gaussian kernel and functional similarity of microbes and drugs respectively, and then adopt random walk and restart (RWR) methods to enhance these similar features to construct a new microbe-drug heterogeneous network HN. At the same time, we would further calculate the cosine similarity of microbes and diseases to construct another microbe-drug heterogeneous network LDIM. Next, we would input HN into GTN to derive the location and structural features of microorganisms and drugs, and input LDIM into FKAN to extract the hidden higher-order features of microorganisms and drugs, respectively. Finally, we would integrate these two features extracted by GTN and FKAN and feed the integrated features into the MLP classifier to infer potential microbial-drug associations. Moreover, to evaluate the performance of GTFKAN, we compared it with state-of-the-art methods based on well-known public datasets, and the experimental results show that GTFKAN can achieve satisfactory predictive performance. In addition, the results of ablation experiments and case studies also demonstrated the superiority of GTFKAN, which means that GTFKAN may be a useful microbial-drug association prediction tool in the future.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"437 17","pages":"Article 169201"},"PeriodicalIF":4.7,"publicationDate":"2025-05-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143955189","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":"Allosteric Modulation of SERCA Pumps in Health and Disease: Structural Dynamics, Posttranslational Modifications, and Therapeutic Potential.","authors":"Jana Viskupicova, L Michel Espinoza-Fonseca","doi":"10.1016/j.jmb.2025.169200","DOIUrl":"10.1016/j.jmb.2025.169200","url":null,"abstract":"<p><p>Sarco/endoplasmic reticulum (SR/ER) Ca²⁺-ATPase (SERCA) pumps are ubiquitous membrane proteins in all eukaryotic cells, playing a central role in maintaining intracellular calcium homeostasis by re-sequestering Ca²⁺ ions from the cytosol into the SR/ER at the expense of ATP hydrolysis. SERCA pumps are well-characterized components of the calcium transport machinery in the cell, playing a role in various physiological processes, including muscle contraction, energy metabolism, secretion exocytosis, gene expression, synaptic transmission, cell survival, and fertilization. Allosteric regulation of SERCA pumps plays a key role in health and disease, and modulation of the SERCA pumps has emerged as a therapeutic approach for the treatment of cardiovascular, muscular, metabolic, and neurodegenerative disorders. In this review, we provide a comprehensive overview of the structural dynamics underlying allosteric modulation of SERCA, focusing on the effects of endogenous regulatory proteins, Ca²⁺ ions, ATP, and small molecules. We also examine in detail the role of posttranslational modifications as allosteric modulators of SERCA function, focusing on the oxidative modifications S-glutathionylation, S-nitrosylation, tyrosine nitration, and carbonylation, and non-oxidative modifications that include SUMOylation, acetylation, O-GlcNAcylation, phosphorylation, and ubiquitination. Finally, we discuss the therapeutic potential and challenges of allosteric modulation of SERCA pumps, including the design of small-molecule effectors, microRNA-based interventions, and targeted strategies that modulate SERCA posttranslational regulation. Overall, this review aims to bridge the gap between the mechanisms underlying allosteric modulation of SERCA and the translation of basic science discoveries into effective therapies targeting SERCA pumps.</p>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":" ","pages":"169200"},"PeriodicalIF":4.7,"publicationDate":"2025-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143955262","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":"TopCysteineDB: A Cysteinome-wide Database Integrating Structural and Chemoproteomics Data for Cysteine Ligandability Prediction","authors":"Michele Bonus ,&nbsp;Julian Greb ,&nbsp;Jaimeen D. Majmudar ,&nbsp;Markus Boehm ,&nbsp;Magdalena Korczynska ,&nbsp;Azadeh Nazemi ,&nbsp;Alan M. Mathiowetz ,&nbsp;Holger Gohlke","doi":"10.1016/j.jmb.2025.169196","DOIUrl":"10.1016/j.jmb.2025.169196","url":null,"abstract":"<div><div>Development of targeted covalent inhibitors and covalent ligand-first approaches have emerged as a powerful strategy in drug design, with cysteines being attractive targets due to their nucleophilicity and relative scarcity. While structural biology and chemoproteomics approaches have generated extensive data on cysteine ligandability, these complementary data types remain largely disconnected. Here, we present <em>TopCysteineDB</em>, a comprehensive resource integrating structural information from the PDB with chemoproteomics data from activity-based protein profiling experiments. Analysis of the complete PDB yielded 264,234 unique cysteines, while the proteomics dataset encompasses 41,898 detectable cysteines across the human proteome. Using <em>TopCovPDB</em>, an automated classification pipeline complemented by manual curation, we identified 787 covalent cysteines and systematically categorized other functional roles, including metal-binding, cofactor-binding, and disulfide bonds. Mapping residue-wise structural information to sequence space enabled cross-referencing between structural and proteomics data, creating a unified view of cysteine ligandability. For <em>TopCySPAL</em>, a machine learning model was developed, integrating structural features and proteomics data, achieving strong predictive performance (AUROC: 0.964, AUPRC: 0.914) and robust generalization to novel cases. <em>TopCysteineDB</em> and <em>TopCySPAL</em> are freely accessible through a webinterface, <em>TopCysteineDBApp</em> (<span><span>https://topcysteinedb.hhu.de/</span><svg><path></path></svg></span>), designed to facilitate exploration of cysteine sites across the human proteome. The interface provides an interactive visualization featuring a color-coded mapping of chemoproteomics data onto cysteine site structures and the highlighting of identified peptide sequences. It offers customizable dataset downloads and ligandability predictions for user-provided structures. This resource advances targeted covalent inhibitor design by providing integrated access to previously dispersed data types and enabling systematic analysis and prediction of cysteine ligandability.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"437 15","pages":"Article 169196"},"PeriodicalIF":4.7,"publicationDate":"2025-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143954853","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":"Insight into the Conformational Ensembles Formed by U–U and T–T Mismatches in RNA and DNA Duplexes From a Structure-based Survey, NMR, and Molecular Dynamics Simulations","authors":"Ainan Geng ,&nbsp;Rohit Roy ,&nbsp;Stephanie Gu ,&nbsp;Serafima Guseva ,&nbsp;Supriya Pratihar ,&nbsp;Yeongjoon Lee ,&nbsp;Linshu Li ,&nbsp;Isaac J. Kimsey ,&nbsp;Mark A. Wilson ,&nbsp;Hashim M. Al-Hashimi","doi":"10.1016/j.jmb.2025.169197","DOIUrl":"10.1016/j.jmb.2025.169197","url":null,"abstract":"<div><div>Nucleic acid base pairs interconvert between alternative conformations on a free energy landscape, and these dynamics play critical roles in recognition, folding, and catalysis. U–U and T–T mismatches can adopt two nearly isoenergetic wobble conformations, distinguished by their relative shearing displacements. Experimental NMR evidence suggests that these conformations dynamically interconvert in RNA motifs containing tandem U–U mismatches. However, whether such motions occur ubiquitously across U–U and T–T mismatches remains unknown, as high-resolution nucleic acid structures typically report only a single conformation. Here, we used NMR spectroscopy, a structure-based survey of the Protein Data Bank, and molecular dynamics (MD) simulations to investigate wobble dynamics in U–U and T–T mismatches when flanked by canonical Watson-Crick base pairs in RNA and DNA duplexes. The structure-based survey revealed that U–U mismatches have propensities to adopt alternative wobble conformations even when controlling for sequence and identified potential intermediates along the wobble transition. Off-resonance <em>R</em>_1ρ relaxation dispersion experiments detected no micro- to millisecond dynamics for U–U mismatches in duplex RNA and T–T mismatches in duplex DNA. However, alternative conformer refinement of the electron density in X-ray structures, inter-proton NOEs, carbonyl carbon chemical shifts, an RDC-derived conformational ensemble, and MD simulations indicated that U–U and T–T mismatches exist in a dynamic equilibrium between two wobble conformations, with the minor state exceeding 30% and the transitions occurring on the nanosecond timescale. Our findings suggest that U–U and T–T ubiquitously undergo sub-microsecond wobble motions, contributing to the energetic landscape and dynamic plasticity of nucleic acids, with important implications for processes that generate and act on these mismatches.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"437 17","pages":"Article 169197"},"PeriodicalIF":4.7,"publicationDate":"2025-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143957904","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":"Mammalian Queuosine tRNA Modification Impacts Translation to Enhance Cell Proliferation and MHC-II Expression","authors":"Olivia N.P. Zbihley ,&nbsp;Katherine Johnson ,&nbsp;Luke R. Frietze ,&nbsp;Wen Zhang ,&nbsp;Marcus Foo ,&nbsp;Hoang Anh V. Tran ,&nbsp;Nicolas Chevrier ,&nbsp;Tao Pan","doi":"10.1016/j.jmb.2025.169188","DOIUrl":"10.1016/j.jmb.2025.169188","url":null,"abstract":"<div><div>Queuosine (Q) is a conserved tRNA modification in the wobble anticodon position of tRNAs that read codons of Tyr/His/Asn/Asp. Eukaryotic tRNA Q-modification requires the metabolite queuine – derived from diet or catabolism of the gut microbiome – and a host-genome encoded enzyme complex, QTRT1/QTRT2. tRNA Q-modification has been shown to regulate translational efficiency, but the response of the mammalian transcriptome and tRNAome to tRNA Q-modification in the context of cell proliferation has not been thoroughly investigated. Using cells that differ only in their tRNA Q-modification levels, we found that both human HEK293T cultures and the primary, murine bone marrow-derived dendritic cells (BMDCs) proliferate faster when tRNA Q-modification level is high. We carried out tRNA-seq and mRNA-seq to elucidate the molecular mechanisms underlying this phenotype, revealing distinct tRNA modification and transcriptome changes associated with altered proliferation. In both cell types, the m²₂G tRNA modification is positively correlated to Q-modification, consistent with its reported role in enhancing translational efficiency. We also find that elevated Q-modification levels result in transcriptome changes, but in a context-dependent manner. In HEK293T cells, upregulated genes are in catabolic processes and signaling pathway activation; whereas in BMDCs, upregulated genes are in immune response mediation, proliferation, and immunoglobulin diversification. Codon usage analysis of differentially expressed transcripts is consistent with Q-modification enhancing the translation of ribosomal proteins, which increases cell proliferation. We also find that tRNA Q-modification increases surface presentation of MHC-II in BMDCs. Our results provide insights into the broader implications of tRNA Q-modifications in regulating diverse biological functions.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"437 16","pages":"Article 169188"},"PeriodicalIF":4.7,"publicationDate":"2025-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143955969","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":"An acetylated Lysine Residue of Its Low-glucose Inhibitory Domain Controls Activity and Protein Interactions of ChREBP","authors":"Konstantin M. Petricek ,&nbsp;Marieluise Kirchner ,&nbsp;Manuela Sommerfeld ,&nbsp;Heike Stephanowitz ,&nbsp;Marie F. Kiefer ,&nbsp;Yueming Meng ,&nbsp;Sarah Dittrich ,&nbsp;Henriette E. Dähnhardt ,&nbsp;Knut Mai ,&nbsp;Eberhard Krause ,&nbsp;Philipp Mertins ,&nbsp;Sylvia J. Wowro ,&nbsp;Michael Schupp","doi":"10.1016/j.jmb.2025.169189","DOIUrl":"10.1016/j.jmb.2025.169189","url":null,"abstract":"<div><div>Carbohydrate response element-binding protein (ChREBP) is a transcription factor activated by glucose metabolites that orchestrates the expression of genes involved in glycolysis, <em>de novo</em> lipogenesis, and ATP homeostasis. Inadequate ChREBP activity impairs the cellular adaptations to glucose exposure and in humans associates with dyslipidemia, fatty liver disease, and type 2 diabetes. ChREBP activity is regulated by cytosolic-nuclear translocation involving its low-glucose inhibitory domain (LID). Whether this domain is targeted by post-translational lysine acetylation is unknown. Here we report a novel LID acetylation site that controls activity and protein interactions of ChREBP. Mutation of this residue increased glucose-induced activity and target gene expression of ChREBP. Mechanistically, mutant ChREBP protein showed more nuclear localization and enhanced genomic binding to a target promoter. Interactions with proteins that exhibit differential binding upon glucose exposure were attenuated by the mutation, demonstrating the importance of the LID in the formation of the protein interactome. Particularly interactions with 14-3-3 proteins, factors that regulate cytosolic/nuclear trafficking of ChREBP, were reduced, whereas interactions with proteins of the nucleosome remodeling deacetylase complex (NuRD) were increased. These molecular insights may shape new therapeutic strategies to target ChREBP activity and counteract metabolic diseases.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"437 17","pages":"Article 169189"},"PeriodicalIF":4.7,"publicationDate":"2025-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143951797","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 Minimal Translation System of the Plasmodium falciparum Apicoplast: Essential tRNA-modifying Enzymes and Their Roles in Organelle Maintenance","authors":"Rubayet Elahi ,&nbsp;Sebastian Mesones Mancilla ,&nbsp;Montana L. Sievert ,&nbsp;Luciana Ribeiro Dinis ,&nbsp;Opeoluwa Adewale-Fasoro ,&nbsp;Alexis Mann ,&nbsp;Yonatan Zur ,&nbsp;Sean T. Prigge","doi":"10.1016/j.jmb.2025.169156","DOIUrl":"10.1016/j.jmb.2025.169156","url":null,"abstract":"<div><div>Post-transcriptional tRNA modifications are essential for accurate and efficient protein translation across all organisms. The apicoplast organelle genome of <em>Plasmodium falciparum</em> contains a minimal set of 25 complete tRNA isotypes, making it an ideal model for studying minimal translational machinery. Efficient decoding of mRNA codons by this limited tRNA set depends on post-transcriptional modifications. In this study, we sought to define the minimal set of tRNA-modifying enzymes. Using comparative genomics and apicoplast protein localization prediction tools, we identified 16 nucleus-encoded tRNA-modifying enzymes predicted to localize to the apicoplast. Experimental studies confirmed apicoplast localization for 14 enzymes, including two with dual localization. Combining an apicoplast metabolic bypass parasite line with gene disruption tools, we disrupted 12 of the 14 apicoplast-localized enzymes. Six of these enzymes were found to be essential for parasite survival, and six were dispensable. All six essential enzymes are thought to catalyze modifications in the anticodon loop of tRNAs, and their deletions resulted in apicoplast disruption. Of the two genes refractory to deletion, one exhibited dual localization, suggesting essential functions outside the apicoplast. The other, which appears to localize solely to the apicoplast, may play an indispensable role that is not circumvented by our metabolic bypass. Our findings suggest the apicoplast translation system relies on a minimal set of tRNA modifications concentrated in the anticodon loop. This work advances our understanding of minimal translational machinery in reduced organelles, such as the apicoplast, with promising applications in synthetic biology.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"437 16","pages":"Article 169156"},"PeriodicalIF":4.7,"publicationDate":"2025-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143955303","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":"Structure of an Unfavorable de Novo DNA Methylation Complex of Plant Methyltransferase ZMET2","authors":"Genevieve Herle ,&nbsp;Jian Fang ,&nbsp;Jikui Song","doi":"10.1016/j.jmb.2025.169186","DOIUrl":"10.1016/j.jmb.2025.169186","url":null,"abstract":"<div><div>DNA methylation is an important epigenetic mechanism that controls the assembly of heterochromatin and gene expression. In plants, DNA methylation occurs in both CG and non-CG contexts, with non-CG methylation showing notable substrate sequence dependence. The plant DNA methyltransferase CMT3 mediates maintenance of CHG (H = A, C, or T) DNA methylation, with a strong substrate preference for the hemimethylated CWG (W = A, T) motif. Yet, the underlying mechanism remains elusive. Here we present a crystal structure of ZMET2, the CMT3 ortholog from <em>Zea mays</em> (maize), in complex with a DNA substrate containing an unmethylated CTG motif and a histone peptide carrying a mimic of the histone H3K9me2 modification. Structural comparison of the ZMET2-CTG complex with the previously reported structure of ZMET2 bound to hemimethylated CAG DNA reveals similar but distinct protein-DNA interactions centered on the CWG motif, providing insight into the methylation state- and substrate sequence-specific ZMET2/CMT3-substrate interaction. Furthermore, our combined structural and biochemical analysis reveals a role for the +3-flanking base of the target cytosine in fine-tuning ZMET2-mediated DNA methylation and its functional interplay with the +1- and +2-flanking sites. Together, these results provide deep mechanistic insights into the substrate specificity of CMT3 DNA methyltransferases in plants.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"437 17","pages":"Article 169186"},"PeriodicalIF":4.7,"publicationDate":"2025-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143948820","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":"Solution AFM Imaging and Coarse-grained Molecular Modeling of Yeast Condensin Structural Variation Coupled to the ATP Hydrolysis Cycle","authors":"Hiroki Koide ,&nbsp;Noriyuki Kodera ,&nbsp;Shoji Takada ,&nbsp;Tsuyoshi Terakawa","doi":"10.1016/j.jmb.2025.169185","DOIUrl":"10.1016/j.jmb.2025.169185","url":null,"abstract":"<div><div>Condensin is a protein complex that regulates chromatin structural changes during mitosis. It varies the molecular conformation through the ATP hydrolysis cycle and extrudes DNA loops into its ring-like structure as a molecular motor. Condensin contains Smc2 and Smc4, in which a coiled-coil arm tethers the hinge and head domains and dimerizes at the hinge. ATPs bind between the heads, induce their engagement, and are hydrolyzed to promote their disengagement. Previously, we performed solution atomic force microscopy (AFM) imaging of yeast condensin holo-complex with ATP and conducted flexible molecular fitting, obtaining the hinge structure with open conformation. However, it has yet to be clarified how the opening/closing of the hinge is coupled to the ATP hydrolysis cycle. In this study, we performed solution AFM imaging in the presence and absence of varying nucleotides, including AMP-PNP, ATPγS, and ADP. Furthermore, we conducted molecular dynamics simulations of an Smc2/4 heterodimer and selected the structure best representing each AFM image. Our results suggested that head engagement upon ATP binding is coupled to hinge opening and that the N-terminal region of Brn1, one of the accessory subunits, re-associates to the Smc2 head after ADP release.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"437 17","pages":"Article 169185"},"PeriodicalIF":4.7,"publicationDate":"2025-05-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143951645","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":"A F420-dependent Single Domain Chemogenetic Tool for Protein De-dimerization","authors":"James Antoney ,&nbsp;Stephanie Kainrath ,&nbsp;Joshua G. Dubowsky ,&nbsp;F.Hafna Ahmed ,&nbsp;Suk Woo Kang ,&nbsp;Emily R.R. Mackie ,&nbsp;Gustavo Bracho Granado ,&nbsp;Tatiana P. Soares da Costa ,&nbsp;Colin J. Jackson ,&nbsp;Harald Janovjak","doi":"10.1016/j.jmb.2025.169184","DOIUrl":"10.1016/j.jmb.2025.169184","url":null,"abstract":"<div><div>Protein-protein interactions (PPIs) mediate many fundamental cellular processes. Control of PPIs through optically or chemically responsive protein domains has had a profound impact on basic research and some clinical applications. Most chemogenetic methods induce the association, i.e., dimerization or oligomerization, of target proteins, whilst the few available dissociation approaches either break large oligomeric protein clusters or heteromeric complexes. Here, we have exploited the controlled dissociation of a homodimeric oxidoreductase from mycobacteria (MSMEG_2027) by its native cofactor, F₄₂₀, which is not present in mammals, as a bioorthogonal monomerization switch. Using X-ray crystallography, we found that in the absence of F₄₂₀ MSMEG_2027 forms a unique domain-swapped dimer that occludes the cofactor binding site. Rearrangement of the N-terminal helix upon F₄₂₀ binding results in the dissolution of the dimer. We then showed that MSMEG_2027 can be fused to proteins of interest in human cells and applied it as a tool to induce and release MAPK/ERK signalling downstream of a chimeric fibroblast growth factor receptor 1 (FGFR1) tyrosine kinase. This F₄₂₀-dependent chemogenetic de-homodimerization tool is stoichiometric and based on a single domain and thus represents a novel mechanism to investigate protein complexes <em>in situ</em>.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"437 17","pages":"Article 169184"},"PeriodicalIF":4.7,"publicationDate":"2025-05-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143958135","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}