Journal of Structural Biology: X最新文献

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Nucleic acid-binding KH domain proteins influence a spectrum of biological pathways including as part of membrane-localized complexes 核酸结合 KH 结构域蛋白影响一系列生物通路,包括作为膜定位复合物的一部分发挥作用
IF 3.5
Journal of Structural Biology: X Pub Date : 2024-06-27 DOI: 10.1016/j.yjsbx.2024.100106
Md Kamrul Hasan , L. Jeannine Brady
{"title":"Nucleic acid-binding KH domain proteins influence a spectrum of biological pathways including as part of membrane-localized complexes","authors":"Md Kamrul Hasan ,&nbsp;L. Jeannine Brady","doi":"10.1016/j.yjsbx.2024.100106","DOIUrl":"https://doi.org/10.1016/j.yjsbx.2024.100106","url":null,"abstract":"<div><p>K-Homology domain (KH domain) proteins bind single-stranded nucleic acids, influence protein–protein interactions of proteins that harbor them, and are found in all kingdoms of life. In concert with other functional protein domains KH domains contribute to a variety of critical biological activities, often within higher order machineries including membrane-localized protein complexes. Eukaryotic KH domain proteins are linked to developmental processes, morphogenesis, and growth regulation, and their aberrant expression is often associated with cancer. Prokaryotic KH domain proteins are involved in integral cellular activities including cell division and protein translocation. Eukaryotic and prokaryotic KH domains share structural features, but are differentiated based on their structural organizations. In this review, we explore the structure/function relationships of known examples of KH domain proteins, and highlight cases in which they function within or at membrane surfaces. We also summarize examples of KH domain proteins that influence bacterial virulence and pathogenesis. We conclude the article by discussing prospective research avenues that could be pursued to better investigate this largely understudied protein category.</p></div>","PeriodicalId":17238,"journal":{"name":"Journal of Structural Biology: X","volume":"10 ","pages":"Article 100106"},"PeriodicalIF":3.5,"publicationDate":"2024-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2590152424000114/pdfft?md5=0e422cb348e848d0c60e6c2df8352de4&pid=1-s2.0-S2590152424000114-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141486539","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Accurate size-based protein localization from cryo-ET tomograms 从低温电子断层扫描图中准确定位蛋白质大小
IF 3.5
Journal of Structural Biology: X Pub Date : 2024-06-26 DOI: 10.1016/j.yjsbx.2024.100104
Weisheng Jin , Ye Zhou , Alberto Bartesaghi
{"title":"Accurate size-based protein localization from cryo-ET tomograms","authors":"Weisheng Jin ,&nbsp;Ye Zhou ,&nbsp;Alberto Bartesaghi","doi":"10.1016/j.yjsbx.2024.100104","DOIUrl":"https://doi.org/10.1016/j.yjsbx.2024.100104","url":null,"abstract":"<div><p>Cryo-electron tomography (cryo-ET) combined with sub-tomogram averaging (STA) allows the determination of protein structures imaged within the native context of the cell at near-atomic resolution. Particle picking is an essential step in the cryo-ET/STA image analysis pipeline that consists in locating the position of proteins within crowded cellular tomograms so that they can be aligned and averaged in 3D to improve resolution. While extensive work in 2D particle picking has been done in the context of single-particle cryo-EM, comparatively fewer strategies have been proposed to pick particles from 3D tomograms, in part due to the challenges associated with working with noisy 3D volumes affected by the missing wedge. While strategies based on 3D template-matching and deep learning are commonly used, these methods are computationally expensive and require either an external template or manual labelling which can bias the results and limit their applicability. Here, we propose a size-based method to pick particles from tomograms that is fast, accurate, and does not require external templates or user provided labels. We compare the performance of our approach against a commonly used algorithm based on deep learning, crYOLO, and show that our method: i) has higher detection accuracy, ii) does not require user input for labeling or time-consuming training, and iii) runs efficiently on non-specialized CPU hardware. We demonstrate the effectiveness of our approach by automatically detecting particles from tomograms representing different types of samples and using these particles to determine the high-resolution structures of ribosomes imaged <em>in vitro</em> and <em>in situ</em>.</p></div>","PeriodicalId":17238,"journal":{"name":"Journal of Structural Biology: X","volume":"10 ","pages":"Article 100104"},"PeriodicalIF":3.5,"publicationDate":"2024-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2590152424000096/pdfft?md5=9bf56ad8420d48d82b350489a5b2005c&pid=1-s2.0-S2590152424000096-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141594447","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Solution structure, dynamics and tetrahedral assembly of Anti-TRAP, a homo-trimeric triskelion-shaped regulator of tryptophan biosynthesis in Bacillus subtilis 枯草芽孢杆菌中色氨酸生物合成的同源三叉戟形调控因子 Anti-TRAP 的溶液结构、动力学和四面体组装
IF 3.5
Journal of Structural Biology: X Pub Date : 2024-06-11 DOI: 10.1016/j.yjsbx.2024.100103
Craig A. McElroy , Elihu C. Ihms , Deepak Kumar Yadav , Melody L. Holmquist , Vibhuti Wadhwa , Vicki H. Wysocki , Paul Gollnick , Mark P. Foster
{"title":"Solution structure, dynamics and tetrahedral assembly of Anti-TRAP, a homo-trimeric triskelion-shaped regulator of tryptophan biosynthesis in Bacillus subtilis","authors":"Craig A. McElroy ,&nbsp;Elihu C. Ihms ,&nbsp;Deepak Kumar Yadav ,&nbsp;Melody L. Holmquist ,&nbsp;Vibhuti Wadhwa ,&nbsp;Vicki H. Wysocki ,&nbsp;Paul Gollnick ,&nbsp;Mark P. Foster","doi":"10.1016/j.yjsbx.2024.100103","DOIUrl":"https://doi.org/10.1016/j.yjsbx.2024.100103","url":null,"abstract":"<div><p>Cellular production of tryptophan is metabolically expensive and tightly regulated. The small <em>Bacillus subtilis</em> zinc binding Anti-TRAP protein (AT), which is the product of the <em>yczA/rtpA</em> gene, is upregulated in response to accumulating levels of uncharged tRNA<sup>Trp</sup> through a T-box antitermination mechanism. AT binds to the undecameric axially symmetric ring-shaped protein TRAP (<em>trp</em> RNA Binding Attenuation Protein), thereby preventing it from binding to the <em>trp</em> leader RNA. This reverses the inhibitory effect of TRAP on transcription and translation of the <em>trp</em> operon. AT principally adopts two symmetric oligomeric states, a trimer (AT<sub>3</sub>) featuring three-fold axial symmetry or a dodecamer (AT<sub>12</sub>) comprising a tetrahedral assembly of trimers, whereas only the trimeric form binds and inhibits TRAP. We apply native mass spectrometry (nMS) and small-angle x-ray scattering (SAXS), together with analytical ultracentrifugation (AUC) to monitor the pH and concentration-dependent equilibrium between the trimeric and dodecameric structural forms of AT. In addition, we use solution nuclear magnetic resonance (NMR) spectroscopy to determine the solution structure of AT<sub>3</sub>, while heteronuclear <sup>15</sup>N relaxation measurements on both oligomeric forms of AT provide insights into the dynamic properties of binding-active AT<sub>3</sub> and binding-inactive AT<sub>12</sub>, with implications for TRAP binding and inhibition.</p></div>","PeriodicalId":17238,"journal":{"name":"Journal of Structural Biology: X","volume":"10 ","pages":"Article 100103"},"PeriodicalIF":3.5,"publicationDate":"2024-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2590152424000084/pdfft?md5=571b0da5dc58532b76dc49e84cbcb4d5&pid=1-s2.0-S2590152424000084-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141486538","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Eliminating the missing cone challenge through innovative approaches 通过创新方法消除缺锥难题
IF 2.9
Journal of Structural Biology: X Pub Date : 2024-06-01 DOI: 10.1016/j.yjsbx.2024.100102
Cody Gillman , Guanhong Bu , Emma Danelius , Johan Hattne , Brent L. Nannenga , Tamir Gonen
{"title":"Eliminating the missing cone challenge through innovative approaches","authors":"Cody Gillman ,&nbsp;Guanhong Bu ,&nbsp;Emma Danelius ,&nbsp;Johan Hattne ,&nbsp;Brent L. Nannenga ,&nbsp;Tamir Gonen","doi":"10.1016/j.yjsbx.2024.100102","DOIUrl":"https://doi.org/10.1016/j.yjsbx.2024.100102","url":null,"abstract":"<div><p>Microcrystal electron diffraction (MicroED) has emerged as a powerful technique for unraveling molecular structures from microcrystals too small for X-ray diffraction. However, a significant hurdle arises with plate-like crystals that consistently orient themselves flat on the electron microscopy grid. If the normal of the plate correlates with the axes of the crystal lattice, the crystal orientations accessible for measurement are restricted because the crystal cannot be arbitrarily rotated. This limits the information that can be acquired, resulting in a missing cone of information. We recently introduced a novel crystallization strategy called suspended drop crystallization and proposed that crystals in a suspended drop could effectively address the challenge of preferred crystal orientation. Here we demonstrate the success of the suspended drop approach in eliminating the missing cone in two samples that crystallize as thin plates: bovine liver catalase and the SARS‑CoV‑2 main protease (Mpro). This innovative solution proves indispensable for crystals exhibiting systematic preferred orientations, unlocking new possibilities for structure determination by MicroED.</p></div>","PeriodicalId":17238,"journal":{"name":"Journal of Structural Biology: X","volume":"9 ","pages":"Article 100102"},"PeriodicalIF":2.9,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2590152424000072/pdfft?md5=7540527cb3411fb26f5be3a6bf21bfcd&pid=1-s2.0-S2590152424000072-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141290118","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Optimizing NMR fragment-based drug screening for membrane protein targets 优化基于核磁共振片段的膜蛋白靶点药物筛选
IF 2.9
Journal of Structural Biology: X Pub Date : 2024-06-01 DOI: 10.1016/j.yjsbx.2024.100100
Geoffrey C. Li , Manuel A. Castro , Thilini Ukwaththage, Charles R. Sanders
{"title":"Optimizing NMR fragment-based drug screening for membrane protein targets","authors":"Geoffrey C. Li ,&nbsp;Manuel A. Castro ,&nbsp;Thilini Ukwaththage,&nbsp;Charles R. Sanders","doi":"10.1016/j.yjsbx.2024.100100","DOIUrl":"https://doi.org/10.1016/j.yjsbx.2024.100100","url":null,"abstract":"<div><p>NMR spectroscopy has played a pivotal role in fragment-based drug discovery by coupling detection of weak ligand-target binding with structural mapping of the binding site. Fragment-based screening by NMR has been successfully applied to many soluble protein targets, but only to a limited number of membrane proteins, despite the fact that many drug targets are membrane proteins. This is partly because of difficulties preparing membrane proteins for NMR—especially human membrane proteins—and because of the inherent complexity associated with solution NMR spectroscopy on membrane protein samples, which require the inclusion of membrane-mimetic agents such as micelles, nanodiscs, or bicelles. Here, we developed a generalizable protocol for fragment-based screening of membrane proteins using NMR. We employed two human membrane protein targets, both in fully protonated detergent micelles: the single-pass C-terminal domain of the amyloid precursor protein, C99, and the tetraspan peripheral myelin protein 22 (PMP22). For both we determined the optimal NMR acquisition parameters, protein concentration, protein-to-micelle ratio, and upper limit to the concentration of D<sub>6</sub>-DMSO in screening samples. Furthermore, we conducted preliminary screens of a plate-format molecular fragment mixture library using our optimized conditions and were able to identify hit compounds that selectively bound to the respective target proteins. It is hoped that the approaches presented here will be useful in complementing existing methods for discovering lead compounds that target membrane proteins.</p></div>","PeriodicalId":17238,"journal":{"name":"Journal of Structural Biology: X","volume":"9 ","pages":"Article 100100"},"PeriodicalIF":2.9,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2590152424000059/pdfft?md5=39c55f7648d09ecd7660ace75e9b5e22&pid=1-s2.0-S2590152424000059-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141240760","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Coordination of bilayer properties by an inward-rectifier K+ channel is a cooperative process driven by protein-lipid interaction 内向整流 K+ 通道对双分子层特性的协调是一个由蛋白质-脂质相互作用驱动的合作过程
IF 2.9
Journal of Structural Biology: X Pub Date : 2024-06-01 DOI: 10.1016/j.yjsbx.2024.100101
Evan J. van Aalst , Maryam Yekefallah , Roy A. M. van Beekveld , Eefjan Breukink , Markus Weingarth , Benjamin J. Wylie
{"title":"Coordination of bilayer properties by an inward-rectifier K+ channel is a cooperative process driven by protein-lipid interaction","authors":"Evan J. van Aalst ,&nbsp;Maryam Yekefallah ,&nbsp;Roy A. M. van Beekveld ,&nbsp;Eefjan Breukink ,&nbsp;Markus Weingarth ,&nbsp;Benjamin J. Wylie","doi":"10.1016/j.yjsbx.2024.100101","DOIUrl":"https://doi.org/10.1016/j.yjsbx.2024.100101","url":null,"abstract":"<div><p>Physical properties of biological membranes directly or indirectly govern biological processes. Yet, the interplay between membrane and integral membrane proteins is difficult to assess due to reciprocal effects between membrane proteins, individual lipids, and membrane architecture. Using solid-state NMR (SSNMR) we previously showed that KirBac1.1, a bacterial Inward-Rectifier K<sup>+</sup> channel, nucleates bilayer ordering and microdomain formation through tethering anionic lipids. Conversely, these lipids cooperatively bind cationic residues to activate the channel and initiate K<sup>+</sup> flux. The mechanistic details governing the relationship between cooperative lipid loading and bilayer ordering are, however, unknown. To investigate, we generated KirBac1.1 samples with different concentrations of <sup>13</sup>C-lableded phosphatidyl glycerol (PG) lipids and acquired a full suite of SSNMR 1D temperature series experiments using the ordered all-trans (AT) and disordered <em>trans</em>-gauche (TG) acyl conformations as markers of bilayer dynamics. We observed increased AT ordered signal, decreased TG disordered signal, and increased bilayer melting temperature with increased PG concentration. Further, we identified cooperativity between ordering and direct binding of PG lipids, indicating KirBac1.1-driven bilayer ordering and microdomain formation is a classically cooperative Hill-type process driven by and predicated upon direct binding of PG lipids. Our results provide unique mechanistic insight into how proteins and lipids in tandem contribute to supramolecular bilayer heterogeneity in the lipid membrane.</p></div>","PeriodicalId":17238,"journal":{"name":"Journal of Structural Biology: X","volume":"9 ","pages":"Article 100101"},"PeriodicalIF":2.9,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2590152424000060/pdfft?md5=93c4cf2e0eae744a1e20dcd4448f8094&pid=1-s2.0-S2590152424000060-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141240761","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The parabasal filaments of Trichomonas vaginalis: A new filament and observations using 0.8 nm-resolution scanning electron microscopy 阴道毛滴虫的副基质丝:一种新的丝状物和使用 0.8 纳米分辨率扫描电子显微镜的观察结果
IF 2.9
Journal of Structural Biology: X Pub Date : 2024-03-06 DOI: 10.1016/j.yjsbx.2024.100099
Sharmila Fiama das Neves Ortiz , Raphael Verdan , Gustavo Miranda Rocha , Kildare Miranda , Marlene Benchimol
{"title":"The parabasal filaments of Trichomonas vaginalis: A new filament and observations using 0.8 nm-resolution scanning electron microscopy","authors":"Sharmila Fiama das Neves Ortiz ,&nbsp;Raphael Verdan ,&nbsp;Gustavo Miranda Rocha ,&nbsp;Kildare Miranda ,&nbsp;Marlene Benchimol","doi":"10.1016/j.yjsbx.2024.100099","DOIUrl":"https://doi.org/10.1016/j.yjsbx.2024.100099","url":null,"abstract":"<div><p><em>Trichomonas vaginalis</em> is the etiologic agent of trichomoniasis, the most common nonviral sexually transmitted infection worldwide, with an estimated 260 million new cases annually. <em>T. vaginalis</em> contains organelles common to all eukaryotic cells, uncommon cell structures such as hydrogenosomes, and a complex and elaborate cytoskeleton constituting the mastigont system. The mastigont system is mainly formed by several proteinaceous structures associated with basal bodies, the pelta-axostylar complex made of microtubules, and striated filaments named the costa and the parabasal filaments (PFs). Although the structural organization of trichomonad cytoskeletons has been analyzed using several techniques, observation using a new generation of scanning electron microscopes with a resolution exceeding 1 nm has allowed more detailed visualization of the three-dimensional organization of the mastigont system. In this study, we have investigated the cytoskeleton of <em>T. vaginalis</em> using a diverse range of scanning probe microscopy techniques, which were complemented by electron tomography and Fast-Fourier methods. This multi-modal approach has allowed us to characterize an unknown parabasal filament and reveal the ultrastructure of other striated fibers that have not been published before. Here, we show the differences in origin, striation pattern, size, localization, and additional details of the PFs, thus improving the knowledge of the cell biology of this parasite.</p></div>","PeriodicalId":17238,"journal":{"name":"Journal of Structural Biology: X","volume":"9 ","pages":"Article 100099"},"PeriodicalIF":2.9,"publicationDate":"2024-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2590152424000047/pdfft?md5=f5be6fd3381454e5b294408c8f1c6d0c&pid=1-s2.0-S2590152424000047-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140051590","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Magic-angle spinning NMR structure of Opa60 in lipid bilayers Opa60 在脂质双分子层中的魔角旋转 NMR 结构
IF 2.9
Journal of Structural Biology: X Pub Date : 2024-02-21 DOI: 10.1016/j.yjsbx.2024.100098
Marcel C. Forster, Kumar Tekwani Movellan, Eszter E. Najbauer, Stefan Becker, Loren B. Andreas
{"title":"Magic-angle spinning NMR structure of Opa60 in lipid bilayers","authors":"Marcel C. Forster,&nbsp;Kumar Tekwani Movellan,&nbsp;Eszter E. Najbauer,&nbsp;Stefan Becker,&nbsp;Loren B. Andreas","doi":"10.1016/j.yjsbx.2024.100098","DOIUrl":"https://doi.org/10.1016/j.yjsbx.2024.100098","url":null,"abstract":"<div><p>Here we report the structure of Opa60 in lipid bilayers using proton-detected magic-angle spinning nuclear magnetic resonance (MAS NMR). Preparations including near-native oligosaccharide lipids reveal a consistent picture of a stable transmembrane beta barrel with a minor increase in the structured region as compared with the previously reported detergent structure. The large variable loops known to interact with host proteins could not be detected, confirming their dynamic nature even in a lipid bilayer environment. The structure provides a starting point for investigation of the functional role of Opa60 in gonococcal infection, which is understood to involve interaction with host proteins. At the same time, it demonstrates the recent advances in proton-detected methodology for membrane protein structure determination at atomic resolution by MAS NMR.</p></div>","PeriodicalId":17238,"journal":{"name":"Journal of Structural Biology: X","volume":"9 ","pages":"Article 100098"},"PeriodicalIF":2.9,"publicationDate":"2024-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2590152424000035/pdfft?md5=bcfa30af962cd69ec03183b9f0718283&pid=1-s2.0-S2590152424000035-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140015902","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Grafting the ALFA tag for structural studies of aquaporin Z 接枝 ALFA 标签用于水蒸发蛋白 Z 的结构研究
IF 2.9
Journal of Structural Biology: X Pub Date : 2024-02-02 DOI: 10.1016/j.yjsbx.2024.100097
Lauren Stover , Hanieh Bahramimoghaddam , Lie Wang , Samantha Schrecke , Gaya P. Yadav , Ming Zhou , Arthur Laganowsky
{"title":"Grafting the ALFA tag for structural studies of aquaporin Z","authors":"Lauren Stover ,&nbsp;Hanieh Bahramimoghaddam ,&nbsp;Lie Wang ,&nbsp;Samantha Schrecke ,&nbsp;Gaya P. Yadav ,&nbsp;Ming Zhou ,&nbsp;Arthur Laganowsky","doi":"10.1016/j.yjsbx.2024.100097","DOIUrl":"https://doi.org/10.1016/j.yjsbx.2024.100097","url":null,"abstract":"<div><p>Aquaporin Z (AqpZ), a bacterial water channel, forms a tetrameric complex and, like many other membrane proteins, activity is regulated by lipids. Various methods have been developed to facilitate structure determination of membrane proteins, such as the use of antibodies. Here, we graft onto AqpZ the ALFA tag (AqpZ-ALFA), an alpha helical epitope, to make use of the high-affinity anti-ALFA nanobody (nB). Native mass spectrometry reveals the AqpZ-ALFA fusion forms a stable, 1:1 complex with nB. Single-particle cryogenic electron microscopy studies reveal the octameric (AqpZ-ALFA)<sub>4</sub>(nB)<sub>4</sub> complex forms a dimeric assembly and the structure was determined to 1.9 Å resolution. Dimerization of the octamer is mediated through stacking of the symmetrically bound nBs. Tube-like density is also observed, revealing a potential cardiolipin binding site. Grafting of the ALFA tag, or other epitope, along with binding and association of nBs to promote larger complexes will have applications in structural studies and protein engineering.</p></div>","PeriodicalId":17238,"journal":{"name":"Journal of Structural Biology: X","volume":"9 ","pages":"Article 100097"},"PeriodicalIF":2.9,"publicationDate":"2024-02-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2590152424000023/pdfft?md5=81782f0ee174ad218a60122e91b9a015&pid=1-s2.0-S2590152424000023-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139714608","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Structure of biomimetic casein micelles: Critical tests of the hydrophobic colloid and multivalent-binding models using recombinant deuterated and phosphorylated β-casein 仿生酪蛋白胶束的结构:使用重组氘化和磷酸化 β -酪蛋白对疏水胶体和多价结合模型进行关键测试
IF 2.9
Journal of Structural Biology: X Pub Date : 2024-01-22 DOI: 10.1016/j.yjsbx.2024.100096
Jared K. Raynes , Jitendra Mata , Karyn L. Wilde , John A. Carver , Sharon M. Kelly , Carl Holt
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