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Biomolecular NMR Assignments最新文献

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Chemical shift assignments of wildtype human leptin 野生型人类瘦素的化学位移分配。
IF 0.9 4区 生物学
Biomolecular NMR Assignments Pub Date : 2023-10-05 DOI: 10.1007/s12104-023-10153-3
Xiao Fan, Ruiqi Qin, Wensu Yuan, Jing-Song Fan, Zhi Lin
{"title":"Chemical shift assignments of wildtype human leptin","authors":"Xiao Fan,&nbsp;Ruiqi Qin,&nbsp;Wensu Yuan,&nbsp;Jing-Song Fan,&nbsp;Zhi Lin","doi":"10.1007/s12104-023-10153-3","DOIUrl":"10.1007/s12104-023-10153-3","url":null,"abstract":"<div><p>Leptin is an adipose tissue-expressed 16-kDa hormone encoded by the ob/ob gene. It serves a crucial role in regulating diverse physiological processes, including body weight control, energy homeostasis regulation, promotion of cell proliferation, and more. Emerging research has also revealed potential implications of leptin in various aging-related diseases, suggesting multifaceted physiological roles of leptin. Structural investigation of wild-type leptin in apo form is of particular importance to understand its conformational plasticity for receptor interaction and recognition. Here, we report backbone and side-chain resonance assignments of wild-type human leptin as a basis for structural and functional studies on leptin-mediated signaling.</p></div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"17 2","pages":"265 - 268"},"PeriodicalIF":0.9,"publicationDate":"2023-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41095982","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Solution-state NMR assignment and secondary structure analysis of the monomeric Pseudomonas biofilm-forming functional amyloid accessory protein FapA 单体假单胞菌生物膜形成功能性淀粉样蛋白辅助蛋白FapA的溶液态NMR定位和二级结构分析。
IF 0.9 4区 生物学
Biomolecular NMR Assignments Pub Date : 2023-10-05 DOI: 10.1007/s12104-023-10155-1
Chang-Hyeock Byeon, Ümit Akbey
{"title":"Solution-state NMR assignment and secondary structure analysis of the monomeric Pseudomonas biofilm-forming functional amyloid accessory protein FapA","authors":"Chang-Hyeock Byeon,&nbsp;Ümit Akbey","doi":"10.1007/s12104-023-10155-1","DOIUrl":"10.1007/s12104-023-10155-1","url":null,"abstract":"<div><p>FapA is an accessory protein within the biofilm forming functional bacterial amyloid related fap-operon in <i>Pseudomonas</i>, and maybe a chaperone for FapC controlling its fibrillization. To allow further structural analysis, here we present a complete sequential assignment of <sup>1</sup>H<sub>amide</sub>, <sup>13</sup>C<sub>α</sub>, <sup>13</sup>C<sub>β</sub>, and <sup>15</sup>N NMR resonances for the functional form of the monomeric soluble FapA protein, comprising amino acids between 29 and 152. From these observed chemical shifts, the secondary structure propensities (SSPs) were determined. FapA predominantly adopts a random coil conformation, however, we also identified small propensities for α-helical and β-strand conformations. Notably, these observed SSPs are smaller compared to the ones we recently observed for the monomeric soluble FapC protein. These NMR results provide valuable insights into the activity of FapA in functional amyloid formation and regulation, that will also aid developing strategies targeting amyloid formation within biofilms and addressing chronic infections.</p></div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"17 2","pages":"275 - 280"},"PeriodicalIF":0.9,"publicationDate":"2023-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41094752","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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: 1
NMR assignment and dynamics of the dimeric form of soluble C-terminal domain major ampullate spidroin 2 from Latrodectus hesperus 赤蛾壶腹蛛素2可溶性c端结构域二聚体的核磁共振分配和动力学研究。
IF 0.9 4区 生物学
Biomolecular NMR Assignments Pub Date : 2023-09-05 DOI: 10.1007/s12104-023-10150-6
Nur Alia Oktaviani, Ali D. Malay, Mami Goto, Toshio Nagashima, Fumiaki Hayashi, Keiji Numata
{"title":"NMR assignment and dynamics of the dimeric form of soluble C-terminal domain major ampullate spidroin 2 from Latrodectus hesperus","authors":"Nur Alia Oktaviani,&nbsp;Ali D. Malay,&nbsp;Mami Goto,&nbsp;Toshio Nagashima,&nbsp;Fumiaki Hayashi,&nbsp;Keiji Numata","doi":"10.1007/s12104-023-10150-6","DOIUrl":"10.1007/s12104-023-10150-6","url":null,"abstract":"<div><p>Spider dragline silk has attracted great interest due to its outstanding mechanical properties, which exceed those of man-made synthetic materials. Dragline silk, which is composed of at least major ampullate spider silk protein 1 and 2 (MaSp1 and MaSp2), contains a long repetitive domain flanked by N-terminal and C-terminal domains (NTD and CTD). Despite the small size of the CTD, this domain plays a crucial role as a molecular switch that regulates and directs spider silk self-assembly. In this study, we report the <sup>1</sup>H, <sup>13</sup>C, and <sup>15</sup>N chemical shift assignments of the <i>Latrodectus hesperus</i> MaSp2 CTD in dimeric form at pH 7. Our solution NMR data demonstrated that this protein contains five helix regions connected by a flexible linker.</p></div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"17 2","pages":"249 - 255"},"PeriodicalIF":0.9,"publicationDate":"2023-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10146098","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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
Backbone and sidechain NMR assignments of residues 1–81 from yeast Sis1 in complex with an Hsp70 C-terminal EEVD peptide 酵母Sis1与Hsp70 c端EEVD肽复合物中残基1-81的主链和侧链NMR定位。
IF 0.9 4区 生物学
Biomolecular NMR Assignments Pub Date : 2023-08-17 DOI: 10.1007/s12104-023-10148-0
Carolina O. Matos, Glaucia M.S. Pinheiro, Carlos H. I. Ramos, Fabio C. L. Almeida
{"title":"Backbone and sidechain NMR assignments of residues 1–81 from yeast Sis1 in complex with an Hsp70 C-terminal EEVD peptide","authors":"Carolina O. Matos,&nbsp;Glaucia M.S. Pinheiro,&nbsp;Carlos H. I. Ramos,&nbsp;Fabio C. L. Almeida","doi":"10.1007/s12104-023-10148-0","DOIUrl":"10.1007/s12104-023-10148-0","url":null,"abstract":"<div><p>Molecular chaperones aid proteins to fold and assemble without modifying their final structure, requiring, in several folding processes, the interplay between members of the Hsp70 and Hsp40 families. Here, we report the NMR chemical shift assignments for <sup>1</sup> H, <sup>15</sup> N, and <sup>13</sup> C nuclei of the backbone and side chains of the J-domain of the class B Hsp40 from <i>Saccharomyces cerevisiae</i>, Sis1, complexed with the C-terminal EEVD motif of Hsp70. The data revealed information on the structure and backbone dynamics that add significantly to the understanding of the J-domain-Hsp70-EEVD mechanism of interaction.</p></div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"17 2","pages":"239 - 242"},"PeriodicalIF":0.9,"publicationDate":"2023-08-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10005545","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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
Backbone and side chain NMR assignments and secondary structure calculation of the pheromone binding protein3 of Ostrinia nubilalis, an agricultural pest 农业害虫nubilalis Ostrinia nubilalis信息素结合蛋白3的主侧链NMR定位和二级结构计算。
IF 0.9 4区 生物学
Biomolecular NMR Assignments Pub Date : 2023-07-27 DOI: 10.1007/s12104-023-10145-3
Omar Al-Danoon, Smita Mohanty
{"title":"Backbone and side chain NMR assignments and secondary structure calculation of the pheromone binding protein3 of Ostrinia nubilalis, an agricultural pest","authors":"Omar Al-Danoon,&nbsp;Smita Mohanty","doi":"10.1007/s12104-023-10145-3","DOIUrl":"10.1007/s12104-023-10145-3","url":null,"abstract":"<div><p><i>Ostrinia nubilalis</i>, also known as European Corn Borer (ECB), is a serious pest in Europe and North America, as well as in Central Asia and Northern Africa. It damages a variety of agricultural crops such as corn, oats, buckwheat, millet, and soybeans. causing annually at least one billion dollars in loss. The <i>Ostrinia nubilalis</i> pheromone-binding protein3 (OnubPBP3), preferentially expressed in the male moth antenna, has been implicated in the detection of the female-secreted pheromone blend during the mating process. Understanding the structure of and function of OnubPBP3, including the mechanism of pheromone binding and its release at the dendritic olfactory neuron (ORN), is essential if integrated pest management through sensory inhibition is to be achieved. We report here the backbone and side-chain resonance assignments of OnubPBP3 at pH 6.5 using various triple resonance NMR experiments on a <sup>13</sup>C, <sup>15</sup>N-labeled protein sample. The secondary structure of OnubPBP3 consists of six α-helices and an unstructured C-terminus based on backbone chemical shifts.</p></div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"17 2","pages":"223 - 227"},"PeriodicalIF":0.9,"publicationDate":"2023-07-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9879801","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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
Chemical shift assignments of dsRBD1 and linker region of R2D2, a siRNA binding protein in the Drosophila RNAi pathway 果蝇RNAi通路中siRNA结合蛋白dsRBD1和R2D2连接区域的化学位移定位。
IF 0.9 4区 生物学
Biomolecular NMR Assignments Pub Date : 2023-07-05 DOI: 10.1007/s12104-023-10143-5
Ramdas Aute, Mandar V. Deshmukh
{"title":"Chemical shift assignments of dsRBD1 and linker region of R2D2, a siRNA binding protein in the Drosophila RNAi pathway","authors":"Ramdas Aute,&nbsp;Mandar V. Deshmukh","doi":"10.1007/s12104-023-10143-5","DOIUrl":"10.1007/s12104-023-10143-5","url":null,"abstract":"<div><p>In the model organism <i>Drosophila melanogaster</i>, one of the Dicer homologs, Dcr-2, initiates the RNA interference pathway by cleaving long double-stranded RNA into small interfering RNA (siRNA). The Dcr-2:R2D2 heterodimer subsequently binds to the 21-nucleotide siRNA to form the R2D2:Dcr-2 Initiator (RDI) complex, which is critical for initiating the assembly of the RNA-induced silencing complex containing guide siRNA strand. During RDI complex formation, R2D2 senses the stability of the 5′ end of the siRNA and a 5′-phosphate group, although the underlying mechanism of siRNA asymmetry sensing and 5′-phosphate recognition by R2D2 is elusive. In this study, we present nearly complete chemical shift assignments of the backbone and the side chain of a construct that comprises the N-terminus dsRBD1 and linker of R2D2 (~ 10.3 kDa; henceforth: R2D2D1L). Our study would further aid in the structural and functional characterization of R2D2.</p></div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"17 2","pages":"211 - 215"},"PeriodicalIF":0.9,"publicationDate":"2023-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10110774","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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
Resonance assignments of the PUB domain of the RNF31 protein RNF31蛋白PUB结构域的共振配位。
IF 0.9 4区 生物学
Biomolecular NMR Assignments Pub Date : 2023-07-03 DOI: 10.1007/s12104-023-10139-1
Lanlan Song, Fumei Zhong, Xiaoming Tu, Jiahai Zhang
{"title":"Resonance assignments of the PUB domain of the RNF31 protein","authors":"Lanlan Song,&nbsp;Fumei Zhong,&nbsp;Xiaoming Tu,&nbsp;Jiahai Zhang","doi":"10.1007/s12104-023-10139-1","DOIUrl":"10.1007/s12104-023-10139-1","url":null,"abstract":"<div><p>E3 ubiquitin protein ligase RNF31 is present in human proteins and is involved in linear ubiquitin chain assembly complex (LUBAC) activity and cell growth. RNF31 is involved in ubiquitination, which is the post-translational modification of proteins. Ubiquitin molecules connect with amino acid residues of target proteins under the action of ubiquitin-activating enzyme E1, ubiquitin binding enzyme E2 and ubiquitin ligase E3, so as to achieve certain physiological functions. The abnormal expression of ubiquitination promotes the formation of cancer. In studies of breast cancer, RNF31 mRNA levels were found to be higher in cancer cells than in other tissues. The PUB domain of RNF31 is the binding site of the ubiquitin thioesterase otulin. Here, we report the backbone and side-chain resonance assignments of the PUB domain of RNF31 and study the backbone relaxation of the domain. These studies will contribute to further understanding of the structural and functional relationship of RNF31 protein, which may also be a target for drug research.</p></div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"17 2","pages":"189 - 192"},"PeriodicalIF":0.9,"publicationDate":"2023-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9731209","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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
Backbone resonance assignments of the C-terminal region of human translation initiation factor eIF4B 人翻译起始因子eIF4B c端区域的主链共振分配。
IF 0.9 4区 生物学
Biomolecular NMR Assignments Pub Date : 2023-06-27 DOI: 10.1007/s12104-023-10141-7
Somnath Mondal, Sabrina Rousseau, Vincent Talenton, Cheikh Ahmadou Bamba Thiam, Mikayel Aznauryan, Cameron D. Mackereth
{"title":"Backbone resonance assignments of the C-terminal region of human translation initiation factor eIF4B","authors":"Somnath Mondal,&nbsp;Sabrina Rousseau,&nbsp;Vincent Talenton,&nbsp;Cheikh Ahmadou Bamba Thiam,&nbsp;Mikayel Aznauryan,&nbsp;Cameron D. Mackereth","doi":"10.1007/s12104-023-10141-7","DOIUrl":"10.1007/s12104-023-10141-7","url":null,"abstract":"<div><p>Translation initiation in eukaryotes is an early step in protein synthesis, requiring multiple factors to recruit the ribosomal small subunit to the mRNA 5’ untranslated region. One such protein factor is the eukaryotic translation initiation factor 4B (eIF4B), which increases the activity of the eIF4A RNA helicase, and is linked to cell survival and proliferation. We report here the protein backbone chemical shift assignments corresponding to the C-terminal 279 residues of human eIF4B. Analysis of the chemical shift values identifies one main helical region in the area previously linked to RNA binding, and confirms that the overall C-terminal region is intrinsically disordered.</p></div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"17 2","pages":"199 - 203"},"PeriodicalIF":0.9,"publicationDate":"2023-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10045915","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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
NMR resonance assignments of 18.5 kDa complex of Arabidopsis thaliana DRB7.2:DRB4 interaction domains 拟南芥DRB7.2:DRB4相互作用结构域18.5kDa复合物的NMR共振归属。
IF 0.9 4区 生物学
Biomolecular NMR Assignments Pub Date : 2023-05-31 DOI: 10.1007/s12104-023-10137-3
Sneha Paturi, Mandar V. Deshmukh
{"title":"NMR resonance assignments of 18.5 kDa complex of Arabidopsis thaliana DRB7.2:DRB4 interaction domains","authors":"Sneha Paturi,&nbsp;Mandar V. Deshmukh","doi":"10.1007/s12104-023-10137-3","DOIUrl":"10.1007/s12104-023-10137-3","url":null,"abstract":"<div><p>In higher eukaryotes, the dsRNA binding proteins (dsRBPs) assist the corresponding Dicer in the cleavage of dsRNA precursors to effect post-transcriptional gene regulation through RNA interference. In contrast, the DRB7.2:DRB4 complex in <i>Arabidopsis thaliana</i> acts as a potent inhibitor of Dicer-like 3 (DCL3) processing by sequestering endogenous inverted-repeat dsRNA precursors. DRB7.2 possesses a single dsRNA Binding Domain (dsRBD) flanked by unstructured N- and C-terminal regions. Whereas, DRB4 has two concatenated N-terminal dsRBDs and a long unstructured C-terminus harboring a small domain of unidentified function, D3. Here, we present near-complete backbone and partial side chain assignments of the interaction domains, DRB7.2M (i.e., DRB7.2 (71–162)) and DRB4D3 (i.e., DRB4 (294–355)) as a complex. Our findings establish the groundwork for future structural, dynamic, and functional research on DRB7.2 and DRB4, and provide clues for the endo-IR pathway in plants.</p></div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"17 2","pages":"173 - 178"},"PeriodicalIF":0.9,"publicationDate":"2023-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10236393","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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
Complete non-proline backbone resonance assignments of the S. aureus neutrophil serine protease inhibitor, EapH1 金黄色葡萄球菌中性粒细胞丝氨酸蛋白酶抑制剂EapH1的完全非脯氨酸骨干共振分配
IF 0.9 4区 生物学
Biomolecular NMR Assignments Pub Date : 2023-05-10 DOI: 10.1007/s12104-023-10131-9
Nitin Mishra, Indrani Pal, Alvaro I. Herrera, Abhinav Dubey, Haribabu Arthanari, Brian V. Geisbrecht, Om Prakash
{"title":"Complete non-proline backbone resonance assignments of the S. aureus neutrophil serine protease inhibitor, EapH1","authors":"Nitin Mishra,&nbsp;Indrani Pal,&nbsp;Alvaro I. Herrera,&nbsp;Abhinav Dubey,&nbsp;Haribabu Arthanari,&nbsp;Brian V. Geisbrecht,&nbsp;Om Prakash","doi":"10.1007/s12104-023-10131-9","DOIUrl":"10.1007/s12104-023-10131-9","url":null,"abstract":"<div><p>The <i>S. aureus</i> extracellular adherence protein (Eap) and its homologs, EapH1 and EapH2, serve roles in evasion of the human innate immune system. EapH1 binds with high-affinity and inhibits the neutrophil azurophilic granule proteases neutrophil elastase, cathepsin-G and proteinase-3. Previous structural studies using X-ray crystallography have shown that EapH1 binds to neutrophil elastase and cathepsin-G using a globally similar binding mode. However, whether the same holds true in solution is unknown and whether the inhibitor experiences dynamic changes following binding remains uncertain. To facilitate solution-phase structural and biochemical studies of EapH1 and its complexes with neutrophil granule proteases, we have characterized EapH1 by multidimensional NMR spectroscopy. Here we report a total of 100% of the non-proline backbone resonance assignments of EapH1 with BMRB accession number 50,304.</p></div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"17 1","pages":"129 - 134"},"PeriodicalIF":0.9,"publicationDate":"2023-05-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s12104-023-10131-9.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4433032","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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: 1
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