{"title":"Structure of an Unfavorable de Novo DNA Methylation Complex of Plant Methyltransferase ZMET2","authors":"Genevieve Herle , Jian Fang , 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 , Noriyuki Kodera , Shoji Takada , 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}
James Antoney , Stephanie Kainrath , Joshua G. Dubowsky , F.Hafna Ahmed , Suk Woo Kang , Emily R.R. Mackie , Gustavo Bracho Granado , Tatiana P. Soares da Costa , Colin J. Jackson , Harald Janovjak
{"title":"A F420-dependent Single Domain Chemogenetic Tool for Protein De-dimerization","authors":"James Antoney , Stephanie Kainrath , Joshua G. Dubowsky , F.Hafna Ahmed , Suk Woo Kang , Emily R.R. Mackie , Gustavo Bracho Granado , Tatiana P. Soares da Costa , Colin J. Jackson , 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, F<sub>420</sub>, which is not present in mammals, as a bioorthogonal monomerization switch. Using X-ray crystallography, we found that in the absence of F<sub>420</sub> MSMEG_2027 forms a unique domain-swapped dimer that occludes the cofactor binding site. Rearrangement of the N-terminal helix upon F<sub>420</sub> 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 F<sub>420</sub>-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}
{"title":"Hepatitis B Virus Nucleocapsid Assembly.","authors":"Xupeng Hong, William M Schneider, Charles M Rice","doi":"10.1016/j.jmb.2025.169182","DOIUrl":"10.1016/j.jmb.2025.169182","url":null,"abstract":"<p><p>Hepatitis B virus (HBV), the prototypical member of the Hepadnaviridae family, is a DNA virus that replicates its genome through reverse transcription of a pregenomic RNA (pgRNA) precursor. The selective packaging of pgRNA and viral polymerase (Pol) into assembling capsids formed by the viral core protein-a process known as nucleocapsid assembly-is an essential step in the HBV lifecycle. Advances in cellular and cell-free systems have provided significant insights into the mechanisms underlying capsid assembly, Pol binding to pgRNA, Pol-pgRNA packaging, and initiation of genome replication. However, the absence of a cell-free system capable of reconstituting selective HBV Pol-pgRNA packaging into fully assembled capsids leaves fundamental questions about nucleocapsid assembly unanswered. This review summarizes the current knowledge of HBV nucleocapsid assembly, focusing on the interplay between Pol-pgRNA interactions, capsid formation, and regulation by host factors. It also highlights the contribution of cellular and cell-free systems to these discoveries and underscores the need for new approaches that reconstitute the complete HBV nucleocapsid assembly process. With the growing interest in developing nucleocapsid assembly inhibitors, some of which are currently in clinical trials, targeting Pol-pgRNA interactions and nucleocapsid assembly represents a promising therapeutic strategy for curing chronic hepatitis B.</p>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":" ","pages":"169182"},"PeriodicalIF":4.7,"publicationDate":"2025-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143956772","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":"Artificial-intelligence-driven Innovations in Mechanistic Computational Modeling and Digital Twins for Biomedical Applications.","authors":"Bhanwar Lal Puniya","doi":"10.1016/j.jmb.2025.169181","DOIUrl":"10.1016/j.jmb.2025.169181","url":null,"abstract":"<p><p>Understanding of complex biological systems remains a significant challenge due to their high dimensionality, nonlinearity, and context-specific behavior. Artificial intelligence (AI) and mechanistic modeling are becoming essential tools for studying such complex systems. Mechanistic modeling can facilitate the construction of simulatable models that are interpretable but often struggle with scalability and parameters estimation. AI can integrate multi-omics data to create predictive models, but it lacks interpretability. The gap between these two modeling methods limits our ability to develop comprehensive and predictive models for biomedical applications. This article reviews the most recent advancements in the integration of AI and mechanistic modeling to fill this gap. Recently, with omics availability, AI has led to new discoveries in mechanistic computational modeling. The mechanistic models can also help in getting insight into the mechanism for prediction made by AI models. This integration is helpful in modeling complex systems, estimating the parameters that are hard to capture in experiments, and creating surrogate models to reduce computational costs because of expensive mechanistic model simulations. This article focuses on advancements in mechanistic computational models and AI models and their integration for scientific discoveries in biology, pharmacology, drug discovery and diseases. The mechanistic models with AI integration can facilitate biological discoveries to advance our understanding of disease mechanisms, drug development, and personalized medicine. The article also highlights the role of AI and mechanistic model integration in the development of more advanced models in the biomedical domain, such as medical digital twins and virtual patients for pharmacological discoveries.</p>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":" ","pages":"169181"},"PeriodicalIF":4.7,"publicationDate":"2025-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143957845","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}
Shuxiang Li, Jie Shu, James C Rober, Austin Macklem, Daniel Espiritu, Tanay Debnath, Samuel Tian, Daniel Tian, Maria J Aristizabal, Anna R Panchenko
{"title":"Deciphering Allosteric Modulation of Cancer-Associated Histone Missense Mutations.","authors":"Shuxiang Li, Jie Shu, James C Rober, Austin Macklem, Daniel Espiritu, Tanay Debnath, Samuel Tian, Daniel Tian, Maria J Aristizabal, Anna R Panchenko","doi":"10.1016/j.jmb.2025.169180","DOIUrl":"10.1016/j.jmb.2025.169180","url":null,"abstract":"<p><p>Histone mutations have been implicated in various cancers, but their mechanistic effects on chromatin dynamics remain largely unexplored. In this study, we investigated allosteric modulation effects induced by 40 cancer-associated histone missense mutations. By combining computational approaches with experimental evidence, we assessed the allosteric and functional impact of these mutations. Our results reveal that the allosteric effects of histone mutations are position-specific, with mutations near the H3 and H4 histone N-terminal tails exhibiting the strongest long-range perturbations. Notably, we predicted seven mutations with significant allosteric effects, potentially altering nucleosome interactions. Experimental verification of H2BS64Y and H2BS64F mutations demonstrated that they disrupted normal histone function, altered H2BK120 ubiquitination levels and genome stability, findings suggestive of their potential carcinogenic effects. Collectively, these results show that allostery may serve as a critical mechanism underlying the oncogenic potential of some histone mutations, highlighting the need for further exploration of allosteric pathways in cancer epigenetics.</p>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":" ","pages":"169180"},"PeriodicalIF":4.7,"publicationDate":"2025-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143962703","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":"The Evolution of Sequence Specificity in a DNA Binding Protein Family","authors":"Meghna Nandy , Madhumitha Krishnaswamy , Mohak Sharda , Aswin Sai Narain Seshasayee","doi":"10.1016/j.jmb.2025.169177","DOIUrl":"10.1016/j.jmb.2025.169177","url":null,"abstract":"<div><div>Transcriptional regulation enables bacteria to adjust to its environment. This is driven by transcription factors (TFs), which display DNA site recognition specificity with some flexibility built in. TFs, however, are not considered essential to a minimal cellular life. How did they evolve? It has been hypothesized that TFs evolve by gaining specificity (and other functions) on a background of non-specific chromosome structuring proteins. We used the IHF/HU family of DNA binding proteins, in which IHF binds DNA in a sequence-specific manner, whereas HU binds more indiscriminately, to test this hypothesis. We show that HUβ has been present from the bacterial root, while both IHF subunits emerged much later and diversified in <em>Proteobacteria</em>, with HUα having possibly arisen from transfer events in <em>Gammaproteobacteria</em>. By reconstructing ancestral sequences <em>in-silico</em> on a rooted phylogeny of IHF/HU we show that the common ancestor of this family was probably HU-like and therefore non-specific in binding DNA. IHF evolved from a branch of HU after HU had substantially diverged. Various residues characteristic of IHFα and shown to be involved in specific sequence recognition (at least in <em>E. coli</em>) have likely been co-opted from preexisting residues in HU, while those residues of IHFβ have likely evolved independently, suggesting that each of the IHF subunits has undergone different trajectories to acquire their DNA binding properties.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"437 14","pages":"Article 169177"},"PeriodicalIF":4.7,"publicationDate":"2025-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143924349","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}
Aron W Fenton, Zoe A Hoffpauir, Tyler A Martin, Robert A Harris, Audrey L Lamb
{"title":"Are Allosteric Mechanisms Conserved Among Homologues?","authors":"Aron W Fenton, Zoe A Hoffpauir, Tyler A Martin, Robert A Harris, Audrey L Lamb","doi":"10.1016/j.jmb.2025.169176","DOIUrl":"https://doi.org/10.1016/j.jmb.2025.169176","url":null,"abstract":"<p><p>Conservation of allosteric mechanisms among homologues is often assumed but seldom tested. This assumption underpins key concepts like coevolution of residues involved in allosteric mechanisms and the comparison of structures of two different homologues to gain insights into allosteric mechanisms. As an initial assessment of whether allosteric mechanisms are conserved among homologues, this work reviews what is known about the allosteric mechanisms of liver pyruvate kinase (LPYK) vs. skeletal muscle pyruvate kinase (M<sub>1</sub>PYK), framed within a two-ligand allosteric energy cycle description of allosteric regulation. Selective observations from other PYK homologues are included when relevant. The primary focus of this review is on functional data, while expressing caution regarding the interpretation of allosteric mechanisms based solely on available X-ray crystallographic structures. Additionally, this review considers types of data that are currently lacking for these two PYK homologues, highlighting potential techniques that could be valuable for evaluating the conservation of allosteric mechanisms among homologues. In particular, a hybrid tetramer technique that has been used to study bacterial phosphofructokinases 1 is summarized. Interestingly, despite a high degree of similarity (66.5% sequence identity) between the LPYK and rM<sub>1</sub>PYK proteins, the available functional comparisons do not provide strong evidence for conserved allosteric mechanisms. Lastly, we consider whether insights into native allosteric mechanisms are relevant to allosteric mechanisms associated with allosteric drug designs.</p>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":" ","pages":"169176"},"PeriodicalIF":4.7,"publicationDate":"2025-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143951325","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}
Paul Campitelli, I Can Kazan, Sean Hamilton, S Banu Ozkan
{"title":"Dynamic Allostery: Evolution's Double-Edged Sword in Protein Function and Disease.","authors":"Paul Campitelli, I Can Kazan, Sean Hamilton, S Banu Ozkan","doi":"10.1016/j.jmb.2025.169175","DOIUrl":"https://doi.org/10.1016/j.jmb.2025.169175","url":null,"abstract":"<p><p>Allostery is a core mechanism in biology that allows proteins to communicate and regulate activity over long structural distances. While classical models of allostery focus on conformational changes triggered by ligand binding, dynamic allostery-where protein function is modulated through alterations in thermal fluctuations without major conformational shifts-has emerged as a critical evolutionary mechanism. This review explores how evolution leverages dynamic allostery to fine-tune protein function through subtle mutations at distal sites, preserving core structural architecture while dramatically altering functional properties. Using a combination of computational approaches including Dynamic Flexibility Index (DFI), Dynamic Coupling Index (DCI), and vibrational density of states (VDOS) analysis, we demonstrate that functional adaptations in proteins often involve \"hinge-shift\" mechanisms, where redistribution of rigid and flexible regions modulates collective motions without changing the overall fold. This evolutionary principle is a double-edged sword: the same mechanisms that enable functional innovation also create vulnerabilities that can be exploited in disease states. Disease-associated variants frequently occur at positions highly coupled to functional sites despite being physically distant, forming Dynamic Allosteric Residue Couples (DARC sites). We demonstrate applications of these principles in understanding viral evolution, drug resistance, and capsid assembly dynamics. Understanding dynamic allostery provides critical insights into protein evolution and offers new avenues for therapeutic interventions targeting allosteric regulation.</p>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":" ","pages":"169175"},"PeriodicalIF":4.7,"publicationDate":"2025-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143951799","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":"Science in the U.S. Is Under Attack – What Can We Do?","authors":"","doi":"10.1016/j.jmb.2025.169165","DOIUrl":"10.1016/j.jmb.2025.169165","url":null,"abstract":"","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"437 14","pages":"Article 169165"},"PeriodicalIF":4.7,"publicationDate":"2025-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143886276","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}