Journal of structural biology最新文献_第2页

Cloneable contrast across all biological length scales 所有生物长度尺度的可克隆对比。

IF 2.7 3区生物学

Journal of structural biology Pub Date : 2026-03-01 Epub Date: 2026-01-11 DOI: 10.1016/j.jsb.2026.108290

Kanda M. Borgognoni , Bradley F. Guilliams , Zachary J. Butz , Christopher J. Ackerson

{"title":"Cloneable contrast across all biological length scales","authors":"Kanda M. Borgognoni , Bradley F. Guilliams , Zachary J. Butz , Christopher J. Ackerson","doi":"10.1016/j.jsb.2026.108290","DOIUrl":"10.1016/j.jsb.2026.108290","url":null,"abstract":"<div><div>Cloneable contrast in biological microscopy is exemplified by Green Fluorescent Protein (GFP) in fluorescence microscopy. There are no similarly useful cloneable contrast agents that function in biological electron microscopy. This paper reports a cloneable Selenium NanoParticle (cSeNP) that produces molecular contrast in imaging modalities including cellular electron microscopy, fluorescence microscopy, and X-ray computed tomography. This set of imaging modalities can image all biologically relevant length scales, from subcellular structure to whole organisms. The cSeNP is a ∼5 nm diameter Selenium nanoparticle that is made and conjugated by a protein. Because the cSeNP is electron dense compared to biological molecules, it has high contrast in biological electron microscopy. DNA encoding the cSeNP protein was concatenated to DNA encoding FtsZ, the procaryotic analog of tubulin. FtsZ is membrane associated throughout the cell cycle and localizes to the cleavage furrow of dividing cells. <em>Escherichia coli</em> cells expressing FtsZ-cSeNP fusion proteins were examined by transmission electron tomography and fluorescence light microscopy. These experiments show cSeNP decorated FtsZ filaments and/or cSeNPs in locations that correlate to known FtsZ locations, with less than 5% of cSeNPs in unexpected locations. X-ray imaging shows contrast attributable to cSeNPs is distinguishable from background in <em>E. coli</em>. The cSeNP, therefore, represents a cloneable imaging contrast agent that facilitates location and correlation of proteins-of-interest across all biological length scales. This is especially useful in biological electron microscopy, where larger-area imaging modalities such as fluorescence microscopy are employed to identify sub-areas containing a protein-of-interest to prepare for electron microscopy study.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"218 1","pages":"Article 108290"},"PeriodicalIF":2.7,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145966383","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Probing the structure and thermodynamics of a multidomain psychrophilic chitinase from Moritella marina 一种多结构域嗜冷几丁质酶的结构和热力学研究。

IF 2.7 3区生物学

Journal of structural biology Pub Date : 2026-03-01 Epub Date: 2025-12-26 DOI: 10.1016/j.jsb.2025.108282

Magdalena Bejger , Piotr H. Małecki , Katarzyna Biniek-Antosiak, Wojciech Rypniewski

{"title":"Probing the structure and thermodynamics of a multidomain psychrophilic chitinase from Moritella marina","authors":"Magdalena Bejger , Piotr H. Małecki , Katarzyna Biniek-Antosiak, Wojciech Rypniewski","doi":"10.1016/j.jsb.2025.108282","DOIUrl":"10.1016/j.jsb.2025.108282","url":null,"abstract":"<div><div>Studies of protein structure and stability have traditionally focused on individual domains, treating them as autonomous units, even though most proteins consist of multiple domains. This raises the question to what extent can multidomain proteins be considered as sums of their individual domains, and how neighboring domains influence one another. Chitinase Chi60 from the psychrophilic bacterium <em>Moritella marina</em> consists of four domains linked in sequence: a catalytic domain, two consecutive Ig-like domains, and a chitin-binding module. The modular architecture of this enzyme provides an opportunity to examine the structure and stability of a protein from which domains are systematically excised. A series of deletion mutants of the chitinase was designed and constructed, and their structures and thermal melting profiles were analyzed. The different domains exhibit distinct melting temperatures. The catalytic domain shows a complex melting profile. Each domain can fold and maintain its structural integrity when isolated, including the two tandem Ig-like domains that share sequence similarity. Although the interfaces between domains in this modular protein are small, it is still possible to detect the influence neighboring domains exert on one another. Some artificial combinations of domains are unstable and prone to degradation. This long, flexible molecule may be stabilized through dimerization when not engaged with the chitin substrate, with two of its domains participating in the interaction.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"218 1","pages":"Article 108282"},"PeriodicalIF":2.7,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145850248","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Biophysical characterization of zinc and DNA binding properties of MRN complex interacting protein MRN复合体相互作用蛋白锌的生物物理特性及DNA结合特性。

IF 2.7 3区生物学

Journal of structural biology Pub Date : 2026-03-01 Epub Date: 2026-01-03 DOI: 10.1016/j.jsb.2026.108287

Samina Kazi , Ezeogo Obaji , Johan Pääkkönen , Carlos Vela-Rodríguez , Bianca Sammer , Philomena Schmid , Albert Galera-Prat , Lari Lehtiö , Renata Prunskaite-Hyyryläinen

{"title":"Biophysical characterization of zinc and DNA binding properties of MRN complex interacting protein","authors":"Samina Kazi , Ezeogo Obaji , Johan Pääkkönen , Carlos Vela-Rodríguez , Bianca Sammer , Philomena Schmid , Albert Galera-Prat , Lari Lehtiö , Renata Prunskaite-Hyyryläinen","doi":"10.1016/j.jsb.2026.108287","DOIUrl":"10.1016/j.jsb.2026.108287","url":null,"abstract":"<div><div>Studies in immortalized human mitotic cells demonstrated that MRN Complex Interacting Protein (MRNIP) plays a critical role in genome stability, replication fork protection, and the detection of DNA double-strand breaks via liquid–liquid phase separation. Our earlier work in mice identified its essential role in meiosis during spermatogenesis, namely, meiotic sex chromosome inactivation, highlighting its critical importance for male fertility. Apart from that, MRNIP is a poorly characterized protein with little to no data-based evidence of its biophysical and biochemical properties.</div><div>In this study, we provide experimental evidence confirming that the N-terminal domain is indeed folded and contains a zinc-ribbon motif. We demonstrate that MRNIP binds a Zn<sup>2+</sup> ion at this site, which plays a structural role in stabilizing the folded domain. Together with structural similarity observed across species, these findings support the conserved nature of the N-terminal domain of MRNIP. Our experimental data confirms that the C-terminal region is disordered.</div><div>Furthermore, we show that both the N- and C-terminal regions exhibit binding specificity for DNA rather than RNA, under low-salt conditions, suggesting low-affinity interactions, whereas no DNA or RNA binding was observed under physiological salt conditions. Our findings provide insight into the biophysical and biochemical properties of MRNIP and offer a foundation for advancing structural and functional studies of MRNIP.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"218 1","pages":"Article 108287"},"PeriodicalIF":2.7,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145906240","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Solution 3D structure and conformational flexibility of the endothelial monocyte activating polypeptide II (EMAP II) revealed by NMR spectroscopy and molecular dynamics simulations 通过核磁共振波谱和分子动力学模拟揭示内皮单核细胞活化多肽II （EMAP II）的三维结构和构象灵活性。

IF 2.7 3区生物学

Journal of structural biology Pub Date : 2026-03-01 Epub Date: 2025-12-13 DOI: 10.1016/j.jsb.2025.108280

Dmytro Lozhko , Lesia Kolomiiets , Lilia Zhukova , Michal Taube , Maciej Kozak , Michał Dadlez , Olexandr Kornelyuk , Igor Zhukov

{"title":"Solution 3D structure and conformational flexibility of the endothelial monocyte activating polypeptide II (EMAP II) revealed by NMR spectroscopy and molecular dynamics simulations","authors":"Dmytro Lozhko , Lesia Kolomiiets , Lilia Zhukova , Michal Taube , Maciej Kozak , Michał Dadlez , Olexandr Kornelyuk , Igor Zhukov","doi":"10.1016/j.jsb.2025.108280","DOIUrl":"10.1016/j.jsb.2025.108280","url":null,"abstract":"<div><div>Endothelial monocyte activating polypeptide II (EMAP II) is the C-terminal domain of its precursor, AIMP1/p43 polypeptide, a multifunctional protein with diverse functional cytokine activities and tRNA-binding abilities. Several X-ray crystallographic structures of EMAP II are available in the PDB database. However, its NMR-based structure, presented in this work indicates partition of its structure into two domains characterized by substantial differences in structural dynamics. Based on <sup>15</sup>N relaxation experiments, hydrogen–deuterium exchange (HDX) data and molecular dynamics simulations we conclude that observed differences in dynamics may enable dual mechanisms of tRNA binding and cytokine function of EMAP II. Although in general in-solution EMAP II structure studied here is highly similar to its in-crystal X-ray structure, the N-terminal segment responsible for cytokine activity exhibited reduced deuterium exchange rate and demonstrated higher accessibility to the solvent compared to X-ray structures and the <em>AlphaFold2</em> model. Such differences may be important for understanding cytokine function of EMAP II. The tRNA-binding motif characterized by different orientation of the side chain of tryptophan 128, which can play a significant role in the regulation of tRNA binding.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"218 1","pages":"Article 108280"},"PeriodicalIF":2.7,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145763008","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Bioinformatic and experimental characterization of the RBM15 RNA binding protein RBM15 RNA结合蛋白的生物信息学和实验表征。

IF 2.7 3区生物学

Journal of structural biology Pub Date : 2026-03-01 Epub Date: 2025-11-24 DOI: 10.1016/j.jsb.2025.108264

Emma Bose , Caleb Mayes , Lance Ellis , Corrine Baker , Sofia Tambalotti , Bryan Eusse , Shengwei Xiong , Yaa Pokua Osei Sarpong , Marwan Shalaby , Lucas Barry , Frank Lewis , Johnson Joseph , Talaidh Isaacs , Derik McCarthy , Dana Katz , Jingyang Wang , Victoria Zirimu , Luis Vargas , Julian Von Hofe , Glen C Aguilar , Alisha N. Jones

{"title":"Bioinformatic and experimental characterization of the RBM15 RNA binding protein","authors":"Emma Bose , Caleb Mayes , Lance Ellis , Corrine Baker , Sofia Tambalotti , Bryan Eusse , Shengwei Xiong , Yaa Pokua Osei Sarpong , Marwan Shalaby , Lucas Barry , Frank Lewis , Johnson Joseph , Talaidh Isaacs , Derik McCarthy , Dana Katz , Jingyang Wang , Victoria Zirimu , Luis Vargas , Julian Von Hofe , Glen C Aguilar , Alisha N. Jones","doi":"10.1016/j.jsb.2025.108264","DOIUrl":"10.1016/j.jsb.2025.108264","url":null,"abstract":"<div><div>The RNA binding motif 15 protein (RBM15) binds both RNA and proteins to regulate a wide repertoire of processes in the cell, including the positing of N6 methyladenosine marks on RNA, the silencing of genes on the inactive X-chromosome, and even hematopoiesis. Although its C-terminal SPOC domain has been found to facilitate protein–protein interactions, the structural mechanism that underlies how its three N-terminal RNA recognition motifs (RRMs) interact with RNA remains to be elucidated. In this crowdsourced study, we bioinformatically assessed publicly available, genome-wide RNA 2D structural probing and RNA binding protein (RBP) cross-linking and immunoprecipitation (CLIP) data to identify RNAs that bind with RBM15. Binding assays reveal that the RRMs work in concert to bind stem-loop structured RNA motifs with nanomolar binding affinity. Structural modeling and nuclear magnetic resonance (NMR) spectroscopy analysis suggest that RRMs 2 and 3 are coaxially stacked to form a heterodimer; they create a sandwich-like motif around structured RNA. Altogether, this work provides insight into the structural mechanism by which RBM15 interacts with RNAs to govern biological function.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"218 1","pages":"Article 108264"},"PeriodicalIF":2.7,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145635050","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Adaptive Gaussian representation for differentiable cryo-electron tomography reconstruction 可微低温电子断层扫描重建的自适应高斯表示。

IF 2.7 3区生物学

Journal of structural biology Pub Date : 2026-03-01 Epub Date: 2025-12-17 DOI: 10.1016/j.jsb.2025.108281

Chi Zhang , Zhidong Yang , Renmin Han , Fa Zhang , Jieqing Feng

{"title":"Adaptive Gaussian representation for differentiable cryo-electron tomography reconstruction","authors":"Chi Zhang , Zhidong Yang , Renmin Han , Fa Zhang , Jieqing Feng","doi":"10.1016/j.jsb.2025.108281","DOIUrl":"10.1016/j.jsb.2025.108281","url":null,"abstract":"<div><div>Cryo-electron tomography (cryo-ET) enables 3D visualization of biological structures in their native state, but high-fidelity tomogram reconstruction remains challenging due to low signal-to-noise ratios and limited angular sampling. In this work, we present CryoETGS, a differentiable learning framework that reconstructs tomograms through adaptive 3D Gaussian representations of biological structures for cryo-ET. This representation enables efficient and interpretable reconstruction through a hardware-accelerated differentiable rendering pipeline aligned with the cryo-ET imaging geometry. CryoETGS incorporates hierarchical initialization, adaptive densification, and a tilt-weighted optimization strategy to enhance convergence and reconstruction fidelity. The framework further supports real-time projection synthesis and bidirectional conversion between voxel-based and Gaussian representations. Extensive experiments on both simulated and experimental datasets demonstrate that CryoETGS achieves state-of-the-art reconstruction performance, effectively mitigates missing wedge artifacts, and exhibits high computational efficiency. Source code is publicly available at <span><span>https://github.com/JachyLikeCoding/ETGS</span><svg><path></path></svg></span>.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"218 1","pages":"Article 108281"},"PeriodicalIF":2.7,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145794230","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Corrigendum to “High-resolution single particle analysis using a scintillator camera XF416 on CRYOARM300II at 300 kV”. [J. Struct. Biol. 218(1) (2026) 108286] “在300千伏的CRYOARM300II上使用闪烁体相机XF416进行高分辨率单粒子分析”的勘误表。[J。结构体。生物学报。218(1)(2026)[88286]。

IF 2.7 3区生物学

Journal of structural biology Pub Date : 2026-03-01 Epub Date: 2026-01-28 DOI: 10.1016/j.jsb.2026.108292

Shinji Aramaki , Tomohito Tanihara , Yuya Yoshida , Naoya Matsunaga , Shigehiro Ohdo , Kouta Mayanagi

引用次数: 0

Structural characterization of Meiothermus ruber LOV domain 微热藻LOV结构域的结构表征。

IF 2.7 3区生物学

Journal of structural biology Pub Date : 2026-03-01 Epub Date: 2025-12-03 DOI: 10.1016/j.jsb.2025.108268

Oleg Semenov , Vera Nazarenko , Anna Yudenko , Kirill Kovalev , Ivan Goncharov , Ilia Natarov , Anatolii Mikhailov , Elizaveta Kuznetsova , Andrey Nikolaev , Yuqi Yang , Nikolai N. Sluchanko , Valentin Borshchevskiy , Alina Remeeva , Ivan Gushchin

{"title":"Structural characterization of Meiothermus ruber LOV domain","authors":"Oleg Semenov , Vera Nazarenko , Anna Yudenko , Kirill Kovalev , Ivan Goncharov , Ilia Natarov , Anatolii Mikhailov , Elizaveta Kuznetsova , Andrey Nikolaev , Yuqi Yang , Nikolai N. Sluchanko , Valentin Borshchevskiy , Alina Remeeva , Ivan Gushchin","doi":"10.1016/j.jsb.2025.108268","DOIUrl":"10.1016/j.jsb.2025.108268","url":null,"abstract":"<div><div>Light Oxygen Voltage (LOV) domains are important widespread receptors of blue light that also found applications in optogenetics and imaging. While LOV domains from mesophiles are relatively well characterized, their counterparts from thermophilic microorganisms remain understudied. Here, we express two constructs of a LOV domain belonging to a histidine kinase from <em>Meiothermus ruber</em>, MrLOV and MrLOVe, and show that they are photoactive, with recovery time values of 21 and 27 min, respectively, and thermostable. Crystal structures reveal that MrLOV, which lacks helices A’α and Jα, forms a parallel dimer, whereas MrLOVe is a tetramer organized as an antiparallel dimer of two parallel dimers interacting via helices Jα. One MrLOVe dimer is symmetric, and the other is asymmetric, with conformational differences mirroring activation-related changes in other LOV domains. Our data provide the structural basis for understanding and engineering of thermophilic LOVs and pave the way for development of thermostable and photostable LOV-derived optogenetic tools and flavin-based fluorescent proteins.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"218 1","pages":"Article 108268"},"PeriodicalIF":2.7,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145687600","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Mechanistic study of PDE5A inhibitors from the prepared folium of Epimedium sagittatum maxim 矮淫羊藿叶中PDE5A抑制剂的作用机制研究。

IF 2.7 3区生物学

Journal of structural biology Pub Date : 2026-03-01 Epub Date: 2025-12-09 DOI: 10.1016/j.jsb.2025.108279

Yuan Fang , Siqi Wu , Jian Xu , Jialiang Chen , Wanyin Shi , Hongji Wang , Senjie Li , Huifang Xie , Houchao Tao , Lifeng Pan , Yunxiang Zang , Guangtao Yao , Xiangwei Zheng

{"title":"Mechanistic study of PDE5A inhibitors from the prepared folium of Epimedium sagittatum maxim","authors":"Yuan Fang , Siqi Wu , Jian Xu , Jialiang Chen , Wanyin Shi , Hongji Wang , Senjie Li , Huifang Xie , Houchao Tao , Lifeng Pan , Yunxiang Zang , Guangtao Yao , Xiangwei Zheng","doi":"10.1016/j.jsb.2025.108279","DOIUrl":"10.1016/j.jsb.2025.108279","url":null,"abstract":"<div><div>Phosphodiesterase-5 (PDE5A) is a critical therapeutic target for treating male erectile dysfunction (ED). PDE5A inhibitors like sildenafil are clinically effective, but exhibit side effects due to non-specific inhibition of related PDE isoforms. This necessitates the discovery of safer and specific PDE5A inhibitors. The prepared folium of Epimedium sagittatum (PFES) is a primary sovereign drug in traditional Chinese medicine (TCM) formulations for ED. As part of ongoing research into its pharmacodynamic basis, this study isolated and identified forty-four flavonoids and organic acids from PFES. The inhibitory activities of these compounds against PDE5A were systematically evaluated, and three compounds (1, 5, and 6) are demonstrated to have significant PDE5A inhibition activities. Notably, the compound 6 (baohuoside I), was previously confirmed the activitywith PDE5A, and its co-crystal structure with PDE5A was also reported. To elucidate the molecular mechanisms underlying the inhibition of PDE5A by compound 1 and 5, we solved the crystal structures of the catalytic domain of PDE5A in complex with compound 1 and 5. Further structural analyses revealed distinct binding modes adopted by 1 and 5 for occupying the PDE5A active site, highlighting their specific interactions with PDE5A compared to each other and to other established inhibitors like sildenafil. In summary, these findings underscore the potential of PFES-derived natural compounds as specific PDE5A inhibitors, and provide crucial insights for the rational development of novel ED therapeutics with potentially improved specificity and reduced side effects based on TCM constituents.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"218 1","pages":"Article 108279"},"PeriodicalIF":2.7,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145743137","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Decoding sequence-structure-function-evolution of basic leucine zippers of aureochromes from heterokont algae 异源藻金黄色色素碱基亮氨酸拉链序列解码-结构-功能-进化。

IF 2.7 3区生物学

Journal of structural biology Pub Date : 2026-03-01 Epub Date: 2025-12-28 DOI: 10.1016/j.jsb.2025.108283

Madhurima Khamaru, Debarshi Bose, Anwesha Deb, Devrani Mitra

{"title":"Decoding sequence-structure-function-evolution of basic leucine zippers of aureochromes from heterokont algae","authors":"Madhurima Khamaru, Debarshi Bose, Anwesha Deb, Devrani Mitra","doi":"10.1016/j.jsb.2025.108283","DOIUrl":"10.1016/j.jsb.2025.108283","url":null,"abstract":"<div><div>The blue light photoreceptor cum transcription factors, aureochromes (Aureos), are present exclusively in photosynthetic stramenopiles. Co-existence of Light-Oxygen-Voltage (LOV) and basic leucine zipper (bZIP) is unique to Aureos – therefore ideal to study light-dependent DNA binding/transcriptional regulation. Further, Aureos’ inverse effector-sensor topology, resembling several sensory eukaryotic transcription factors, makes them prototypical optogenetic scaffolds. In absence of 3D data, this study aims for a thorough investigation of the bZIP domains from Aureos and others, and their interaction with substrate DNA using tools from sequence/structural bioinformatics, network theory, molecular dynamics simulation and <em>in vitro</em> experiments. An in-depth comparison of 173 Aureo/plant/opisthokont bZIPs reveals Aureos’ uniqueness and evolutionary significance in DNA binding specificity as well as dimer stability. An all-atom network analysis on representative bZIP-DNA co-crystal structures, especially the measurement of eigenvector centrality, further adds importance to hydrophobic interactions in the zipper region to stabilize bZIP dimer and facilitate DNA binding in Aureos and other bZIPs. The most notable finding is the unique presence of histidine at the basic region of Aureos unlike other bZIPs. Histidine not just promotes blue light independent substrate DNA-binding affinity but also serves as a potential switch point in Aureo/bZIP evolution.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"218 1","pages":"Article 108283"},"PeriodicalIF":2.7,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145862904","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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