Journal of structural biology最新文献

Selective signal enhancement in Fourier space as a tool for discovering ultrastructural organization of macromolecules from in situ TEM. 傅立叶空间的选择性信号增强，作为从原位 TEM 发现大分子超微结构组织的工具。

IF 3 3区生物学

Journal of structural biology Pub Date : 2024-09-14 DOI: 10.1016/j.jsb.2024.108128

Nadejda B Matsko, Martin Schorb, Yannick Schwab

{"title":"Selective signal enhancement in Fourier space as a tool for discovering ultrastructural organization of macromolecules from in situ TEM.","authors":"Nadejda B Matsko, Martin Schorb, Yannick Schwab","doi":"10.1016/j.jsb.2024.108128","DOIUrl":"https://doi.org/10.1016/j.jsb.2024.108128","url":null,"abstract":"We present a Fourier transform (FT) based analytical method that allows to obtain of ultrastructural details from TEM images at sub-nanometer scale applying a selective filtering for singular macromolecule electron microscopy density information. It can be applied to high-pressure frozen, frozen hydrated and epoxy freeze substituted and embedded biological species. Both 2D projections and orthoslices from reconstructed tomograms can be used as a source of structural information. The key to the method is to select the macromolecule or organelle of interest with an accuracy of ≥ 7 - 3 nm (depending on pixel size of initial tilt series or singular image acquisition) and explore both the central low frequency FT intensity and diffraction regions to obtain the spatial structural organization and its dimensional characteristics, respectively. We also introduce a structure-specific selective mask FT filtering approach that can significantly improve image information even in poorly contrasted TEM of resin sections without heavy-metal been used. The described method elucidates chromatin architecture without the need of averaging. A zigzag symmetry of 30 nm diameter chromatin fibers which in general is a controversial topic of research has been identified for C. elegans cells in vivo with sub-nanometer details being preserved in the images.","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2024-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142289841","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

Three-dimensional cellular architecture of the sigmoid filament in Trichomonas vaginalis 阴道毛滴虫乙状结肠丝的三维细胞结构。

IF 3 3区生物学

Journal of structural biology Pub Date : 2024-09-06 DOI: 10.1016/j.jsb.2024.108127

引用次数: 0

Comparison of the global crystallographic texture of minerals in the shells of Bathymodiolus thermophilus Kenk et B.R. Wilson, 1985 and species of the genus Mytilus Linnaeus, 1758 Bathymodiolus thermophilus Kenk et B.R. Wilson，1985 年与林奈（Mytilus Linnaeus，1758 年）属物种贝壳中矿物的总体结晶学纹理比较。

IF 3 3区生物学

Journal of structural biology Pub Date : 2024-09-06 DOI: 10.1016/j.jsb.2024.108126

{"title":"Comparison of the global crystallographic texture of minerals in the shells of Bathymodiolus thermophilus Kenk et B.R. Wilson, 1985 and species of the genus Mytilus Linnaeus, 1758","authors":"","doi":"10.1016/j.jsb.2024.108126","DOIUrl":"10.1016/j.jsb.2024.108126","url":null,"abstract":"<div>The global crystallographic texture of calcite and aragonite in the shells of the bivalves Bathymodiolus thermophilus, Mytilus galloprovincialis, M. edulis and M. trossulus was studied by means of neutron diffraction. It was revealed that the general appearance of pole figures isolines of both minerals coincides for the studied species. The crystallographic texture sharpness evaluated by means of pole density on the calcite pole figures ((0006), <math><mrow><mo>(</mo><mn>10</mn><mover><mrow><mn>1</mn></mrow><mrow><mo>¯</mo></mrow></mover><mn>4</mn><mo>)</mo></mrow></math>) and aragonite pole figures ((012)/(121), (040)/(221)) coincides or has close values for deep-sea hydrothermal species B. thermophilus and the studied shallow-water species of the genus Mytilus. The calcite pole figures (0006) and <math><mrow><mo>(</mo><mn>10</mn><mover><mrow><mn>1</mn></mrow><mrow><mo>¯</mo></mrow></mover><mn>4</mn><mo>)</mo></mrow></math> of B. thermophilus show a shift in the position of texture maximum values compared to corresponding pole figures of other mussels. The shell microstructure of all studied mollusks is similar, only the shape of the fibers of B. thermophilus differs. Global crystallographic texture is a stable feature of the family Mytilidae. The extreme habitat conditions of the hydrothermal biotope do not significantly affect the crystallographic texture of B. thermophilus.</div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2024-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142145838","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

Studying protein–protein interactions: Latest and most popular approaches 研究蛋白质与蛋白质之间的相互作用：最新和最流行的方法

IF 3 3区生物学

Journal of structural biology Pub Date : 2024-08-28 DOI: 10.1016/j.jsb.2024.108118

{"title":"Studying protein–protein interactions: Latest and most popular approaches","authors":"","doi":"10.1016/j.jsb.2024.108118","DOIUrl":"10.1016/j.jsb.2024.108118","url":null,"abstract":"<div>PPIs, or protein–protein interactions, are essential for many biological processes. According to the findings, abnormal PPIs have been linked to several diseases, such as cancer and infectious and neurological disorders. Consequently, focusing on PPIs is a path toward disease treatment and a crucial tool for producing novel medications. Many methods exist to investigate PPIs, including low- and high-throughput studies. Since many PPIs have been discovered using in vitro and in vivo experimental approaches, the use of computational methods to predict PPIs has grown due to the expanding scale of PPI data and the intrinsic complexity of interacting mechanisms. Recognizing PPI networks offers a systematic means of predicting protein functions, and pathways that are included. These investigations can help uncover the underlying molecular mechanisms of complex phenotypes and clarify the biological processes related to health and diseases. Therefore, our goal in this study is to provide an overview of the latest and most popular approaches for investigating PPIs. We also overview some important clinical approaches based on the PPIs and how these interactions can be targeted.</div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2024-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142108532","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

Structural analysis of the human C5a-C5aR1 complex using cryo-electron microscopy 利用低温电子显微镜对人类 C5a-C5aR1 复合物进行结构分析。

IF 3 3区生物学

Journal of structural biology Pub Date : 2024-08-15 DOI: 10.1016/j.jsb.2024.108117

{"title":"Structural analysis of the human C5a-C5aR1 complex using cryo-electron microscopy","authors":"","doi":"10.1016/j.jsb.2024.108117","DOIUrl":"10.1016/j.jsb.2024.108117","url":null,"abstract":"<div>The complement system is a complex network of proteins that plays a crucial role in the innate immune response. One important component of this system is the C5a-C5aR1 complex, which is critical in the recruitment and activation of immune cells. In-depth investigation of the activation mechanism as well as biased signaling of the C5a-C5aR1 system will facilitate the elucidation of C5a-mediated pathophysiology. In this study, we determined the structure of C5a-C5aR1-Gi complex at a high resolution of 3 Å using cryo-electron microscopy (Cryo-EM). Our results revealed the binding site of C5a, which consists of a polar recognition region on the extracellular side and an amphipathic pocket within the transmembrane domain. Furthermore, we found that C5a binding induces conformational changes of C5aR1, which subsequently leads to the activation of G protein signaling pathways. Notably, a key residue (M265) located on transmembrane helix 6 (TM6) was identified to play a crucial role in regulating the recruitment of β-arrestin driven by C5a. This study provides more information about the structure and function of the human C5a-C5aR1 complex, which is essential for the proper functioning of the complement system. The findings of this study can also provide a foundation for the design of new pharmaceuticals targeting this receptor with bias or specificity.</div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2024-08-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141995955","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

Cryo-EM reconstruction of oleate hydratase bound to a phospholipid membrane bilayer 油酸水解酶与磷脂膜双分子层结合的冷冻电子显微镜重建。

IF 3 3区生物学

Journal of structural biology Pub Date : 2024-08-14 DOI: 10.1016/j.jsb.2024.108116

{"title":"Cryo-EM reconstruction of oleate hydratase bound to a phospholipid membrane bilayer","authors":"","doi":"10.1016/j.jsb.2024.108116","DOIUrl":"10.1016/j.jsb.2024.108116","url":null,"abstract":"<div>Oleate hydratase (OhyA) is a bacterial peripheral membrane protein that catalyzes FAD-dependent water addition to membrane bilayer-embedded unsaturated fatty acids. The opportunistic pathogen Staphylococcus aureus uses OhyA to counteract the innate immune system and support colonization. Many Gram-positive and Gram-negative bacteria in the microbiome also encode OhyA. OhyA is a dimeric flavoenzyme whose carboxy terminus is identified as the membrane binding domain; however, understanding how OhyA binds to cellular membranes is not complete until the membrane-bound structure has been elucidated. All available OhyA structures depict the solution state of the protein outside its functional environment. Here, we employ liposomes to solve the cryo-electron microscopy structure of the functional unit: the OhyA•membrane complex. The protein maintains its structure upon membrane binding and slightly alters the curvature of the liposome surface. OhyA preferentially associates with 20–30 nm liposomes with multiple copies of OhyA dimers assembling on the liposome surface resulting in the formation of higher-order oligomers. Dimer assembly is cooperative and extends along a formed ridge of the liposome. We also solved an OhyA dimer of dimers structure that recapitulates the intermolecular interactions that stabilize the dimer assembly on the membrane bilayer as well as the crystal contacts in the lattice of the OhyA crystal structure. Our work enables visualization of the molecular trajectory of membrane binding for this important interfacial enzyme.</div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2024-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S104784772400056X/pdfft?md5=9988fe164241cbab00e0c3e8f1b152bc&pid=1-s2.0-S104784772400056X-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141995954","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A glimpse into the hidden world of the flexible C-terminal protein binding domains of human RAD52 人类 RAD52 灵活的 C 端蛋白结合域的隐秘世界一瞥。

IF 3 3区生物学

Journal of structural biology Pub Date : 2024-08-06 DOI: 10.1016/j.jsb.2024.108115

引用次数: 0

Relationship between thermal stability of collagens and the fraction of hydrophobic residues in their molecules 胶原蛋白的热稳定性与其分子中疏水残基比例之间的关系。

IF 3 3区生物学

Journal of structural biology Pub Date : 2024-07-31 DOI: 10.1016/j.jsb.2024.108114

引用次数: 0

Crystal structure of the GluK1 ligand-binding domain with kainate and the full-spanning positive allosteric modulator BPAM538 GluK1 配体结合结构域与凯恩酸盐和全跨度正异构调节剂 BPAM538 的晶体结构。

IF 3 3区生物学

Journal of structural biology Pub Date : 2024-07-28 DOI: 10.1016/j.jsb.2024.108113

{"title":"Crystal structure of the GluK1 ligand-binding domain with kainate and the full-spanning positive allosteric modulator BPAM538","authors":"","doi":"10.1016/j.jsb.2024.108113","DOIUrl":"10.1016/j.jsb.2024.108113","url":null,"abstract":"<div>Kainate receptors play an important role in the central nervous system by mediating postsynaptic excitatory neurotransmission and modulating the release of the inhibitory neurotransmitter GABA through a presynaptic mechanism. To date, only three structures of the ligand-binding domain (LBD) of the kainate receptor subunit GluK1 in complex with positive allosteric modulators have been determined by X-ray crystallography, all belonging to class II modulators. Here, we report a high-resolution structure of GluK1-LBD in complex with kainate and BPAM538, which belongs to the full-spanning class III. One BPAM538 molecule binds at the GluK1 dimer interface, thereby occupying two allosteric binding sites simultaneously. BPAM538 stabilizes the active receptor conformation with only minor conformational changes being introduced to the receptor. Using a calcium-sensitive fluorescence-based assay, a 5-fold potentiation of the kainate response (100 μM) was observed in presence of 100 μM BPAM538 at GluK1(Q)b, whereas no potentiation was observed at GluK2(VCQ)a. Using electrophysiology recordings of outside-out patches excised from HEK293 cells, BPAM538 increased the peak response of GluK1(Q)b co-expressed with NETO2 to rapid application of 10 mM L-glutamate with 130 ± 20 %, and decreased desensitization determined as the steady-state/peak response ratio from 23 ± 2 % to 90 ± 4 %. Based on dose–response relationship experiments on GluK1(Q)b the EC50 of BPAM538 was estimated to be 58 ± 29 μM.</div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2024-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1047847724000534/pdfft?md5=fd36f2c650fe072db6eace68cdb0888f&pid=1-s2.0-S1047847724000534-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141855872","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

From viruses to humans – Exploring the structure–function relationship of the Kesv protein for the future of biomedicine 从病毒到人类--探索 Kesv 蛋白的结构与功能关系，开创生物医学的未来。

IF 3 3区生物学

Journal of structural biology Pub Date : 2024-07-26 DOI: 10.1016/j.jsb.2024.108112

引用次数: 0