Journal of structural biology最新文献_第8页

The role of bone sialoprotein in bone healing 骨唾液蛋白在骨愈合中的作用

IF 3 3区生物学

Journal of structural biology Pub Date : 2024-10-05 DOI: 10.1016/j.jsb.2024.108132

B.L. Foster

{"title":"The role of bone sialoprotein in bone healing","authors":"B.L. Foster","doi":"10.1016/j.jsb.2024.108132","DOIUrl":"10.1016/j.jsb.2024.108132","url":null,"abstract":"<div><div>Bone sialoprotein (BSP) is a multi-functional extracellular matrix (ECM) protein associated with mineralized tissues, particularly bone and cementum. The amino acid sequence of BSP includes three evolutionarily conserved sequences which contribute to functions of the protein: an N-terminal collagen-binding domain, polyglutamic acid (polyE) sequences involved in hydroxyapatite nucleation and crystal growth, and a C-terminal arginine-glycine-aspartic acid (RGD) integrin-binding domain. BSP promotes attachment and differentiation of osteogenic and osteoclastic cells. Genetic ablation of BSP in mice results in skeletal and dental developmental defects and impaired bone healing in both appendicular bone and alveolar bone of the jaw.</div><div>Several studies demonstrated positive effects of BSP on bone healing in rodent models, though other experiments show negligible results. Native (harvested from rat bones) BSP cross-linked to collagen induced slight improvements in calvarial bone healing in rats. Recombinant BSP and collagen delivered in a polylactide (PLA) cylinder improved bone defect healing in rat femurs. Both native and recombinant BSP delivered in a collagen gel improved alveolar bone healing in wild-type and BSP-deficient mice. These advances suggest BSP is a new player in bone healing that has potential to be an alternative or complimentary to other bioactive factors. Future studies are necessary to understand mechanisms of how BSP influences bone healing and optimize delivery and dose in different types of bone defects and injuries.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"216 4","pages":"Article 108132"},"PeriodicalIF":3.0,"publicationDate":"2024-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142381098","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

SAXS of murine amelogenin identifies a persistent dimeric species from pH 5.0 to 8.0 小鼠淀粉样蛋白的 SAXS 发现了一种在 pH 值 5.0 到 8.0 之间持续存在的二聚体物种。

IF 3 3区生物学

Journal of structural biology Pub Date : 2024-10-04 DOI: 10.1016/j.jsb.2024.108131

Sebastian T. Mergelsberg , Hoshin Kim , Garry W. Buchko , Bojana Ginovska

{"title":"SAXS of murine amelogenin identifies a persistent dimeric species from pH 5.0 to 8.0","authors":"Sebastian T. Mergelsberg , Hoshin Kim , Garry W. Buchko , Bojana Ginovska","doi":"10.1016/j.jsb.2024.108131","DOIUrl":"10.1016/j.jsb.2024.108131","url":null,"abstract":"<div><div>Amelogenin is an intrinsically disordered protein essential to tooth enamel formation in mammals. Using advanced small angle X-ray scattering (SAXS) capabilities at synchrotrons and computational models, we revisited measuring the quaternary structure of murine amelogenin as a function of pH and phosphorylation at serine-16. The SAXS data shows that at the pH extremes, amelogenin exists as an extended monomer at pH 3.0 (R<sub>g</sub> = 38.4 Å) and nanospheres at pH 8.0 (R<sub>g</sub> = 84.0 Å), consistent with multiple previous observations. At pH 5.0 and above there was no evidence for a significant population of monomeric species. Instead, at pH 5.0, ∼80 % of the population is a heterogenous dimeric species that increases to ∼100 % at pH 5.5. The dimer population was observed at all pH > 5 conditions in dynamic equilibrium with a species in the pentamer range at pH < 6.5 and nanospheres at pH 8.0. At pH 8.0, ∼40 % of the amelogenin remained in the dimeric state. In general, serine-16 phosphorylation of amelogenin appears to modestly stabilize the population of the dimeric species.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"216 4","pages":"Article 108131"},"PeriodicalIF":3.0,"publicationDate":"2024-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142378031","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

On the abundance and importance of AXXXA sequence motifs in globular proteins and their involvement in CβCβ interaction 论球蛋白中 AXXXA 序列基序的丰度和重要性及其在 CβCβ 相互作用中的参与。

IF 3 3区生物学

Journal of structural biology Pub Date : 2024-09-27 DOI: 10.1016/j.jsb.2024.108129

Surbhi Vilas Tajane , Abhilasha Thakur , Srijita Acharya , Pinak Chakrabarti , Sucharita Dey

{"title":"On the abundance and importance of AXXXA sequence motifs in globular proteins and their involvement in CβCβ interaction","authors":"Surbhi Vilas Tajane , Abhilasha Thakur , Srijita Acharya , Pinak Chakrabarti , Sucharita Dey","doi":"10.1016/j.jsb.2024.108129","DOIUrl":"10.1016/j.jsb.2024.108129","url":null,"abstract":"<div><div>The AXXXA and GXXXG motifs are frequently observed in helices, especially in membrane proteins. The motif GXXXG is known to stabilize helix-helix association in membrane proteins via C<sub>α</sub>H<img>O bonding. AXXXA sequence motif additionally stabilizes the folded state of proteins. We found 27,000 and 18,000 occurrences of AXXXA and GXXXG motifs in a non-redundant set of 6000 obligate homodimeric (OD) complexes. Interestingly, this is less pronounced in transient homodimers (TD) and heterodimers (HetD). On average each obligate homodimer contains four AXXXA motifs, it is 2 and 3.5 for HetD and TD, respectively. Focusing on the binding surface it is seen that 27 % of the ODs contain at least one AXXXA motif at the interface, whereas it is 17 % and 15 % for HetD and TD respectively. AXXXA predominantly stabilizes the OD quaternary structure via the side chain C<sub>β</sub><img>C<sub>β</sub> interactions. This interaction is energetically favorable and is found to be a major driving force for OD quaternary structure stability. C<sub>β-</sub>C<sub>β</sub> interactions are observed ∼6 times higher than the known C<sub>α</sub>H<img>O interaction for helix-helix stabilization. Two additional new interactions of C<sub>β</sub><img>O and O<img>O are observed at the AXXXA containing interface regions. The occurrence of the motif gets drastically reduced if any of the terminal Ala residues are replaced by Gly. Our findings show the importance of AXXXA in providing stability to the quaternary structure through specific hydrophobic interactions and the specificity of the Ala residue at motif termini. The knowledge gained can be used for designing synthetic proteins of improved stability and for designing peptide-based therapeutics.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"216 4","pages":"Article 108129"},"PeriodicalIF":3.0,"publicationDate":"2024-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142349012","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

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":"10.1016/j.jsb.2024.108128","url":null,"abstract":"<div><div>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 <em>C. elegans</em> cells <em>in vivo</em> with sub-nanometer details being preserved in the images.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"216 4","pages":"Article 108128"},"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":"OA","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

Sharmila Ortiz , Raphael Verdan , Marlene Benchimol

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

Alexey Pakhnevich , Dmitry Nikolayev , Tatiana Lychagina

{"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":"Alexey Pakhnevich , Dmitry Nikolayev , Tatiana Lychagina","doi":"10.1016/j.jsb.2024.108126","DOIUrl":"10.1016/j.jsb.2024.108126","url":null,"abstract":"<div><p>The global crystallographic texture of calcite and aragonite in the shells of the bivalves <em>Bathymodiolus thermophilus</em>, <em>Mytilus galloprovincialis</em>, <em>M. edulis</em> and <em>M. trossulus</em> 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), <span><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></span>) and aragonite pole figures ((012)/(121), (040)/(221)) coincides or has close values for deep-sea hydrothermal species <em>B. thermophilus</em> and the studied shallow-water species of the genus <em>Mytilus</em>. The calcite pole figures (0006) and <span><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></span> of <em>B. thermophilus</em> 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 <em>B. thermophilus</em> 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 <em>B. thermophilus</em>.</p></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"216 4","pages":"Article 108126"},"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

Sama Akbarzadeh , Özlem Coşkun , Başak Günçer

{"title":"Studying protein–protein interactions: Latest and most popular approaches","authors":"Sama Akbarzadeh , Özlem Coşkun , Başak Günçer","doi":"10.1016/j.jsb.2024.108118","DOIUrl":"10.1016/j.jsb.2024.108118","url":null,"abstract":"<div><p>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 <em>in vitro</em> and <em>in vivo</em> 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.</p></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"216 4","pages":"Article 108118"},"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

Tingting Yang , Jian Li , Xinyu Cheng , Qiuyuan Lu , Zara Farooq , Ying Fu , Sijia Lv , Weiwei Nan , Boming Yu , Jingjing Duan , Yuting Zhang , Yang Fu , Haihai Jiang , Peter J McCormick , Yanyan Li , Jin Zhang

{"title":"Structural analysis of the human C5a-C5aR1 complex using cryo-electron microscopy","authors":"Tingting Yang , Jian Li , Xinyu Cheng , Qiuyuan Lu , Zara Farooq , Ying Fu , Sijia Lv , Weiwei Nan , Boming Yu , Jingjing Duan , Yuting Zhang , Yang Fu , Haihai Jiang , Peter J McCormick , Yanyan Li , Jin Zhang","doi":"10.1016/j.jsb.2024.108117","DOIUrl":"10.1016/j.jsb.2024.108117","url":null,"abstract":"<div><p>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.</p></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"216 3","pages":"Article 108117"},"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

Michael L. Oldham , M. Zuhaib Qayyum , Ravi C. Kalathur , Charles O. Rock , Christopher D. Radka

{"title":"Cryo-EM reconstruction of oleate hydratase bound to a phospholipid membrane bilayer","authors":"Michael L. Oldham , M. Zuhaib Qayyum , Ravi C. Kalathur , Charles O. Rock , Christopher D. Radka","doi":"10.1016/j.jsb.2024.108116","DOIUrl":"10.1016/j.jsb.2024.108116","url":null,"abstract":"<div><p>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 <em>Staphylococcus aureus</em> 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.</p></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"216 3","pages":"Article 108116"},"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

Lucas R. Struble, Jeffrey J. Lovelace, Gloria E.O. Borgstahl

引用次数: 0