Pub Date : 2026-03-01Epub Date: 2025-08-11DOI: 10.1016/j.jmb.2025.169385
Wilma K. Olson , Nicolas Clauvelin , Stefjord Todolli , Xiang-Jun Lu
The three-dimensional architecture of the genome is intimately tied to fundamental biological processes. How the primary sequence of DNA base pairs leads to the complex folding and dynamics of a full chromosome is an open question. Here we present a picture of chromatin folding that is emerging from the combination of fine structural data with novel experimental measurements and increasingly coarse grained, interconnected levels of DNA modeling. We draw attention to the role of DNA twist in the spacing of nucleosomes and the effects of nucleosome spacing and the surprising influence of nucleosomal twist on the expansion and compression of short simulated chromatin arrays. We also discuss the connection between base-pair and nucleosome-level treatments of DNA and the direct connection between protein and DNA fine structure, with investigations of chromatin looping based on these treatments.
{"title":"Contributions of Local Structural and Energetic Features of DNA to Large-scale Genomic Organization","authors":"Wilma K. Olson , Nicolas Clauvelin , Stefjord Todolli , Xiang-Jun Lu","doi":"10.1016/j.jmb.2025.169385","DOIUrl":"10.1016/j.jmb.2025.169385","url":null,"abstract":"<div><div>The three-dimensional architecture of the genome is intimately tied to fundamental biological processes. How the primary sequence of DNA base pairs leads to the complex folding and dynamics of a full chromosome is an open question. Here we present a picture of chromatin folding that is emerging from the combination of fine structural data with novel experimental measurements and increasingly coarse grained, interconnected levels of DNA modeling. We draw attention to the role of DNA twist in the spacing of nucleosomes and the effects of nucleosome spacing and the surprising influence of nucleosomal twist on the expansion and compression of short simulated chromatin arrays. We also discuss the connection between base-pair and nucleosome-level treatments of DNA and the direct connection between protein and DNA fine structure, with investigations of chromatin looping based on these treatments.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"438 5","pages":"Article 169385"},"PeriodicalIF":4.5,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144843978","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}
Pub Date : 2026-03-01Epub Date: 2025-12-18DOI: 10.1016/j.jmb.2025.169599
Raoul E. Herzog, Isabelle F. Harvey-Seutcheu, Philipp Janke, Wenzhao Dai, Paul M. Fischer, Peter Hamm, Philipp J. Heckmeier
Light-sensitive proteins allow organisms to perceive and respond to their environment, and have diversified over billions of years. Among these, Light-Oxygen-Voltage (LOV) domains are widespread photosensors that control diverse physiological processes and are increasingly used in optogenetics. Yet, the evolutionary constraints that shaped their protein dynamics and thereby their functional diversity remain poorly resolved. Here we systematically characterize the dynamics of 21 natural LOV core domains, significantly extending the spectroscopically resolved catalog through the addition of 18 previously unstudied variants. Using time-resolved spectroscopy, we uncover an exceptional kinetic diversity spanning from picoseconds to days and identify distinct functional clusters within the LOV family. These clusters reflect evolutionary branching, including a divergence of 1.0 billion years between investigatedLOV variants from plants and 0.4 billion years of separation within one of these functional clusters. Individual variants with extreme photocycles emerge as promising anchor points for optogenetic applications, ranging from highly efficient adduct formation to ultrafast recovery. Beyond natural diversity, we introduce a LOV domain generated by artificial intelligence-guided protein design. Despite being sequentially remote from its maternal template, this variant retains core photocycle function while exhibiting unique biophysical properties, thereby occupying a new region on the biophysical landscape. Our work emphasizes how billions of years of evolution defined LOV protein dynamics, and how protein design can expand this repertoire, engineering next-generation optogenetic tools.
{"title":"Evolution and design shape protein dynamics in LOV domains – spanning picoseconds to days","authors":"Raoul E. Herzog, Isabelle F. Harvey-Seutcheu, Philipp Janke, Wenzhao Dai, Paul M. Fischer, Peter Hamm, Philipp J. Heckmeier","doi":"10.1016/j.jmb.2025.169599","DOIUrl":"10.1016/j.jmb.2025.169599","url":null,"abstract":"<div><div>Light-sensitive proteins allow organisms to perceive and respond to their environment, and have diversified over billions of years. Among these, Light-Oxygen-Voltage (LOV) domains are widespread photosensors that control diverse physiological processes and are increasingly used in optogenetics. Yet, the evolutionary constraints that shaped their protein dynamics and thereby their functional diversity remain poorly resolved. Here we systematically characterize the dynamics of 21 natural LOV core domains, significantly extending the spectroscopically resolved catalog through the addition of 18 previously unstudied variants. Using time-resolved spectroscopy, we uncover an exceptional kinetic diversity spanning from picoseconds to days and identify distinct functional clusters within the LOV family. These clusters reflect evolutionary branching, including a divergence of <span><math><mrow><mo>≈</mo></mrow></math></span>1.0 billion years between investigatedLOV variants from plants and <span><math><mrow><mo>≈</mo></mrow></math></span>0.4 billion years of separation within one of these functional clusters. Individual variants with extreme photocycles emerge as promising anchor points for optogenetic applications, ranging from highly efficient adduct formation to ultrafast recovery. Beyond natural diversity, we introduce a LOV domain generated by artificial intelligence-guided protein design. Despite being sequentially remote from its maternal template, this variant retains core photocycle function while exhibiting unique biophysical properties, thereby occupying a new region on the biophysical landscape. Our work emphasizes how billions of years of evolution defined LOV protein dynamics, and how protein design can expand this repertoire, engineering next-generation optogenetic tools.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"438 5","pages":"Article 169599"},"PeriodicalIF":4.5,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145800341","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}
Pub Date : 2026-03-01Epub Date: 2026-01-07DOI: 10.1016/j.jmb.2026.169636
Jimin Pei, Jing Zhang, Qian Cong
Intrinsically disordered regions (IDRs) in proteins play a pivotal role in protein–protein interactions (PPIs). Using AlphaFold2 and enriched multiple sequence alignments, we predicted and investigated PPIs across the human proteome, focusing on those involving disordered regions. Our predictions show that disordered regions predominantly interact with ordered domains, whereas predicted disordered–disordered interactions are relatively rare. Although disordered regions typically lack annotated domains, certain regions—such as the keratin type II head domain and the Krüppel-associated box (KRAB)—mediate specific interactions. In contrast, their predicted binding partners frequently feature diverse Pfam domains, including protein kinase, WD40 repeat, and nuclear hormone receptor domains. These domains are enriched in nuclear localization and α-helical repeat motifs. Disordered regions involved in predicted PPIs exhibit higher sequence conservation than non-interacting disordered regions, suggesting evolutionary constraints at interaction interfaces. Moreover, certain posttranslational modifications (e.g., phosphorylation and acetylation) in disordered regions are enriched within predicted interaction interfaces, likely modulating binding affinities. Notably, we identified a significant enrichment of disease-associated mutations in predicted PPI interfaces involving disordered regions, underscoring their functional and pathological relevance. Together, these findings highlight the intricate interplay between disordered and ordered regions in mediating PPIs and provide insights into their structural and functional contributions to human health and disease.
{"title":"A Survey of Predicted Protein–Protein Interactions Involving Disordered Regions in Humans","authors":"Jimin Pei, Jing Zhang, Qian Cong","doi":"10.1016/j.jmb.2026.169636","DOIUrl":"10.1016/j.jmb.2026.169636","url":null,"abstract":"<div><div>Intrinsically disordered regions (IDRs) in proteins play a pivotal role in protein–protein interactions (PPIs). Using AlphaFold2 and enriched multiple sequence alignments, we predicted and investigated PPIs across the human proteome, focusing on those involving disordered regions. Our predictions show that disordered regions predominantly interact with ordered domains, whereas predicted disordered–disordered interactions are relatively rare. Although disordered regions typically lack annotated domains, certain regions—such as the keratin type II head domain and the Krüppel-associated box (KRAB)—mediate specific interactions. In contrast, their predicted binding partners frequently feature diverse Pfam domains, including protein kinase, WD40 repeat, and nuclear hormone receptor domains. These domains are enriched in nuclear localization and α-helical repeat motifs. Disordered regions involved in predicted PPIs exhibit higher sequence conservation than non-interacting disordered regions, suggesting evolutionary constraints at interaction interfaces. Moreover, certain posttranslational modifications (e.g., phosphorylation and acetylation) in disordered regions are enriched within predicted interaction interfaces, likely modulating binding affinities. Notably, we identified a significant enrichment of disease-associated mutations in predicted PPI interfaces involving disordered regions, underscoring their functional and pathological relevance. Together, these findings highlight the intricate interplay between disordered and ordered regions in mediating PPIs and provide insights into their structural and functional contributions to human health and disease.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"438 5","pages":"Article 169636"},"PeriodicalIF":4.5,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145941994","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}
Pub Date : 2026-03-01Epub Date: 2026-01-14DOI: 10.1016/j.jmb.2026.169638
William R.K. Talley , Daniel Bazan , Jaroslaw Majewski , Herbert Kaltner , Crystal M. Vander Zanden
Tandem-repeat galectins are a family of proteins containing two carbohydrate recognition domains (CRDs) with affinity to various glycoproteins and glycolipids involved in cell signaling. Galectin-4 is expressed in intestinal epithelial cells, and galectin-8 is essential in regulating cell adhesion and immune response. Misregulation of both tandem-repeat galectins is linked to variable cancer cell behavior. Structure models for the membrane-bound forms of galectin-4 and galectin-8 were constructed from X-ray reflectivity measurements coupled with molecular dynamics for galectin-4. The proteins were bound to lipid monolayers containing their respective ligands, gangliosides GM1 or GM3, to determine the membrane-bound structure. Galectin-4 contains two CRDs with weak affinity for GM1, and it bound with both CRDs arranged near the membrane while dynamically sampling alternative conformations. Galectin-8, in contrast, contains only one CRD with tight binding to GM3, and one CRD was pointed towards the membrane while the other oriented away from the membrane. Shortening the peptide linker between the CRDs altered protein binding to the membrane, suggesting the linker likely facilitates stabilizing contacts between the CRDs. Overall, this work helps to illustrate the conformational dynamics of tandem-repeat galectins, emphasizing the roles of ligand affinity, linker peptide dynamics, and contacts between CRDs.
{"title":"Structure of Two Tandem-Repeat Galectin Proteins Binding a Model Glycolipid Membrane","authors":"William R.K. Talley , Daniel Bazan , Jaroslaw Majewski , Herbert Kaltner , Crystal M. Vander Zanden","doi":"10.1016/j.jmb.2026.169638","DOIUrl":"10.1016/j.jmb.2026.169638","url":null,"abstract":"<div><div>Tandem-repeat galectins are a family of proteins containing two carbohydrate recognition domains (CRDs) with affinity to various glycoproteins and glycolipids involved in cell signaling. Galectin-4 is expressed in intestinal epithelial cells, and galectin-8 is essential in regulating cell adhesion and immune response. Misregulation of both tandem-repeat galectins is linked to variable cancer cell behavior. Structure models for the membrane-bound forms of galectin-4 and galectin-8 were constructed from X-ray reflectivity measurements coupled with molecular dynamics for galectin-4. The proteins were bound to lipid monolayers containing their respective ligands, gangliosides GM1 or GM3, to determine the membrane-bound structure. Galectin-4 contains two CRDs with weak affinity for GM1, and it bound with both CRDs arranged near the membrane while dynamically sampling alternative conformations. Galectin-8, in contrast, contains only one CRD with tight binding to GM3, and one CRD was pointed towards the membrane while the other oriented away from the membrane. Shortening the peptide linker between the CRDs altered protein binding to the membrane, suggesting the linker likely facilitates stabilizing contacts between the CRDs. Overall, this work helps to illustrate the conformational dynamics of tandem-repeat galectins, emphasizing the roles of ligand affinity, linker peptide dynamics, and contacts between CRDs.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"438 5","pages":"Article 169638"},"PeriodicalIF":4.5,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145987685","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}
Pub Date : 2026-03-01Epub Date: 2025-08-21DOI: 10.1016/j.jmb.2025.169401
Annapoorna Venkatachalam, Scott H. Kaufmann
As an enzyme that relaxes torsionally strained DNA, TOP1 is present in all nucleated human somatic cells. Even though this ubiquity makes TOP1 an unlikely anticancer drug target, six FDA-approved antineoplastic treatments, including two approved in the past five years, and a variety of experimental agents inhibit the TOP1 catalytic cycle. To provide insight into the continuing effort to develop TOP1-directed agents, here we briefly review the biology of TOP1, the cellular effects of stabilizing TOP1-DNA covalent complexes, mechanisms of resistance to TOP1 poisons, and strategies to overcome this resistance before describing efforts to develop TOP1 catalytic inhibitors as well as an exciting new generation of tumor targeting nanoparticles and antibody-drug conjugates that deliver TOP1-directed agents to cancers at high concentrations while sparing normal tissues. When paired with inhibitors of DNA damage response pathways, epigenetic therapies, or immune modulators, these new TOP1-directed agents promise to improve the therapy of a wide range of solid tumors.
{"title":"Targeting DNA Topoisomerase I for the Treatment of Cancer: Past, Present and Future","authors":"Annapoorna Venkatachalam, Scott H. Kaufmann","doi":"10.1016/j.jmb.2025.169401","DOIUrl":"10.1016/j.jmb.2025.169401","url":null,"abstract":"<div><div>As an enzyme that relaxes torsionally strained DNA, TOP1 is present in all nucleated human somatic cells. Even though this ubiquity makes TOP1 an unlikely anticancer drug target, six FDA-approved antineoplastic treatments, including two approved in the past five years, and a variety of experimental agents inhibit the TOP1 catalytic cycle. To provide insight into the continuing effort to develop TOP1-directed agents, here we briefly review the biology of TOP1, the cellular effects of stabilizing TOP1-DNA covalent complexes, mechanisms of resistance to TOP1 poisons, and strategies to overcome this resistance before describing efforts to develop TOP1 catalytic inhibitors as well as an exciting new generation of tumor targeting nanoparticles and antibody-drug conjugates that deliver TOP1-directed agents to cancers at high concentrations while sparing normal tissues. When paired with inhibitors of DNA damage response pathways, epigenetic therapies, or immune modulators, these new TOP1-directed agents promise to improve the therapy of a wide range of solid tumors.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"438 5","pages":"Article 169401"},"PeriodicalIF":4.5,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144937881","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}
Pub Date : 2026-03-01Epub Date: 2025-12-23DOI: 10.1016/j.jmb.2025.169614
Caralyn E. Flack, John S. Parkinson
Tracking ligand-induced conformational changes through transmembrane sensory proteins remains a challenge in signal transduction research. Our study followed propagation of stimulus signals through a bacterial transmembrane chemoreceptor (Tsr) that controls a cytoplasmic signaling kinase (CheA). We marked relay elements in the ∼200-Å long cytoplasmic four-helix bundle signaling domain with amino acid replacements that locked Tsr in kinase-ON or -OFF output and characterized the mutant receptors with in vivo assays that monitored Tsr structure (crosslinking) and function (kinase control). We found that conformational changes emanating from the mutant lesions propagated bidirectionally throughout the Tsr signaling domain and did not dissipate appreciably with distance, implying conformational coupling between subdomains. These behaviors proved intrinsic to Tsr homodimers and independent of higher order signaling complexes. AlphaFold 3 atomic models of the mutant receptors exhibited structural changes that would likely affect local helix packing interactions at the mutant sites. One member of each ON-OFF mutant pair appeared to reduce packing stability, whereas the other enhanced packing stability. This analysis pinpointed two sites of structural logic inversion (“entropic switches”) in the Tsr transmission path. Kinase-OFF lesions appeared to be stabilizing at the input and output segments of the cytoplasmic domain but destabilizing in the intervening signaling region that contains the modification sites for sensory adaptation. These findings support the notion of chemoreceptor signaling through opposed dynamic switches and provide new insights into the mechanism of kinase output control. This work also highlights the powerful interplay possible between cellular signaling readouts and AF3-generated models of mutant proteins.
{"title":"Bacterial Chemoreceptors Transmit Stimulus Signals Through Coupled Entropic Switches","authors":"Caralyn E. Flack, John S. Parkinson","doi":"10.1016/j.jmb.2025.169614","DOIUrl":"10.1016/j.jmb.2025.169614","url":null,"abstract":"<div><div>Tracking ligand-induced conformational changes through transmembrane sensory proteins remains a challenge in signal transduction research. Our study followed propagation of stimulus signals through a bacterial transmembrane chemoreceptor (Tsr) that controls a cytoplasmic signaling kinase (CheA). We marked relay elements in the ∼200-Å long cytoplasmic four-helix bundle signaling domain with amino acid replacements that locked Tsr in kinase-ON or -OFF output and characterized the mutant receptors with <em>in vivo</em> assays that monitored Tsr structure (crosslinking) and function (kinase control). We found that conformational changes emanating from the mutant lesions propagated bidirectionally throughout the Tsr signaling domain and did not dissipate appreciably with distance, implying conformational coupling between subdomains. These behaviors proved intrinsic to Tsr homodimers and independent of higher order signaling complexes. AlphaFold 3 atomic models of the mutant receptors exhibited structural changes that would likely affect local helix packing interactions at the mutant sites. One member of each ON-OFF mutant pair appeared to reduce packing stability, whereas the other enhanced packing stability. This analysis pinpointed two sites of structural logic inversion (“entropic switches”) in the Tsr transmission path. Kinase-OFF lesions appeared to be stabilizing at the input and output segments of the cytoplasmic domain but destabilizing in the intervening signaling region that contains the modification sites for sensory adaptation. These findings support the notion of chemoreceptor signaling through opposed dynamic switches and provide new insights into the mechanism of kinase output control. This work also highlights the powerful interplay possible between cellular signaling readouts and AF3-generated models of mutant proteins.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"438 5","pages":"Article 169614"},"PeriodicalIF":4.5,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145832080","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}
The type IA topoisomerase subfamily includes bacterial topoisomerase I and topoisomerase III encoded by topA and topB genes, reverse gyrase found in thermophilic bacteria and archaea, as well as eukaryotic topoisomerase III. Type IA topoisomerases also act on RNA as substrate. Important functions in neurological development have been demonstrated for human TOP3B. Type IA topoisomerase present in all bacterial pathogens should be a novel target that can be utilized for the discovery of new antibacterial agents. Naturally produced bacterial toxins have been shown to inhibit cell growth by targeting topoisomerase I. Topoisomerase III in human and other eukaryotes could potentially also be targeted for treatment of cancer and viral or parasitic infections. Docking, machine-learning, enzyme or cell-based screening campaigns have identified compounds that can inhibit the catalytic activity of type IA topoisomerases, or poisons that can trap the covalent complex of the targeted type IA topoisomerase. Small molecule inhibitors identified thus far for bacterial topoisomerase I or human TOP3B have not been viable candidates as drug leads mostly due to lack of sufficient potency and selectivity. The barriers for obtaining better inhibitors include the lack of an X-ray or cryo-EM structure of topoisomerase-ligand complex and mutations in the topoisomerase gene that can confirm the topoisomerase as primary cellular target. Well-designed combination of virtual and experiment screening to explore large chemical space in future studies may improve the likelihood of success for identifying small molecule inhibitors of type IA topoisomerases that can form specific protein–ligand complexes amenable for structure determination.
{"title":"Search for Specific Inhibitors Targeting Type IA Topoisomerases","authors":"Somaia Haque Chadni , Shomita Ferdous , Yuk-Ching Tse-Dinh","doi":"10.1016/j.jmb.2025.169349","DOIUrl":"10.1016/j.jmb.2025.169349","url":null,"abstract":"<div><div>The type IA topoisomerase subfamily includes bacterial topoisomerase I and topoisomerase III encoded by <em>topA</em> and <em>topB</em> genes, reverse gyrase found in thermophilic bacteria and archaea, as well as eukaryotic topoisomerase III. Type IA topoisomerases also act on RNA as substrate. Important functions in neurological development have been demonstrated for human TOP3B. Type IA topoisomerase present in all bacterial pathogens should be a novel target that can be utilized for the discovery of new antibacterial agents. Naturally produced bacterial toxins have been shown to inhibit cell growth by targeting topoisomerase I. Topoisomerase III in human and other eukaryotes could potentially also be targeted for treatment of cancer and viral or parasitic infections. Docking, machine-learning, enzyme or cell-based screening campaigns have identified compounds that can inhibit the catalytic activity of type IA topoisomerases, or poisons that can trap the covalent complex of the targeted type IA topoisomerase. Small molecule inhibitors identified thus far for bacterial topoisomerase I or human TOP3B have not been viable candidates as drug leads mostly due to lack of sufficient potency and selectivity. The barriers for obtaining better inhibitors include the lack of an X-ray or cryo-EM structure of topoisomerase-ligand complex and mutations in the topoisomerase gene that can confirm the topoisomerase as primary cellular target. Well-designed combination of virtual and experiment screening to explore large chemical space in future studies may improve the likelihood of success for identifying small molecule inhibitors of type IA topoisomerases that can form specific protein–ligand complexes amenable for structure determination.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"438 5","pages":"Article 169349"},"PeriodicalIF":4.5,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144666754","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}
Topoisomerases are essential enzymes that resolve DNA topological stress during replication and transcription. In mammalian cells, the two isoforms, TOP2A and TOP2B, differ in expression profiles and functions. TOP2A is a key regulator of cell division, mainly expressed in rapidly dividing cells, such as cancer cells, and is therefore the primary target of several chemotherapeutic molecules. In contrast, TOP2B is ubiquitously expressed in both dividing and non-dividing cells and is not directly implicated in tumorigenesis. Despite their functional differences, the high homology of the two isoforms contributes to unwanted off-target effects of TOP2-directed therapies, sometimes leading to secondary cancer. Both isoforms can harbor naturally occurring or cancer-associated point mutations, which could confer altered sensitivity or resistance to chemotherapy agents. Using data from cancer genomic databases, we analyzed hotspot mutations of both isoforms found in human tumors and conducted a molecular analysis based on structural and functional data. We identified TOP2 variants in high-grade serous ovarian carcinoma, a malignancy frequently treated with TOP2-targeting agents, such as doxorubicin or etoposide. Our analysis emphasizes the importance of modeling somatic mutations to assess enzyme conformation and therapeutic response. Additionally, this review provides insights that underline the potential value of including TOP2A and TOP2B in companion diagnostic gene panels used in personalized oncology, notably in cancers where TOP2-directed agents are part of the standard therapy.
{"title":"DNA Topoisomerase II Mutations in Cancer: Structural Impact and Drug Response in High-grade Serous Ovarian Carcinoma","authors":"Viola Mazzoleni , Amélie Boichard , Valérie Lamour","doi":"10.1016/j.jmb.2025.169384","DOIUrl":"10.1016/j.jmb.2025.169384","url":null,"abstract":"<div><div>Topoisomerases are essential enzymes that resolve DNA topological stress during replication and transcription. In mammalian cells, the two isoforms, TOP2A and TOP2B, differ in expression profiles and functions. TOP2A is a key regulator of cell division, mainly expressed in rapidly dividing cells, such as cancer cells, and is therefore the primary target of several chemotherapeutic molecules. In contrast, TOP2B is ubiquitously expressed in both dividing and non-dividing cells and is not directly implicated in tumorigenesis. Despite their functional differences, the high homology of the two isoforms contributes to unwanted off-target effects of TOP2-directed therapies, sometimes leading to secondary cancer. Both isoforms can harbor naturally occurring or cancer-associated point mutations, which could confer altered sensitivity or resistance to chemotherapy agents. Using data from cancer genomic databases, we analyzed hotspot mutations of both isoforms found in human tumors and conducted a molecular analysis based on structural and functional data. We identified TOP2 variants in high-grade serous ovarian carcinoma, a malignancy frequently treated with TOP2-targeting agents, such as doxorubicin or etoposide. Our analysis emphasizes the importance of modeling somatic mutations to assess enzyme conformation and therapeutic response. Additionally, this review provides insights that underline the potential value of including <em>TOP2A</em> and <em>TOP2B</em> in companion diagnostic gene panels used in personalized oncology, notably in cancers where TOP2-directed agents are part of the standard therapy.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"438 5","pages":"Article 169384"},"PeriodicalIF":4.5,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144843979","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}
Pub Date : 2026-03-01Epub Date: 2025-12-24DOI: 10.1016/j.jmb.2025.169615
Evgeny V. Mymrikov , Christophe Wirth , Jonas I. Heinicke , Julian Goll , Bianca A. Kern , Christoph Steck , Anastasiia K. Iaroslavtceva , Tobias Mühlethaler , Anna Köttgen , Carola Hunte
The renal solute carrier URAT1 (SLC22A12) is essential for urate homeostasis, with loss-of-function linked to renal hypouricemia, nephrolithiasis and lower gout risk. URAT1 function depends on binding the multi-PDZ domain scaffold protein PDZK1 (NHERF3), with a similar role suggested for the related NHERF1. The molecular basis of these interactions remains poorly understood. Using fluorescence anisotropy, we show that full-length human PDZK1 binds the C-terminal peptide of URAT1 with high affinity (KD 170 nM), unlike NHERF1 (KD > 70 µM). The PDZ1 domain of PDZK1 alone is sufficient for high-affinity binding (KD 160 nM), while PDZ4 provides a secondary site (KD 1.35 µM), with both interactions characterized by rapid kinetics. Gel filtration shows that PDZK1 can bind two URAT1 peptides. X-ray structures of individual PDZ domains from PDZK1 and NHERF1 complexed with the URAT1 peptide reveal the underlying molecular basis for selectivity and broad affinity range. Murine Pdzk1 and Nherf1 bind Urat1 with high affinity indicating species-specific interactions. These data provide insights into URAT1 regulation by PDZ scaffold proteins with relevance for understanding urate homeostasis regulation and related disorders.
{"title":"Molecular Determinants of Selective and High-affinity Binding of the Scaffold Protein PDZK1 to the Urate Transporter URAT1","authors":"Evgeny V. Mymrikov , Christophe Wirth , Jonas I. Heinicke , Julian Goll , Bianca A. Kern , Christoph Steck , Anastasiia K. Iaroslavtceva , Tobias Mühlethaler , Anna Köttgen , Carola Hunte","doi":"10.1016/j.jmb.2025.169615","DOIUrl":"10.1016/j.jmb.2025.169615","url":null,"abstract":"<div><div>The renal solute carrier URAT1 (SLC22A12) is essential for urate homeostasis, with loss-of-function linked to renal hypouricemia, nephrolithiasis and lower gout risk. URAT1 function depends on binding the multi-PDZ domain scaffold protein PDZK1 (NHERF3), with a similar role suggested for the related NHERF1. The molecular basis of these interactions remains poorly understood. Using fluorescence anisotropy, we show that full-length human PDZK1 binds the C-terminal peptide of URAT1 with high affinity (<em>K</em><sub>D</sub> 170 nM), unlike NHERF1 (<em>K</em><sub>D</sub> > 70 µM). The PDZ1 domain of PDZK1 alone is sufficient for high-affinity binding (<em>K</em><sub>D</sub> 160 nM), while PDZ4 provides a secondary site (<em>K</em><sub>D</sub> 1.35 µM), with both interactions characterized by rapid kinetics. Gel filtration shows that PDZK1 can bind two URAT1 peptides. X-ray structures of individual PDZ domains from PDZK1 and NHERF1 complexed with the URAT1 peptide reveal the underlying molecular basis for selectivity and broad affinity range. Murine Pdzk1 and Nherf1 bind Urat1 with high affinity indicating species-specific interactions. These data provide insights into URAT1 regulation by PDZ scaffold proteins with relevance for understanding urate homeostasis regulation and related disorders.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"438 5","pages":"Article 169615"},"PeriodicalIF":4.5,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145843309","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}
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