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Doxorubicin Recognition and Transport by the MATE Multidrug Transporter NorM From Vibrio cholerae 霍乱弧菌MATE多药转运体NorM对阿霉素的识别和转运。
IF 4.5 2区 生物学
Journal of Molecular Biology Pub Date : 2026-01-15 Epub Date: 2025-11-17 DOI: 10.1016/j.jmb.2025.169549
Pei-Yu Hsieh , Ksenija Romane , Julia Kowal , Kaspar P. Locher , Hendrik W. van Veen
{"title":"Doxorubicin Recognition and Transport by the MATE Multidrug Transporter NorM From Vibrio cholerae","authors":"Pei-Yu Hsieh ,&nbsp;Ksenija Romane ,&nbsp;Julia Kowal ,&nbsp;Kaspar P. Locher ,&nbsp;Hendrik W. van Veen","doi":"10.1016/j.jmb.2025.169549","DOIUrl":"10.1016/j.jmb.2025.169549","url":null,"abstract":"<div><div>Multidrug and toxic compound extrusion (MATE) transport proteins contribute to multidrug resistance in human pathogens by extruding various cytotoxic compounds from the cellular interior. Despite their importance across all domains of life, the specificities and mechanisms of substrate transport of these proteins remain poorly understood due to limited structural and functional information. Here, we determined the cryo-electron microscopy structure of NorM from <em>Vibrio cholerae</em> (NorM-VC) in complex with the anthracycline antibiotic doxorubicin, using the NabFab approach. The structure reveals that the doxorubicin-binding pocket is located halfway through the membrane, within the C-lobe of the protein. Functional studies targeting the doxorubicin-interacting residues validated the binding pocket and enabled detailed analysis of the doxorubicin transport reaction. Our findings indicate doxorubicin binding within a multisite binding chamber engaged in a general transport mechanism for a variety of substrates.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"438 2","pages":"Article 169549"},"PeriodicalIF":4.5,"publicationDate":"2026-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145556012","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}
引用次数: 0
Structural Basis of Redox-Dependent Affinities of Dihydroorotate Dehydrogenase for Its Substrates and Products 二氢乙酸脱氢酶对底物和产物的氧化还原依赖亲和力的结构基础。
IF 4.5 2区 生物学
Journal of Molecular Biology Pub Date : 2026-01-15 Epub Date: 2025-11-13 DOI: 10.1016/j.jmb.2025.169544
Osamu Tani , Tomomi Kubota , Tomoko Yamasaki , Takatsugu Hirokawa , Koji Furukawa , Kazuhiko Yamasaki
{"title":"Structural Basis of Redox-Dependent Affinities of Dihydroorotate Dehydrogenase for Its Substrates and Products","authors":"Osamu Tani ,&nbsp;Tomomi Kubota ,&nbsp;Tomoko Yamasaki ,&nbsp;Takatsugu Hirokawa ,&nbsp;Koji Furukawa ,&nbsp;Kazuhiko Yamasaki","doi":"10.1016/j.jmb.2025.169544","DOIUrl":"10.1016/j.jmb.2025.169544","url":null,"abstract":"<div><div>Dihydroorotate dehydrogenase (DHODH), containing a cofactor, flavin mononucleotide (FMN), catalyzes the oxidation of dihydroorotate to orotate. In <em>Trypanosoma brucei</em>, the causative parasite of African trypanosomiasis, the DHODH enzyme (TbDHODH) couples this reaction with the reduction of fumarate to succinate. These reactions occur successively in the same catalytic site through a ping-pong bi–bi mechanism. FMN is reduced in the first step and re-oxidized in the second one. Here, we investigated how the redox state of FMN influences the binding of substrates and products to TbDHODH by NMR analyses of a catalytically impaired mutant. The affinities for the substrates, dihydroorotate and fumarate, were redox-dependent: dihydroorotate preferred the oxidized state, whereas fumarate preferred the reduced state. One of the products, succinate, exhibited no detectable binding to either of the redox states, suggesting its efficient product release. In contrast, the product of the first-half reaction, orotate, showed stronger binding to the oxidized state, suggesting that product inhibition may occur unless orotate is rapidly consumed in the subsequent biosynthetic step. The structural basis of these findings was elucidated by crystallography of the complexes with the above ligands in both redox states, along with quantitative analyses of the interactions using quantum chemical calculations. Upon reduction, the FMN isoalloxazine ring gains two additional hydrogens and becomes more bent at its center. These changes perturb the interactions among the ligands, flavin, and surrounding residues (notably Lys44, Asn68, and Asn195), primarily in the electrostatic term, which quantitatively explains the difference in binding affinities.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"438 2","pages":"Article 169544"},"PeriodicalIF":4.5,"publicationDate":"2026-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145530301","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}
引用次数: 0
Kaptin Functions as a Barbed-End Binding Protein to Control Actin Filament Dynamics Kaptin作为钩端结合蛋白控制肌动蛋白丝动力学。
IF 4.5 2区 生物学
Journal of Molecular Biology Pub Date : 2026-01-15 Epub Date: 2025-11-20 DOI: 10.1016/j.jmb.2025.169554
Priyanka Dutta , Ipshita Maiti , Krishna Chandra Mondal , Aurnab Ghose , Radha Chauhan , Sankar Maiti
{"title":"Kaptin Functions as a Barbed-End Binding Protein to Control Actin Filament Dynamics","authors":"Priyanka Dutta ,&nbsp;Ipshita Maiti ,&nbsp;Krishna Chandra Mondal ,&nbsp;Aurnab Ghose ,&nbsp;Radha Chauhan ,&nbsp;Sankar Maiti","doi":"10.1016/j.jmb.2025.169554","DOIUrl":"10.1016/j.jmb.2025.169554","url":null,"abstract":"<div><div>Precise regulation of the actin cytoskeleton is fundamental to cellular morphology, motility, and intracellular transport. While key classes of actin-binding proteins, including nucleators, capping proteins, and bundlers, have been well characterized, additional modulators likely contribute to the spatial and temporal control of actin dynamics. Here, we identify Kaptin (KPTN), a protein localized to actin-rich structures at the cell periphery, as a novel regulator of actin filament dynamics. Using biochemical reconstitution and single-molecule TIRF microscopy, we demonstrate that KPTN binds to actin filament barbed ends and suppresses filament elongation. This activity leads to filament stabilization and bundling, suggesting a dual role in filament architecture maintenance. Structural prediction via AlphaFold classifies KPTN within the WD-repeat-containing protein family and highlights a conserved, positively charged residue within its predicted N-terminal β-propeller domain as essential for actin interaction. These findings uncover a novel mechanism by which KPTN regulates actin dynamics and establish it as both a barbed-end and side–binding protein within the actin cytoskeletal network.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"438 2","pages":"Article 169554"},"PeriodicalIF":4.5,"publicationDate":"2026-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145581497","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}
引用次数: 0
Cracking Controls ATP Hydrolysis in the Catalytic Unit of a P-type ATPase 裂解控制p型ATP酶催化单元中的ATP水解。
IF 4.5 2区 生物学
Journal of Molecular Biology Pub Date : 2026-01-15 Epub Date: 2025-11-20 DOI: 10.1016/j.jmb.2025.169551
M. Agueda Placenti , Santiago A. Martinez-Gache , Rodolfo M. González-Lebrero , Peter G. Wolynes , F. Luis González Flecha , Ernesto A. Roman
{"title":"Cracking Controls ATP Hydrolysis in the Catalytic Unit of a P-type ATPase","authors":"M. Agueda Placenti ,&nbsp;Santiago A. Martinez-Gache ,&nbsp;Rodolfo M. González-Lebrero ,&nbsp;Peter G. Wolynes ,&nbsp;F. Luis González Flecha ,&nbsp;Ernesto A. Roman","doi":"10.1016/j.jmb.2025.169551","DOIUrl":"10.1016/j.jmb.2025.169551","url":null,"abstract":"<div><div>Membrane transporters are essential for homeostasis and among them P-type ATPases are key players. Despite extensive research, conformational changes in their catalytic unit and their coupling to ATP hydrolysis are not explored in detail. In this work, we analyzed the effect of ATP, temperature, and urea on the steady-state ATPase activity, tryptophan fluorescence and far-UV ellipticity of the catalytic unit of the thermophilic Cu(I) transport P<sub>1B</sub>-ATPase from <em>Archaeoglobus fulgidus</em>. Combining local frustration analysis with AlphaFold2 structure prediction, we identified an open conformation which we used to perform structure-based model simulations of the open-closed transition. We developed a mechanistic model that fully describes all of our experimental observations. Our results revealed a “cracking”-like mechanism involved in the catalysis of ATP hydrolysis. These findings reinforce that, although simple, the isolated catalytic unit is a relevant model to study the role of local unfolding in the catalytic mechanism of these proteins.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"438 2","pages":"Article 169551"},"PeriodicalIF":4.5,"publicationDate":"2026-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145581547","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}
引用次数: 0
Distinct Cis-acting Elements Combinatorically Mediate Co-localization of mRNAs Encoding for Co-translational Interactors in Cytoplasmic Clusters in S. cerevisiae 不同的顺式作用元件组合介导酿酒酵母细胞质簇中编码共翻译相互作用物的mrna的共定位。
IF 4.5 2区 生物学
Journal of Molecular Biology Pub Date : 2026-01-15 Epub Date: 2025-11-14 DOI: 10.1016/j.jmb.2025.169546
Qamar Shhade , Marianna E. Estrada , Rawad Hanna , Muhammad Makhzumy , Hagit Bar-Yosef , Guenter Kramer , Bernd Bukau , Ayala Shiber
{"title":"Distinct Cis-acting Elements Combinatorically Mediate Co-localization of mRNAs Encoding for Co-translational Interactors in Cytoplasmic Clusters in S. cerevisiae","authors":"Qamar Shhade ,&nbsp;Marianna E. Estrada ,&nbsp;Rawad Hanna ,&nbsp;Muhammad Makhzumy ,&nbsp;Hagit Bar-Yosef ,&nbsp;Guenter Kramer ,&nbsp;Bernd Bukau ,&nbsp;Ayala Shiber","doi":"10.1016/j.jmb.2025.169546","DOIUrl":"10.1016/j.jmb.2025.169546","url":null,"abstract":"<div><div>Many newly synthesized proteins assemble co-translationally, providing a vital mechanism to prevent subunit misfolding in the crowded cytoplasm. Initial evidence indicates that the spatial organization of mRNAs aids this assembly, but it is unclear how these mRNAs are organized and how common this mechanism is. We used single-molecule Fluorescence in situ Hybridization in <em>Saccharomyces cerevisiae</em> to examine the spatial organization of mRNAs encoding subunits of various cytosolic complexes involved in critical cellular functions, such as fatty acid synthesis, glycolysis, translation and various amino acid biosynthesis. We found that mRNAs of the same protein complex often co-localize in specific cytoplasmic clusters. Additionally, we observed that the mRNAs encoding enzymes of biosynthetic pathways are organized in cytosolic clusters. Focusing on mRNAs encoding fatty acid synthase complex subunits, we discovered that non-coding cis elements significantly influence mRNA localization in an additive manner. Specifically, 5′ and 3′ UTRs, together with further upstream and downstream regions, facilitate co-localization. Inhibiting mRNA co-localization impaired growth when complex activity was essential, highlighting the importance of mRNA spatial organization for cellular survival. Transiently disrupting mRNA translation also affected clustering, indicating that both the nascent chains and mRNA sequence targeting cues are combinatorically contributing to spatial organization. Proteomics analysis demonstrates the impact of <em>cis</em>-elements on the abundance of the encoded subunits, as well as the entire pathway. In summary, we provide evidence that mRNA co-localization in cytoplasmic foci is coordinated by complementary mechanisms crucial for co-translational assembly, allowing efficient regulation of protein complex formation and entire pathways.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"438 2","pages":"Article 169546"},"PeriodicalIF":4.5,"publicationDate":"2026-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145534035","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}
引用次数: 0
Selective eIF4E–eIF4G Pairing and Cap-4 Recognition Mechanisms in Trypanosomatids: Insights From EIF4E5–EIF4G1 and EIF4E6–EIF4G5 Complexes 锥体虫的选择性eIF4E-eIF4G配对和cap-4识别机制:来自EIF4E5-EIF4G1和EIF4E6-EIF4G5复合物的见解
IF 4.5 2区 生物学
Journal of Molecular Biology Pub Date : 2026-01-15 Epub Date: 2025-11-18 DOI: 10.1016/j.jmb.2025.169550
Renato Ferras Penteado , Sophie Vichier-Guerre , Beatriz Maria da Silva Pereira , Laurence Dugué , Eloise Pavão Guerra Slompo , Tatiana Reichert Assunção de Matos , Sylvie Pochet , Nilson Ivo Tonin Zanchin , Beatriz Gomes Guimarães
{"title":"Selective eIF4E–eIF4G Pairing and Cap-4 Recognition Mechanisms in Trypanosomatids: Insights From EIF4E5–EIF4G1 and EIF4E6–EIF4G5 Complexes","authors":"Renato Ferras Penteado ,&nbsp;Sophie Vichier-Guerre ,&nbsp;Beatriz Maria da Silva Pereira ,&nbsp;Laurence Dugué ,&nbsp;Eloise Pavão Guerra Slompo ,&nbsp;Tatiana Reichert Assunção de Matos ,&nbsp;Sylvie Pochet ,&nbsp;Nilson Ivo Tonin Zanchin ,&nbsp;Beatriz Gomes Guimarães","doi":"10.1016/j.jmb.2025.169550","DOIUrl":"10.1016/j.jmb.2025.169550","url":null,"abstract":"<div><div>Translation initiation in eukaryotes is a highly regulated process involving the assembly of several transient protein complexes. A key step in this process is recognition of the mRNA 5′ cap structure by the initiation factor eIF4E, a core component of the eIF4F complex. In trypanosomatids, this mechanism diverges from canonical eukaryotic systems, featuring five distinct eIF4F-like complexes formed through specific pairings of eIF4E and eIF4G homologs. Additionally, trypanosomatid mRNAs exhibit a unique hypermethylated cap-4 structure at the 5′ end. To elucidate the molecular basis of selective eIF4E–eIF4G interactions and the modulation of cap binding upon eIF4G engagement, we determined high-resolution crystal structures of EIF4E5–EIF4G1 complexes from <em>Trypanosoma brucei</em> and <em>T. cruzi</em>, and the EIF4E6–EIF4G5 complex from <em>T. cruzi</em>. These structural studies, supported by biophysical analyses in the presence and absence of a cap-4 analog, reveal key determinants of cap recognition associated with cap-4 structural flexibility and plasticity in the cap-binding pockets. We observe conformational rearrangements upon eIF4G binding and propose a relationship between these structural changes and increased cap-4 affinity. In addition, comparative structural analysis of the EIF4E5–EIF4G1 and EIF4E6–EIF4G5 complexes offers atomic-level insights into the molecular determinants of specificity that govern selective eIF4E–eIF4G pairings in trypanosomatids.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"438 2","pages":"Article 169550"},"PeriodicalIF":4.5,"publicationDate":"2026-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145562254","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}
引用次数: 0
Both Domains of APOBEC3F Recognize AA RNA Motifs to Support HIV-1 Virion Encapsidation and Antiviral Function APOBEC3F的两个结构域识别AA RNA基序以支持HIV-1病毒粒子的包封和抗病毒功能。
IF 4.5 2区 生物学
Journal of Molecular Biology Pub Date : 2026-01-15 Epub Date: 2025-11-07 DOI: 10.1016/j.jmb.2025.169536
Josue Pacheco , Maria Yousefi , Hanjing Yang , Shuxing Li , Linda Chelico , Xiaojiang S. Chen
{"title":"Both Domains of APOBEC3F Recognize AA RNA Motifs to Support HIV-1 Virion Encapsidation and Antiviral Function","authors":"Josue Pacheco ,&nbsp;Maria Yousefi ,&nbsp;Hanjing Yang ,&nbsp;Shuxing Li ,&nbsp;Linda Chelico ,&nbsp;Xiaojiang S. Chen","doi":"10.1016/j.jmb.2025.169536","DOIUrl":"10.1016/j.jmb.2025.169536","url":null,"abstract":"<div><div>The anti-HIV-1 activity of the double-domain cytidine deaminases APOBEC3G (A3G) and APOBEC3F (A3F) depends on their encapsidation into progeny virions. While A3G requires AA-dinucleotide recognition by its N-terminal deaminase domain (CD1) for packaging, the mechanism for A3F encapsidation has remained unclear. Here, we present the structure of an A3F CD1 variant, revealing AA-binding pocket residues nearly identical to those of A3G CD1. Modeling further shows that A3F’s C-terminal deaminase domain (CD2) harbors a similarly conserved AA-binding pocket. Both A3F CD1 and CD2 preferentially bind AA/GA-containing RNA, and mutations in the AA-binding pocket of either domain in full-length A3F do not impair virion packaging or antiviral activity, indicating functional redundancy. Consistently, double-domain chimeras with A3F CD1 or CD2 at either terminus are efficiently packaged and restrict HIV-1 through both deaminase-dependent and -independent mechanisms. In contrast, A3G exhibits strict domain-position dependence: only constructs with A3G CD1 at the N-terminus support packaging, and HIV-restriction activity varies with the particular domain at the C-terminus. A3G CD1 at the C-terminus is inactive, but the A3G CD2 at the C-terminus is active with either the A3F CD1 or A3F CD2 at the N-terminus. These findings highlight the mechanistic flexibility of A3F, in which either domain can mediate RNA recognition, virion encapsidation, and antiviral activity.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"438 2","pages":"Article 169536"},"PeriodicalIF":4.5,"publicationDate":"2026-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145480274","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}
引用次数: 0
Synthetic Type III-E CRISPR-Cas Effectors for Programmable RNA-targeting 用于可编程rna靶向的III-E型CRISPR-Cas效应物的合成。
IF 4.5 2区 生物学
Journal of Molecular Biology Pub Date : 2026-01-15 Epub Date: 2025-11-27 DOI: 10.1016/j.jmb.2025.169566
Daniel J. Brogan , Calvin P. Lin , Elena Dalla Benetta , Tianqi Wang , Fangying Chen , Harry Li , Claire Lin , Elizabeth A. Komives , Omar S. Akbari
{"title":"Synthetic Type III-E CRISPR-Cas Effectors for Programmable RNA-targeting","authors":"Daniel J. Brogan ,&nbsp;Calvin P. Lin ,&nbsp;Elena Dalla Benetta ,&nbsp;Tianqi Wang ,&nbsp;Fangying Chen ,&nbsp;Harry Li ,&nbsp;Claire Lin ,&nbsp;Elizabeth A. Komives ,&nbsp;Omar S. Akbari","doi":"10.1016/j.jmb.2025.169566","DOIUrl":"10.1016/j.jmb.2025.169566","url":null,"abstract":"<div><div>The recent discovery of the type III-E class of CRISPR-Cas effectors has reshaped our fundamental understanding of CRISPR-Cas evolution and classification. Type III-E effectors are composed of several Cas7-like domains and a single Cas11-like domain naturally fused together to create a single polypeptide capable of targeting and degrading RNA. Here we identified a novel type III-E-like effector composed of three Cas7 domains and a Cas1 domain which was not active but could be engineered into an active chimeric RNA-targeting Cas effector by domain additions and swaps from other type III-E effectors. The results reveal that various domains in type III-E effectors can be swapped for the equivalent domain from a different type III-E effector. Remarkably, the Cas1 domain located at the C-terminus of Cas7-1 could be swapped in place of the Cas11 domain located between the Cas7.1 and the Cas7.2 domains of <em>Di</em>Cas7-11. The results reveal a new modality for engineering type III-E effectors from the blueprints found in nature.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"438 2","pages":"Article 169566"},"PeriodicalIF":4.5,"publicationDate":"2026-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145627328","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}
引用次数: 0
Molecular Insights Into the Binding Dynamics of Transcription Factor TBR1 to T-box DNA Sequences 转录因子TBR1与T-box DNA序列结合动力学的分子洞察。
IF 4.5 2区 生物学
Journal of Molecular Biology Pub Date : 2026-01-15 Epub Date: 2025-11-12 DOI: 10.1016/j.jmb.2025.169543
Raymond Hartman , Ashleigh Blane , Fillmon Kubrom , Riyaadh Mayet , J. Carlos Penedo , Sylvia Fanucchi
{"title":"Molecular Insights Into the Binding Dynamics of Transcription Factor TBR1 to T-box DNA Sequences","authors":"Raymond Hartman ,&nbsp;Ashleigh Blane ,&nbsp;Fillmon Kubrom ,&nbsp;Riyaadh Mayet ,&nbsp;J. Carlos Penedo ,&nbsp;Sylvia Fanucchi","doi":"10.1016/j.jmb.2025.169543","DOIUrl":"10.1016/j.jmb.2025.169543","url":null,"abstract":"<div><div>TBR1 is a transcription factor critical for brain development that recognises a specific nucleotide sequence, the T-box binding element (TBE). Dysregulation or mutation of TBR1 is linked to a spectrum of neurodevelopmental disorders, including autism, speech delay, and intellectual disability, yet the molecular mechanism underlying its DNA recognition remains poorly defined. Here, we examine how the TBR1 T-box domain recognises DNA containing either a single TBE or a palindromic arrangement of two adjacent TBEs. Both sequences are derived from naturally occurring TBR1 binding motifs located within genomic regions annotated as candidate enhancers of autism-associated genes. The TBR1 T-box binds its cognate element in a sequence-specific, enthalpically driven, and entropically opposed manner. Single-molecule Förster resonance energy transfer (smFRET) reveals that the single-site sequence binds one monomer, whereas the palindromic sequence can recruit a second monomer and exhibits additional dynamic events unique to this architecture. These include short-range transitions of a monomer along the palindromic DNA before dissociation or before the arrival of a second monomer. Molecular docking and dynamics simulations support these observations, predicting fewer stabilising contacts per TBE and hence greater conformational flexibility for the palindromic complex. Together, our findings reveal how DNA architecture modulates affinity and kinetics within the T-box family: single TBEs promote stable monomeric binding, whereas palindromic arrangements enable dual occupancy and dynamic exchange. This study provides the first detailed mechanistic insight into DNA recognition by a T-box transcription factor, advancing understanding of its role in neurodevelopmental gene regulation.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"438 2","pages":"Article 169543"},"PeriodicalIF":4.5,"publicationDate":"2026-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145522592","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}
引用次数: 0
Binding and Translocation of Substrate Allosterically Promotes Functional Interactions Within the AlkB–AlkG Electron Transfer Complex 底物的结合和易位变构地促进了AlkB-AlkG电子转移复合物内的功能相互作用。
IF 4.5 2区 生物学
Journal of Molecular Biology Pub Date : 2026-01-15 Epub Date: 2025-11-14 DOI: 10.1016/j.jmb.2025.169548
Karolina Mikulska-Ruminska , Matthew Licht , Mehmed Z. Ertem , John Shanklin , Qun Liu , Ivet Bahar
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