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Correction: Backbone resonance assignments of the CPEB3 [101-200] and CPEB3 [294-410]. 修正：CPEB3[101-200]和CPEB3[294-410]的主干共振分配。
IF 0.8 4区 生物学
Biomolecular NMR Assignments Pub Date : 2025-05-09 DOI: 10.1007/s12104-025-10237-2
Harunobu Saito, Yujin Lee, Motoharu Ueno, Naotaka Sekiyama, Masatomo So, Ayako Furukawa, Kenji Sugase
{"title":"Correction: Backbone resonance assignments of the CPEB3 [101-200] and CPEB3 [294-410].","authors":"Harunobu Saito, Yujin Lee, Motoharu Ueno, Naotaka Sekiyama, Masatomo So, Ayako Furukawa, Kenji Sugase","doi":"10.1007/s12104-025-10237-2","DOIUrl":"https://doi.org/10.1007/s12104-025-10237-2","url":null,"abstract":"","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":" ","pages":""},"PeriodicalIF":0.8,"publicationDate":"2025-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143952655","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 1H, 13C, and 15N resonance assignments of the oncogenic Q61R variant of human NRAS in the active, GTP-bound conformation. 人类NRAS活性gtp结合构象的致癌Q61R变体的NMR 1H， 13C和15N共振分配。
IF 0.8 4区 生物学
Biomolecular NMR Assignments Pub Date : 2025-05-02 DOI: 10.1007/s12104-025-10236-3
Alok K Sharma, Marco Tonelli, Marcin Dyba, William K Gillette, Dominic Esposito, Dwight V Nissley, Frank McCormick, Anna E Maciag
{"title":"NMR <sup>1</sup>H, <sup>13</sup>C, and <sup>15</sup>N resonance assignments of the oncogenic Q61R variant of human NRAS in the active, GTP-bound conformation.","authors":"Alok K Sharma, Marco Tonelli, Marcin Dyba, William K Gillette, Dominic Esposito, Dwight V Nissley, Frank McCormick, Anna E Maciag","doi":"10.1007/s12104-025-10236-3","DOIUrl":"https://doi.org/10.1007/s12104-025-10236-3","url":null,"abstract":"<p><p>NRAS<sup>Q61R</sup> is a frequent mutation in melanoma. Hydrolysis of GTP by NRAS<sup>Q61R</sup> is reported to be much slower than other KRAS and NRAS mutants. Recent structural biology efforts for KRAS and NRAS proteins have been limited to X-ray crystallography and therefore lack insight into the structure and dynamics of these proteins in solution. Here we report the <sup>1</sup>H<sup>N</sup>, <sup>15</sup>N, and <sup>13</sup>C backbone and sidechain resonance assignments of the G-domain of oncogenic NRAS<sup>Q61R</sup>-GTP (MW 19.3 kDa; aa 1-169) using heteronuclear, multidimensional NMR spectroscopy. NRAS<sup>Q61R</sup>-GTP is a conformationally stable protein in solution. The <sup>1</sup>H-<sup>15</sup>N correlation cross-peaks in a 2D <sup>1</sup>H-<sup>15</sup>N HSQC spectrum collected after 48 h at 298 K remained intact and only minimal signs of peak-broadening were noted for select residues. High resolution NMR allowed unambiguous assignments of the <sup>1</sup>H-<sup>15</sup>N correlation cross-peaks for all aa residues, except Y40, in addition to a significantly large number of aliphatic and aromatic sidechain resonances. NRAS<sup>Q61R</sup>-GTP exhibits canonical secondary structural elements in the 5 (five) α-helices, 6 (six) β-strands, and associated loop regions as predicted in TALOS-N and CSI. Order parameter (RCI-S<sup>2</sup>) values predicted by TALOS-N indicate that the NRAS<sup>Q61R</sup>-GTP switch (SW) regions and overall backbone are less flexible than observed in KRAS4b-GTP. The SW region rigidification was validated in heteronuclear NOE measurements. <sup>31</sup>P NMR experiments indicate that the G-domain of NRAS<sup>Q61R</sup>-GTP is in a predominant state 2 (active) conformation.</p>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":" ","pages":""},"PeriodicalIF":0.8,"publicationDate":"2025-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143951965","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 and 15N resonance assignments for the acetyltransferase domain of the kinetoplastid kinetochore protein KKT23 from Trypanosoma brucei. 布鲁氏锥虫着丝粒蛋白KKT23乙酰转移酶结构域的1H， 13C和15N共振分配。
IF 0.8 4区 生物学
Biomolecular NMR Assignments Pub Date : 2025-05-02 DOI: 10.1007/s12104-025-10235-4
Patryk Ludzia, Charlotte Nugent, Bungo Akiyoshi, Christina Redfield
{"title":"<sup>1</sup>H, <sup>13</sup>C and <sup>15</sup>N resonance assignments for the acetyltransferase domain of the kinetoplastid kinetochore protein KKT23 from Trypanosoma brucei.","authors":"Patryk Ludzia, Charlotte Nugent, Bungo Akiyoshi, Christina Redfield","doi":"10.1007/s12104-025-10235-4","DOIUrl":"https://doi.org/10.1007/s12104-025-10235-4","url":null,"abstract":"<p><p>KKT23 is a kinetoplastid-specific kinetochore protein that has a C-terminal GCN5-related histone acetyltransferase domain that acetylates the C-terminal tail of histone H2A. Here, we present the <sup>1</sup>H, <sup>13</sup>C and <sup>15</sup>N resonance assignments for the C-terminal region of KKT23 (KKT23<sup>125-348</sup>) from Trypanosoma brucei in complex with known cofactors for acetyltransferases, acetyl coenzyme A and coenzyme A. These assignments provide the starting point for detailed investigation of the structure, dynamics and interactions of KKT23 in solution.</p>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":" ","pages":""},"PeriodicalIF":0.8,"publicationDate":"2025-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143956149","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, and 15N resonance assignment of the 5'SL-bound La domain of the human La-related protein 6. 人La相关蛋白5' l结合的La结构域的1H， 13C和15N共振分配
IF 0.8 4区 生物学
Biomolecular NMR Assignments Pub Date : 2025-04-30 DOI: 10.1007/s12104-025-10232-7
Blaine H Gordon, Robert Silvers
{"title":"<sup>1</sup>H, <sup>13</sup>C, and <sup>15</sup>N resonance assignment of the 5'SL-bound La domain of the human La-related protein 6.","authors":"Blaine H Gordon, Robert Silvers","doi":"10.1007/s12104-025-10232-7","DOIUrl":"https://doi.org/10.1007/s12104-025-10232-7","url":null,"abstract":"<p><p>Human La-related protein 6 (HsLARP6) participates in the post-transcriptional regulation of type I collagen biosynthesis and is involved in the onset and progression of fibroproliferative disease. The RNA-binding protein HsLARP6 recognizes a hairpin structure known as the 5' stem-loop (5'SL) located at the junction of 5' untranslated and coding regions of type I collagen mRNA. Despite extensive biochemical and functional studies of the interaction between HsLARP6 and the 5'SL motif, the lack of high-resolution molecular data significantly hampers our understanding of the binding mechanism. Here, we introduced a shorter 5'SL model, named A2M5, reducing the molecular size of the protein-RNA complex as well as spectral overlap in RNA-based spectra. Furthermore, we reported the near-complete backbone and side chain resonance assignment of the La domain of HsLARP6 in a 1:1 complex with the A2M5 model RNA. These results will provide a significant platform for future NMR spectroscopic studies of 5'SL binding to the La domain of HsLARP6.</p>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":" ","pages":""},"PeriodicalIF":0.8,"publicationDate":"2025-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143956315","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
13C and 15N resonance assignments of the DNA binding domain of interferon regulatory factor-3. 干扰素调节因子-3 DNA结合域的13C和15N共振分配。
IF 0.8 4区 生物学
Biomolecular NMR Assignments Pub Date : 2025-04-28 DOI: 10.1007/s12104-025-10234-5
Nitin Dhaka, Sunirmala Sahoo, Biswajit Samal, Sulakshana P Mukherjee
{"title":"<sup>13</sup>C and <sup>15</sup>N resonance assignments of the DNA binding domain of interferon regulatory factor-3.","authors":"Nitin Dhaka, Sunirmala Sahoo, Biswajit Samal, Sulakshana P Mukherjee","doi":"10.1007/s12104-025-10234-5","DOIUrl":"https://doi.org/10.1007/s12104-025-10234-5","url":null,"abstract":"<p><p>The Interferon Regulatory Factor (IRF) family of transcription factors is well known for its anti-viral activity in vertebrates. The IRF family comprises nine members (IRF1-9) which have the ability to induce the Interferon beta (IFNβ) promotor. The IRF3 and IRF7 are the key family members involved in the production of type I and type III IFN. IRF3 and IRF7 both comprise of a DNA binding domain (DBD) which binds to its cognate interferon responsive element (IRE) on its target gene promoters. Here, we report near complete backbone and partial side-chain resonance assignments of the DBD domain of the IRF3 subunit of the IRF family. The predicted secondary structure using the backbone chemical shifts largely conforms with that obtained from the crystal structure, with the TALOS-N predicted secondary structures showing slightly elongated β-strands.</p>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":" ","pages":""},"PeriodicalIF":0.8,"publicationDate":"2025-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143962704","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 and 15N backbone resonance assignment of the catalytic domain of human PTPN22. 人PTPN22催化结构域的1H， 13C和15N骨架共振分配。
IF 0.8 4区 生物学
Biomolecular NMR Assignments Pub Date : 2025-04-25 DOI: 10.1007/s12104-025-10233-6
Bryan T Martin, Michael W Clarkson, Ping Wu, Paola Di Lello
{"title":"<sup>1</sup>H, <sup>13</sup>C and <sup>15</sup>N backbone resonance assignment of the catalytic domain of human PTPN22.","authors":"Bryan T Martin, Michael W Clarkson, Ping Wu, Paola Di Lello","doi":"10.1007/s12104-025-10233-6","DOIUrl":"https://doi.org/10.1007/s12104-025-10233-6","url":null,"abstract":"<p><p>Protein Tyrosine Phosphatase Non-receptor type 22 (PTPN22) is a tyrosine-phosphatase that plays a major role in inhibiting T-cell activation in immune cells. Recent studies have revealed that downregulation of PTPN22 triggers T-cell activation and enhances antitumor immune response, thereby identifying PTPN22 as a potential pharmacological target in cancer-immunology.Here we report the <sup>1</sup>H, <sup>15</sup>N and <sup>13</sup>C backbone resonance assignment for the 35.6 kDa catalytic domain of human PTPN22. This assignment will provide an essential experimental tool to identify and characterize potential PTPN22 inhibitors.</p>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":" ","pages":""},"PeriodicalIF":0.8,"publicationDate":"2025-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143958375","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 chemical shift assignment of the IMLV methyl groups of a di-domain of the Tomaymycin non-ribosomal peptide synthetase. 托马霉素非核糖体肽合成酶双结构域的IMLV甲基核磁共振化学移位分配。
IF 0.8 4区 生物学
Biomolecular NMR Assignments Pub Date : 2025-04-25 DOI: 10.1007/s12104-025-10231-8
John P Kirkpatrick, Megha N Karanth, Teresa Carlomagno
{"title":"NMR chemical shift assignment of the IMLV methyl groups of a di-domain of the Tomaymycin non-ribosomal peptide synthetase.","authors":"John P Kirkpatrick, Megha N Karanth, Teresa Carlomagno","doi":"10.1007/s12104-025-10231-8","DOIUrl":"https://doi.org/10.1007/s12104-025-10231-8","url":null,"abstract":"<p><p>Non-ribosomal peptide synthetases (NRPSs) are macromolecular enzymatic complexes responsible for the biosynthesis of an array of microbial natural products, many of which have important applications for human health. The nature of the NRPS machinery, which has been likened to an assembly line, should be amenable to bio-engineering efforts directed towards efficient synthesis of novel and tailored molecules. However, the success of such endeavours depends on a detailed understanding of the mechanistic principles governing the various steps in the peptide assembly-line. Here, we report the near-complete assignment of the Ile, Met, Leu and Val methyl-groups of the 59-kDa adaptor-condensation di-domain (BN-BC) from the Tomaymycin NRPS. These assignments will provide the foundation for future NMR studies of the complex dynamic behaviour of the condensation domain both in isolation and in the context of the enzymatic cycle, which will themselves form the basis for developing a complete mechanistic description of the central condensation reaction in this prototypical NRPS.</p>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":" ","pages":""},"PeriodicalIF":0.8,"publicationDate":"2025-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143956314","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 the rib domain in a cell surface protein from Limosilactobacillus reuteri. 罗伊氏芽孢杆菌细胞表面蛋白肋结构域的化学位移分配。
IF 0.8 4区 生物学
Biomolecular NMR Assignments Pub Date : 2025-04-07 DOI: 10.1007/s12104-025-10228-3
Yi Xue, Xue Kang
{"title":"Chemical shift assignments of the rib domain in a cell surface protein from Limosilactobacillus reuteri.","authors":"Yi Xue, Xue Kang","doi":"10.1007/s12104-025-10228-3","DOIUrl":"https://doi.org/10.1007/s12104-025-10228-3","url":null,"abstract":"<p><p>The Rib domain, a conserved structural element found in Gram-positive bacterial cell surface proteins, plays a role in bacterial virulence and is a potential target for vaccine development. Despite the availability of high-resolution crystallographic structures, the precise functional role of the Rib domain remains elusive. Here, we report the chemical shift assignments of the Rib domain from a cell surface protein of Limosilactobacillus reuteri, providing a foundational step toward understanding its potential involvement in host-bacteria interactions.</p>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":" ","pages":""},"PeriodicalIF":0.8,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143794309","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 and 15N chemical shift assignments of Rubella virus macro domain in the free and in the ADPr bound state. 风疹病毒宏域在自由和 ADPr 结合状态下的 1H、13C 和 15N 化学位移分布。
IF 0.8 4区 生物学
Biomolecular NMR Assignments Pub Date : 2025-04-05 DOI: 10.1007/s12104-025-10227-4
Danai Moschidi, Nikolaos K Fourkiotis, Christos Sideras-Bisdekis, Aikaterini C Tsika, Georgios A Spyroulias
{"title":"<sup>1</sup>H, <sup>13</sup>C and <sup>15</sup>N chemical shift assignments of Rubella virus macro domain in the free and in the ADPr bound state.","authors":"Danai Moschidi, Nikolaos K Fourkiotis, Christos Sideras-Bisdekis, Aikaterini C Tsika, Georgios A Spyroulias","doi":"10.1007/s12104-025-10227-4","DOIUrl":"https://doi.org/10.1007/s12104-025-10227-4","url":null,"abstract":"<p><p>Prokaryotes, eukaryotes, and certain viruses with positive single-stranded RNA genomes are among the forms of life that have been found to possess macro domains (MDs). There are claims that viral MDs inhibit the immune response mediated by PARPs, such as PARP12 and PARP14, and are involved in the formation of the viral replication transcription complex (RTC). Rubella virus (RuV) is included in this group of viruses. Its MD acts as an \"eraser\" of the posttranslation modification (PTM) ADP-ribosylation by binding to and hydrolyzing ADP-ribose (ADPr) from ADP-ribosylated substrates including proteins and nucleic acids. Consequently, it represents an attractive pharmacological target. Currently, no inhibitors exist for RuV MD's de-ADP-ribosylation activity, which may play a crucial role in viral replication and pathogenesis, as observed in severe acute respiratory syndrome coronavirus (SARS-CoV) and Chikungunya virus (CHIKV). RuV remains a serious threat, particularly to unvaccinated children, with approximately 10,000 of the 18,000 global cases in 2022 reported in Africa. Alarmingly, no FDA-approved drugs are available for RuV treatment. In this study, we present the almost complete NMR backbone and side-chain resonance assignment of RuV MD in both free and ADPr bound forms, along with the NMR chemical shift-based secondary structure element prediction. These findings will support the efficient screening of fragments or chemical libraries using NMR spectroscopy to identify compounds that are strong binders and potentially exhibit antiviral activity.</p>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":" ","pages":""},"PeriodicalIF":0.8,"publicationDate":"2025-04-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143787668","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 and 15N resonance assignments of the third intracellular loop of the muscarinic acetylcholine receptor M1. 毒蕈碱乙酰胆碱受体M1细胞内第三环的1H， 13C和15N共振分配。
IF 0.8 4区 生物学
Biomolecular NMR Assignments Pub Date : 2025-04-03 DOI: 10.1007/s12104-025-10230-9
Jiannan Wang, Xiaogang Niu, Changwen Jin, Yunfei Hu
{"title":"<sup>1</sup>H, <sup>13</sup>C and <sup>15</sup>N resonance assignments of the third intracellular loop of the muscarinic acetylcholine receptor M1.","authors":"Jiannan Wang, Xiaogang Niu, Changwen Jin, Yunfei Hu","doi":"10.1007/s12104-025-10230-9","DOIUrl":"https://doi.org/10.1007/s12104-025-10230-9","url":null,"abstract":"<p><p>G protein-coupled receptors (GPCRs) are highly dynamic seven-transmembrane (7TM) proteins that respond to various extracellular stimuli and elicit diverse intracellular signaling cascades. The third intracellular loops (ICL3s) of the GPCRs are intrinsically disordered and play important roles in signaling. The muscarinic acetylcholine receptors (mAChRs) harbor extremely long ICL3s, which comprise over a hundred amino acid residues and contain multiple phosphorylation sites. Due to their intrinsic flexibility, ICL3s are commonly absent or unobservable in cryo-EM or X-ray structures, and there has been a lack of structural and dynamics study of these regions. Herein, we report the <sup>1</sup>H, <sup>13</sup>C and <sup>15</sup>N chemical shift assignments of the M1 muscarinic receptor ICL3, which provides a basis for further NMR studies of its conformational dynamics, post-translational modifications and interactions.</p>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":" ","pages":""},"PeriodicalIF":0.8,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143770846","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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