Journal of Structural Biology: X最新文献

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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
{"title":"Structure of biomimetic casein micelles: Critical tests of the hydrophobic colloid and multivalent-binding models using recombinant deuterated and phosphorylated β-casein","authors":"Jared K. Raynes ,&nbsp;Jitendra Mata ,&nbsp;Karyn L. Wilde ,&nbsp;John A. Carver ,&nbsp;Sharon M. Kelly ,&nbsp;Carl Holt","doi":"10.1016/j.yjsbx.2024.100096","DOIUrl":"10.1016/j.yjsbx.2024.100096","url":null,"abstract":"<div><p>Milk contains high concentrations of amyloidogenic casein proteins and is supersaturated with respect to crystalline calcium phosphates such as apatite. Nevertheless, the mammary gland normally remains unmineralized and free of amyloid. Unlike κ-casein, β- and α<sub>S</sub>-caseins are highly effective mineral chaperones that prevent ectopic and pathological calcification of the mammary gland. Milk invariably contains a mixture of two to five different caseins that act on each other as molecular chaperones. Instead of forming amyloid fibrils, several thousand caseins and hundreds of nanoclusters of amorphous calcium phosphate combine to form fuzzy complexes called casein micelles. To understand the biological functions of the casein micelle its structure needs to be understood better than at present. The location in micelles of the highly amyloidogenic κ-casein is disputed. In traditional hydrophobic colloid models, it, alone, forms a stabilizing surface coat that also determines the average size of the micelles. In the recent multivalent-binding model, κ-casein is present throughout the micelle, in intimate contact with the other caseins. To discriminate between these models, a range of biomimetic micelles was prepared using a fixed concentration of the mineral chaperone β-casein and nanoclusters of calcium phosphate, with variable concentrations of κ-casein. A biomimetic micelle was also prepared using a highly deuterated and <em>in vivo</em> phosphorylated recombinant β-casein with calcium phosphate and unlabelled κ-casein. Neutron and X-ray scattering experiments revealed that κ-casein is distributed throughout the micelle, in quantitative agreement with the multivalent-binding model but contrary to the hydrophobic colloid models.</p></div>","PeriodicalId":17238,"journal":{"name":"Journal of Structural Biology: X","volume":"9 ","pages":"Article 100096"},"PeriodicalIF":2.9,"publicationDate":"2024-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2590152424000011/pdfft?md5=e8fc9848e4965cd95d0dfe026d8062cf&pid=1-s2.0-S2590152424000011-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139634123","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
Peptoid-based macrodiscs of variable lipid composition for structural studies of membrane proteins by oriented-sample solid-state NMR 基于蛋白胨的可变脂质成分大圆盘,用于通过定向样品固态核磁共振进行膜蛋白结构研究
IF 2.9
Journal of Structural Biology: X Pub Date : 2023-12-04 DOI: 10.1016/j.yjsbx.2023.100095
Azamat R. Galiakhmetov, Adit A. Shah, Addison Lane, Carolynn M. Davern, Caroline Proulx, Alexander A. Nevzorov
{"title":"Peptoid-based macrodiscs of variable lipid composition for structural studies of membrane proteins by oriented-sample solid-state NMR","authors":"Azamat R. Galiakhmetov,&nbsp;Adit A. Shah,&nbsp;Addison Lane,&nbsp;Carolynn M. Davern,&nbsp;Caroline Proulx,&nbsp;Alexander A. Nevzorov","doi":"10.1016/j.yjsbx.2023.100095","DOIUrl":"https://doi.org/10.1016/j.yjsbx.2023.100095","url":null,"abstract":"<div><p>Solid-state Nuclear Magnetic Resonance (NMR) in combination with magnetically aligned discoidal lipid mimics allows for studying the conformations of membrane proteins in planar, lipid-rich bilayer environments and at the physiological temperature. We have recently demonstrated the general applicability of macrodiscs composed of DMPC lipids and peptoid belts, which yield magnetic alignment and NMR spectroscopic resolution comparable or superior to detergent-containing bicelles. Here we report on a considerable improvement in the magnetic alignment and NMR resolution of peptoid-based macrodiscs consisting of a mixture of the zwitterionic and negatively charged lipids (DMPC/DMPG at the 85% to 15% molar ratio). The resulting linewidths are about 30% sharper due to the higher orientational order parameter likely arising from the stabilizing electrostatic repulsion between the discs. Moreover, highly aligned, detergent-free macrodiscs can be formed with a longer-chain lipid, DPPC. Interestingly, the spectra of Pf1 in the two lipid mimetics are almost indistinguishable, which would mean that the overall transmembrane helix tilt might be governed not only by the hydrophobic matching but also possibly by the interactions of the flanking lysine and arginine residues at the membrane interface.</p></div>","PeriodicalId":17238,"journal":{"name":"Journal of Structural Biology: X","volume":"9 ","pages":"Article 100095"},"PeriodicalIF":2.9,"publicationDate":"2023-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2590152423000119/pdfft?md5=facf5798311ccfe84d39976a2b84f0fc&pid=1-s2.0-S2590152423000119-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138549264","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
NMR structure verifies the eponymous zinc finger domain of transcription factor ZNF750 核磁共振结构证实了转录因子ZNF750的同名锌指结构域
IF 2.9
Journal of Structural Biology: X Pub Date : 2023-08-12 DOI: 10.1016/j.yjsbx.2023.100093
Antonio J. Rua, Richard D. Whitehead 3rd, Andrei T. Alexandrescu
{"title":"NMR structure verifies the eponymous zinc finger domain of transcription factor ZNF750","authors":"Antonio J. Rua,&nbsp;Richard D. Whitehead 3rd,&nbsp;Andrei T. Alexandrescu","doi":"10.1016/j.yjsbx.2023.100093","DOIUrl":"10.1016/j.yjsbx.2023.100093","url":null,"abstract":"<div><p>ZNF750 is a nuclear transcription factor that activates skin differentiation and has tumor suppressor roles in several cancers. Unusually, ZNF750 has only a single zinc-finger (ZNF) domain, Z*, with an amino acid sequence that differs markedly from the CCHH family consensus. Because of its sequence differences Z* is classified as degenerate, presumed to have lost the ability to bind the zinc ion required for folding. AlphaFold predicts an irregular structure for Z* with low confidence. Low confidence predictions are often inferred to be intrinsically disordered regions of proteins, which would be the case if Z* did not bind Zn<sup>2+</sup>. We use NMR and CD spectroscopy to show that a 25–51 segment of ZNF750 corresponding to the Z* domain folds into a well-defined antiparallel ββα tertiary structure with a pM dissociation constant for Zn<sup>2+</sup> and a thermal stability &gt;80 °C. Of three alternative Zn<sup>2+</sup> ligand sets, Z* uses a CCHC rather than the expected CCHH ligating motif. The switch in the last ligand maintains the folding topology and hydrophobic core of the classical ZNF motif. CCHC ZNFs are typically associated with protein–protein interactions, raising the possibility that ZNF750 interacts with DNA through other proteins rather than directly. The structure of Z* provides context for understanding the function of the domain and its cancer-associated mutations. We expect other ZNFs currently classified as degenerate could be CCHC-type structures like Z*.</p></div>","PeriodicalId":17238,"journal":{"name":"Journal of Structural Biology: X","volume":"8 ","pages":"Article 100093"},"PeriodicalIF":2.9,"publicationDate":"2023-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/4d/b7/main.PMC10465944.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10231213","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
Cryo-EM of a heterogeneous biochemical fraction elucidates multiple protein complexes from a multicellular thermophilic eukaryote 异质生化组分的低温电镜分析阐明了来自多细胞嗜热真核生物的多种蛋白质复合物
IF 2.9
Journal of Structural Biology: X Pub Date : 2023-08-09 DOI: 10.1016/j.yjsbx.2023.100094
Dmitry A. Semchonok , Fotis L. Kyrilis , Farzad Hamdi , Panagiotis L. Kastritis
{"title":"Cryo-EM of a heterogeneous biochemical fraction elucidates multiple protein complexes from a multicellular thermophilic eukaryote","authors":"Dmitry A. Semchonok ,&nbsp;Fotis L. Kyrilis ,&nbsp;Farzad Hamdi ,&nbsp;Panagiotis L. Kastritis","doi":"10.1016/j.yjsbx.2023.100094","DOIUrl":"10.1016/j.yjsbx.2023.100094","url":null,"abstract":"<div><p>Biomolecular complexes and their interactions govern cellular structure and function. Understanding their architecture is a prerequisite for dissecting the cell's inner workings, but their higher-order assembly is often transient and challenging for structural analysis. Here, we performed cryo-EM on a single, highly heterogeneous biochemical fraction derived from <em>Chaetomium thermophilum</em> cell extracts to visualize the biomolecular content of the multicellular eukaryote. After cryo-EM single-particle image processing, results showed that a simultaneous three-dimensional structural characterization of multiple chemically diverse biomacromolecules is feasible. Namely, the thermophilic, eukaryotic complexes of (a) ATP citrate-lyase, (b) Hsp90, (c) 20S proteasome, (d) Hsp60 and (e) UDP-glucose pyrophosphorylase were characterized. In total, all five complexes have been structurally dissected in a thermophilic eukaryote in a total imaged sample area of 190.64 μm<sup>2</sup>, and two, in particular, 20S proteasome and Hsp60, exhibit side-chain resolution features. The <em>C. thermophilum</em> Hsp60 near-atomic model was resolved at 3.46 Å (FSC = 0.143) and shows a hinge-like conformational change of its equatorial domain, highly similar to the one previously shown for its bacterial orthologue, GroEL. This work demonstrates that cryo-EM of cell extracts will greatly accelerate the structural analysis of cellular complexes and provide unprecedented opportunities to annotate architectures of biomolecules in a holistic approach.</p></div>","PeriodicalId":17238,"journal":{"name":"Journal of Structural Biology: X","volume":"8 ","pages":"Article 100094"},"PeriodicalIF":2.9,"publicationDate":"2023-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10451023/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10107408","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
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