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Biomolecular NMR Assignments最新文献

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Backbone and side‑chain 1H, 13C and 15N resonance assignments and secondary structure determination of the rhizobial FixJ. 根瘤菌FixJ的主链和侧链1H、13C和15N共振赋值和二级结构测定。
IF 0.8 4区 生物学
Biomolecular NMR Assignments Pub Date : 2025-02-01 DOI: 10.1007/s12104-025-10221-w
Akio Horikawa, Rika Okubo, Naoki Hishikura, Riki Watanabe, Kaori Kurashima-Ito, Pooppadi Maxin Sayeesh, Kohsuke Inomata, Masaki Mishima, Hiroyasu Koteishi, Hitomi Sawai, Yoshitsugu Shiro, Teppei Ikeya, Yutaka Ito
{"title":"Backbone and side‑chain <sup>1</sup>H, <sup>13</sup>C and <sup>15</sup>N resonance assignments and secondary structure determination of the rhizobial FixJ.","authors":"Akio Horikawa, Rika Okubo, Naoki Hishikura, Riki Watanabe, Kaori Kurashima-Ito, Pooppadi Maxin Sayeesh, Kohsuke Inomata, Masaki Mishima, Hiroyasu Koteishi, Hitomi Sawai, Yoshitsugu Shiro, Teppei Ikeya, Yutaka Ito","doi":"10.1007/s12104-025-10221-w","DOIUrl":"https://doi.org/10.1007/s12104-025-10221-w","url":null,"abstract":"<p><p>The symbiotic nitrogen-fixing bacterium Bradyrhizobium japonicum (B.japonicum) enables high soybean yields with little or no nitrogen fertiliser. A two component regulatory system comprising FixL, a histidine kinase with O<sub>2</sub>-sensing activity, and FixJ, a response regulator, controls the expression of genes involved in nitrogen fixation, such as fixK and nifA. Only under anaerobic conditions, the monophosphate group is transferred from FixL to the N-terminal receiver domain of FixJ (FixJ<sub>N</sub>), which eventually promote the association of the C-terminal effector domain (FixJ<sub>C</sub>) to the promoter regions of the nitrogen-fixation-related genes. Structural biological analyses carried out so far for rhizobial FixJ molecules have proposed a solution structure for FixJ that differs from the crystal structures, in which the two domains are extended. To understand the FixJ activation caused by phosphorylation of the N-terminal domain, which presumably regulates through the interactions between FixJ<sub>N</sub> and FixJ<sub>C</sub>, here we have performed backbone and sidechain resonance assignments of the unphosphorylated state of B. japonicum FixJ.</p>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":" ","pages":""},"PeriodicalIF":0.8,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143073384","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
1H, 13C, 15N and 31P chemical shift assignment of the first stem-loop Guanidine-II riboswitch from Escherichia coli. 大肠杆菌第一个茎环Guanidine-II核开关的1H， 13C， 15N和31P化学位移分配
IF 0.8 4区 生物学
Biomolecular NMR Assignments Pub Date : 2025-02-01 DOI: 10.1007/s12104-025-10217-6
Tatjana Koob, Silas Döpp, Harald Schwalbe
{"title":"<sup>1</sup>H, <sup>13</sup>C, <sup>15</sup>N and <sup>31</sup>P chemical shift assignment of the first stem-loop Guanidine-II riboswitch from Escherichia coli.","authors":"Tatjana Koob, Silas Döpp, Harald Schwalbe","doi":"10.1007/s12104-025-10217-6","DOIUrl":"https://doi.org/10.1007/s12104-025-10217-6","url":null,"abstract":"<p><p>A comprehensive understanding of RNA-based gene regulation is a fundamental aspect for the development of innovative therapeutic options in medicine and for a more targeted response to environmental problems. Within the different mechanisms of RNA-based gene regulation, riboswitches are particularly interesting as they change their structure in response to the interaction with a low molecular weight ligand, often a well-known metabolite. Four distinct classes of riboswitches recognize the very small guanidinium cation. We are focused on the Guanidine-II riboswitch with the mini-ykkC motif. We report here the assignment of the <sup>1</sup>H, <sup>13</sup>C, <sup>15</sup>N and <sup>31</sup>P chemical shifts of the 23 nucleotide-long sequence of the first stem-loop of the Guanidine-II riboswitch aptamer from Escherichia coli. Despite its small size, the assignment of the NMR signals of this RNA proved to be challenging as it has symmetrical base pairs and palindromic character.</p>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":" ","pages":""},"PeriodicalIF":0.8,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143073383","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
1H, 15N, 13C backbone resonance assignment of human Alkbh7. 人Alkbh7的1H， 15N， 13C骨干共振分配。
IF 0.8 4区 生物学
Biomolecular NMR Assignments Pub Date : 2025-01-29 DOI: 10.1007/s12104-025-10219-4
Baboucarr Faal, Jeffrey A Purslow, Vincenzo Venditti
{"title":"<sup>1</sup>H, <sup>15</sup>N, <sup>13</sup>C backbone resonance assignment of human Alkbh7.","authors":"Baboucarr Faal, Jeffrey A Purslow, Vincenzo Venditti","doi":"10.1007/s12104-025-10219-4","DOIUrl":"10.1007/s12104-025-10219-4","url":null,"abstract":"<p><p>The Alkbh7 protein, a member of the Alkylation B (AlkB) family of dioxygenases, plays a crucial role in epigenetic regulation of cellular metabolism. This paper focuses on the NMR backbone resonance assignment of Alkbh7, a fundamental step in understanding its three-dimensional structure and dynamic behavior at the atomic level. Herein, we report the backbone <sup>1</sup>H, <sup>15</sup>N, <sup>13</sup>C chemical shift assignment of the full-length human Alkbh7. Experiments were acquired at 25 °C by heteronuclear multidimensional NMR spectroscopy. Collectively, 70% of the backbone NH resonances were assigned, with 144 out of a possible 205 residues assigned in the <sup>1</sup>H-<sup>15</sup>N TROSY spectrum. Interestingly, peaks from the active site and the C-terminal end of Alkbh7 are not NMR visible, suggesting that these regions are dynamic on the intermediate exchange regime. Using the program TALOS+, a secondary structure prediction was generated from the assigned backbone resonance that is consistent with the previously reported X-ray structure of the enzyme. The reported assignment will permit investigations of the protein structural dynamics anticipated to provide crucial insight regarding fundamental aspects in the recognition and enzyme regulation processes.</p>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":" ","pages":""},"PeriodicalIF":0.8,"publicationDate":"2025-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143062988","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 DRB2 domains, a dsRNA binding protein in A. thaliana RNAi pathway. 拟南芥RNAi通路中dsRNA结合蛋白DRB2结构域的化学位移定位。
IF 0.8 4区 生物学
Biomolecular NMR Assignments Pub Date : 2025-01-29 DOI: 10.1007/s12104-025-10220-x
Upasana Rai, Debadutta Patra, Mandar V Deshmukh
{"title":"Chemical shift assignments of DRB2 domains, a dsRNA binding protein in A. thaliana RNAi pathway.","authors":"Upasana Rai, Debadutta Patra, Mandar V Deshmukh","doi":"10.1007/s12104-025-10220-x","DOIUrl":"https://doi.org/10.1007/s12104-025-10220-x","url":null,"abstract":"<p><p>In Arabidopsis thaliana, micro-RNA regulation is primarily controlled by DCL1, an RNase III enzyme, and its associated proteins. DCL1, together with DRB2, governs a specific group of miRNAs that induce the inhibition of target mRNA translation. DRB2 is a multi-domain protein containing two N-terminal dsRNA binding domains (dsRBD) separated by a linker, followed by an unstructured C-terminal tail. The two dsRBDs in DRB2 are involved in recognizing the miRNA precursor and aiding DCL1 in generating 21-nucleotide-long miRNA. Our study presents a nearly complete backbone chemical shift assignment of both dsRBDs and the side-chain assignment of the first dsRBD in DRB2. The data presented here lays the groundwork for future investigations into the structural, dynamic, and functional aspects of DRB2.</p>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":" ","pages":""},"PeriodicalIF":0.8,"publicationDate":"2025-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143063058","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 PhoCl, a photocleavable protein. PhoCl蛋白的主链共振配位。
IF 0.8 4区 生物学
Biomolecular NMR Assignments Pub Date : 2025-01-18 DOI: 10.1007/s12104-025-10215-8
Runhan Wang, Lina Zhu, Junfeng Wang, Lei Zhu
{"title":"Backbone resonance assignments of PhoCl, a photocleavable protein.","authors":"Runhan Wang, Lina Zhu, Junfeng Wang, Lei Zhu","doi":"10.1007/s12104-025-10215-8","DOIUrl":"https://doi.org/10.1007/s12104-025-10215-8","url":null,"abstract":"<p><p>PhoCl is a photocleavable protein engineered from a green-to-red photoconvertible fluorescent protein by circular permutation, and has been used in various optogenetic applications including precise control of protein localization and activity in cells. Upon violet light illumination, PhoCl undergoes a β-elimination reaction to be cleaved at the chromophore, resulting in spontaneous dissociation into a large empty barrel and a small C-terminal peptide. However, the structural determinants and the mechanism of the PhoCl photocleavage remain elusive, hindering the further development of more robust photocleavable optogenetic tools. Here, we report the backbone resonance assignments of PhoCl as a basis for studying the violet-light-induced self-cleavage mechanism of PhoCl.</p>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":" ","pages":""},"PeriodicalIF":0.8,"publicationDate":"2025-01-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142998056","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 assignment of the N-terminal domain of the A subunit of the Bacillus cereus GerI germinant receptor. 蜡样芽孢杆菌GerI生发受体A亚基n端结构域的骨架分配。
IF 0.8 4区 生物学
Biomolecular NMR Assignments Pub Date : 2025-01-18 DOI: 10.1007/s12104-025-10216-7
Yulia Pustovalova, Yunfeng Li, Jeffrey C Hoch, Bing Hao
{"title":"Backbone assignment of the N-terminal domain of the A subunit of the Bacillus cereus GerI germinant receptor.","authors":"Yulia Pustovalova, Yunfeng Li, Jeffrey C Hoch, Bing Hao","doi":"10.1007/s12104-025-10216-7","DOIUrl":"https://doi.org/10.1007/s12104-025-10216-7","url":null,"abstract":"<p><p>The nutrient germinant receptors (GRs) in spores of Bacillus species consist of a cluster of three proteins- designated A, B, and C subunits- that play a critical role in initiating the germination of dormant spores in response to specific nutrient molecules. The Bacillus cereus GerI GR is essential for inosine-induced germination; however, the roles of the individual subunits and the mechanism by which germinant binding activates GR function remain unclear. In this study, we report the backbone chemical shift assignments of the N-terminal domain (NTD) of the A subunit of GerI (GerIA<sup>NTD</sup>). Furthermore, we derive the secondary structure of GerIA<sup>NTD</sup> in solution and compare it with the crystal structure of the NTD of the A subunit of a Bacillus megaterium GR. These findings lay the foundation for further NMR studies aimed at investigating the structure-function relationship of the GerI subunits, with a broader goal of understanding the molecular mechanism underlying germinant recognition and signal transduction in GRs across Bacillus species.</p>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":" ","pages":""},"PeriodicalIF":0.8,"publicationDate":"2025-01-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142998052","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
Assignment of the N-terminal domain of mouse cGAS. 小鼠cGAS n端结构域的定位。
IF 0.8 4区 生物学
Biomolecular NMR Assignments Pub Date : 2025-01-04 DOI: 10.1007/s12104-024-10213-2
Hanna Aucharova, Rasmus Linser
{"title":"Assignment of the N-terminal domain of mouse cGAS.","authors":"Hanna Aucharova, Rasmus Linser","doi":"10.1007/s12104-024-10213-2","DOIUrl":"https://doi.org/10.1007/s12104-024-10213-2","url":null,"abstract":"<p><p>Cyclic GMP-AMP synthase (cGAS) is a DNA-sensing enzyme that is a member of the nucleotidyltransferase (NTase) family and functions as a DNA sensor. The protein is comprised of a catalytic NTase core domain and an unstructured hypervariable N-terminal domain (NTD) that was reported to increase protein activity by providing an additional DNA-binding surface. We report nearly complete <sup>1</sup>H, <sup>15</sup>N, and <sup>13</sup>C backbone chemical-shift assignments of mouse cGAS NTD (residues 5-146), obtained with a set of 3D and 4D solution NMR experiments. Analysis of the chemical-shift values confirms that the NTD is intrinsically disordered. These resonance assignments can provide the basis for further studies such as activation by DNA and protein-protein interactions.</p>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":" ","pages":""},"PeriodicalIF":0.8,"publicationDate":"2025-01-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142926178","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 NMR resonance assignment of Sis1, a type B J-domain protein from Saccharomyces cerevisiae. 酿酒酵母菌B型j结构域蛋白Sis1的核磁共振骨架结构。
IF 0.8 4区 生物学
Biomolecular NMR Assignments Pub Date : 2024-12-30 DOI: 10.1007/s12104-024-10212-3
Glaucia M S Pinheiro, Gisele C Amorim, Carolina O Matos, Carlos H I Ramos, Fabio C L Almeida
{"title":"Backbone NMR resonance assignment of Sis1, a type B J-domain protein from Saccharomyces cerevisiae.","authors":"Glaucia M S Pinheiro, Gisele C Amorim, Carolina O Matos, Carlos H I Ramos, Fabio C L Almeida","doi":"10.1007/s12104-024-10212-3","DOIUrl":"https://doi.org/10.1007/s12104-024-10212-3","url":null,"abstract":"<p><p>J-domain proteins (JDPs) are essential cochaperones of heat shock protein 70 (Hsp70), as they bind and deliver misfolded polypeptides while also stimulating ATPase activity, thereby mediating the refolding process and assisting Hsp70 in maintaining cellular proteostasis. Despite their importance, detailed structural information about JDP‒Hsp70 complexes is still being explored due to various technical challenges. One major challenge is the lack of more detailed structural data on full-length JDPs. Class A and B JDPs, the most extensively studied, are typically dimers of 300-400 residue polypeptides with central intrinsically disordered regions. These features complicate structural analysis via NMR and X-ray crystallography techniques. This work presents the <sup>1</sup>H, <sup>15</sup>N, and <sup>13</sup>C backbone resonance assignments of the full-length (352 residues long) Sis1, a dimeric class B JDP from S. cerevisiae. Our study achieved 70.5% residue assignment distributed across the entire protein, providing probes in all Sis1 domains for the first time. To overcome this challenging task, strategies such as deuteration and 3D BEST-TROSY correlation experiments were used. The methods and results are detailed within the text. We are confident that this achievement will significantly benefit both the structural biology and the proteostasis scientific communities.</p>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":" ","pages":""},"PeriodicalIF":0.8,"publicationDate":"2024-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142908932","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
Correction: 1H, 13C, and 15N resonance assignments of the amyloidogenic peptide SEM2(49-107) by NMR spectroscopy. 修正：核磁共振波谱对淀粉样蛋白肽SEM2（49-107）的1H， 13C和15N共振分配。
IF 0.8 4区 生物学
Biomolecular NMR Assignments Pub Date : 2024-12-27 DOI: 10.1007/s12104-024-10214-1
Anastasia A Troshkina, Vladimir V Klochkov, Aydar G Bikmullin, Evelina A Klochkova, Dmitriy S Blokhin
{"title":"Correction: <sup>1</sup>H, <sup>13</sup>C, and <sup>15</sup>N resonance assignments of the amyloidogenic peptide SEM2(49-107) by NMR spectroscopy.","authors":"Anastasia A Troshkina, Vladimir V Klochkov, Aydar G Bikmullin, Evelina A Klochkova, Dmitriy S Blokhin","doi":"10.1007/s12104-024-10214-1","DOIUrl":"https://doi.org/10.1007/s12104-024-10214-1","url":null,"abstract":"","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":" ","pages":""},"PeriodicalIF":0.8,"publicationDate":"2024-12-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142890903","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 assignment of a ligand-binding domain of ephrin receptor A2. ephrin受体A2配体结合域的核磁共振配位。
IF 0.8 4区 生物学
Biomolecular NMR Assignments Pub Date : 2024-12-19 DOI: 10.1007/s12104-024-10211-4
Konstantin S Mineev, Santosh L Gande, Verena Linhard, Sattar Khashkhashi Moghaddam, Harald Schwalbe
{"title":"NMR resonance assignment of a ligand-binding domain of ephrin receptor A2.","authors":"Konstantin S Mineev, Santosh L Gande, Verena Linhard, Sattar Khashkhashi Moghaddam, Harald Schwalbe","doi":"10.1007/s12104-024-10211-4","DOIUrl":"https://doi.org/10.1007/s12104-024-10211-4","url":null,"abstract":"<p><p>Ephrin receptors regulate intercellular communication and are thus involved in tumor development. Ephrin receptor A2 (EphA2), in particular, is overexpressed in a variety of cancers and is a proven target for anti-cancer drugs. The N-terminal ligand-binding domain of ephrin receptors is responsible for the recognition of their ligands, ephrins, and is directly involved in receptor activation. Here, we report on the complete <sup>1</sup>H, <sup>15</sup>N and <sup>13</sup>C NMR chemical shift assignment of EphA2 ligand binding domain that provides the basis for NMR-assisted drug design.</p>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":" ","pages":""},"PeriodicalIF":0.8,"publicationDate":"2024-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142851992","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
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