Biomolecular NMR Assignments最新文献

{"title":"1 H, 15 N and 13 C resonance assignments of the Q61H mutant of human KRAS bound to GDP","authors":"Qiwei Huang,&nbsp;Elizabeth Yihui Ng,&nbsp;Qingxin Li,&nbsp;CongBao Kang","doi":"10.1007/s12104-021-10058-z","DOIUrl":"10.1007/s12104-021-10058-z","url":null,"abstract":"<div><p>KRAS proteins are small GTPases binding to the cell membrane and playing important roles in signal transduction. KRAS proteins form complexes with GTP and GDP to result in active and inactive conformations favouring interactions with different proteins. Mutations in KRAS have impact on the GTPase activity and some mutants are related to certain types of cancers. In addition to mutation at position 12, the Q61H mutant is also identified as an oncogenic mutant. Here, we describe resonance assignment for Q61H mutant of human KRAS-4B. A construct containing 1-169 residues of KRAS with a point mutation at position 61 (Q to H) was made for solution NMR studies. The backbone and some side chain resonance assignments were obtained using conventional multi-dimensional experiments. The secondary structures were analysed based on the assigned residues. As NMR is a powerful tool in probing target and ligand interactions, the assignment will be useful for later compound binding studies.</p></div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"16 1","pages":"51 - 56"},"PeriodicalIF":0.9,"publicationDate":"2021-11-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4701785","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}

{"title":"1H, 13C and 15N resonance assignments and solution structures of the two RRM domains of Matrin-3","authors":"Fahu He,&nbsp;Kanako Kuwasako,&nbsp;Masayuki Takizawa,&nbsp;Mari Takahashi,&nbsp;Kengo Tsuda,&nbsp;Takashi Nagata,&nbsp;Satoru Watanabe,&nbsp;Akiko Tanaka,&nbsp;Naohiro Kobayashi,&nbsp;Takanori Kigawa,&nbsp;Peter Güntert,&nbsp;Mikako Shirouzu,&nbsp;Shigeyuki Yokoyama,&nbsp;Yutaka Muto","doi":"10.1007/s12104-021-10057-0","DOIUrl":"10.1007/s12104-021-10057-0","url":null,"abstract":"<div><p>Matrin-3 is a multifunctional protein that binds to both DNA and RNA. Its DNA-binding activity is linked to the formation of the nuclear matrix and transcriptional regulation, while its RNA-binding activity is linked to mRNA metabolism including splicing, transport, stabilization, and degradation. Correspondingly, Matrin-3 has two zinc finger domains for DNA binding and two consecutive RNA recognition motif (RRM) domains for RNA binding. Matrin-3 has been reported to cause amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) when its disordered region contains pathogenic mutations. Simultaneously, it has been shown that the RNA-binding activity of Matrin-3 mediated by its RRM domains, affects the formation of insoluble cytoplasmic granules, which are related to the pathogenic mechanism of ALS/FTD. Thus, the effect of the RRM domains on the phase separation of condensed protein/RNA mixtures has to be clarified for a comprehensive understanding of ALS/FTD. Here, we report the ¹H, ¹⁵N, and ¹³C resonance assignments of the two RNA binding domains and their solution structures. The resonance assignments and the solution structures obtained in this work will contribute to the elucidation of the molecular basis of Matrin-3 in the pathogenic mechanism of ALS and/or FTD.</p></div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"16 1","pages":"41 - 49"},"PeriodicalIF":0.9,"publicationDate":"2021-11-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4659932","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}

{"title":"Backbone 1H, 15N, and 13C resonance assignments of the Phafin2 pleckstrin homology domain","authors":"Jeffrey F. Ellena,&nbsp;Tuo-Xian Tang,&nbsp;Narasimhamurthy Shanaiah,&nbsp;Daniel G. S. Capelluto","doi":"10.1007/s12104-021-10054-3","DOIUrl":"10.1007/s12104-021-10054-3","url":null,"abstract":"<div><p>Phafin2 is a peripheral protein that triggers cellular signaling from endosomal and lysosomal compartments. The specific subcellular localization of Phafin2 is mediated by the presence of a tandem of phosphatidylinositol 3-phosphate (PtdIns3P)-binding domains, the pleckstrin homology (PH) and the Fab-1, YOTB, Vac1, and EEA1 (FYVE) domains. The requirement for both domains for binding to PtdIns3P still remains unclear. To understand the molecular interactions of the Phafin2 PH domain in detail, we report its nearly complete ¹H, ¹⁵N, and ¹³C backbone resonance assignments.</p></div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"16 1","pages":"27 - 30"},"PeriodicalIF":0.9,"publicationDate":"2021-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s12104-021-10054-3.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4226807","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}

{"title":"NMR study of macro domains (MDs) from betacoronavirus: backbone resonance assignments of SARS–CoV and MERS–CoV MDs in the free and the ADPr-bound state","authors":"Aikaterini C. Tsika,&nbsp;Nikolaos K. Fourkiotis,&nbsp;Periklis Charalampous,&nbsp;Angelo Gallo,&nbsp;Georgios A. Spyroulias","doi":"10.1007/s12104-021-10052-5","DOIUrl":"10.1007/s12104-021-10052-5","url":null,"abstract":"<div><p>SARS-CoV and MERS-CoV Macro Domains (MDs) exhibit topological and conformational features that resemble the nsP3b macro (or “X”) domain of SARS-CoV-2. Indeed, all the three domains (SARS-CoV-2, SARS-CoV and MERS-CoV MDs) fold in a three-layer α/β/α sandwich structure, as reported by crystallographic structural investigation of SARS-CoV MD and MERS-CoV MD. These viral MDs are able to bind ADP-ribose as many other MDs from different kingdoms. They have been characterized also as de-ADP-ribosylating enzymes. For this reason, these viral macrodomains recently emerged as important drug targets since they can counteract antiviral ADP-ribosylation mediated by poly-ADP-ribose polymerase (PARPs). Even in presence of the 3D structures of SARS-CoV MD and of MERS-CoV MD, we report herein the almost complete NMR backbone (¹H, ¹³C, ¹⁵N) of SARS-CoV MD and MERS-CoV proteins in the free and ADPr bound forms, and the NMR chemical shift-based prediction of their secondary structure elements. These NMR data will help to further understanding of the atomic-level conformational dynamics of these proteins and will allow an extensive screening of small molecules as potential antiviral drugs.</p></div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"16 1","pages":"9 - 16"},"PeriodicalIF":0.9,"publicationDate":"2021-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s12104-021-10052-5.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4875249","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}

{"title":"NMR 1H, 13C, 15N backbone resonance assignments of the T35S and oncogenic T35S/Q61L mutants of human KRAS4b in the active, GppNHp-bound conformation","authors":"Alok K. Sharma,&nbsp;Marcin Dyba,&nbsp;Marco Tonelli,&nbsp;Brian Smith,&nbsp;William K. Gillette,&nbsp;Dominic Esposito,&nbsp;Dwight V. Nissley,&nbsp;Frank McCormick,&nbsp;Anna E. Maciag","doi":"10.1007/s12104-021-10050-7","DOIUrl":"10.1007/s12104-021-10050-7","url":null,"abstract":"<div><p>RAS proteins cycling between the active-form (GTP-bound) and inactive-form (GDP-bound) play a key role in cell signaling pathways that control cell survival, proliferation, and differentiation. Mutations at codon 12, 13, and 61 in RAS are known to attenuate its GTPase activity favoring the RAS active state and constitutively active downstream signaling. This hyperactivation accounts for various malignancies including pancreatic, lung, and colorectal cancers. Active KRAS is found to exist in equilibrium between two rapidly interconverting conformational states (State1–State2) in solution. Due to this dynamic feature of the protein, the ¹H–¹⁵N correlation cross-peak signals of several amino acid (AA) residues of KRAS belonging to the flexible loop regions are absent from its 2D ¹H–¹⁵N HSQC spectrum within and near physiological solution pH. A threonine to serine mutation at position 35 (T35S) shifts the interconverting equilibrium to State1 conformation and enables the emergence of such residues in the 2D ¹H–¹⁵N HSQC spectrum due to gained conformational rigidity. We report here the ¹H^N, ¹⁵N, and ¹³C backbone resonance assignments for the 19.2 kDa (AA 1–169) protein constructs of KRAS-GppNHp harboring T35S mutation (KRAS^T35S/C118S-GppNHp) and of its oncogenic counterpart harboring the Q61L mutation (KRAS^{T35S/Q61L/C118S}-GppNHp) using heteronuclear, multidimensional NMR spectroscopy at 298 K. High resolution NMR data allowed the unambiguous assignments of ¹H–¹⁵N correlation cross-peaks for all the residues except for Met1. Furthermore, 2D ¹H–¹⁵N HSQC overlay of two proteins assisted in determination of Q61L mutation-induced chemical shift perturbations for select residues in the regions of P-loop, Switch-II, and helix α3.</p></div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"16 1","pages":"1 - 8"},"PeriodicalIF":0.9,"publicationDate":"2021-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s12104-021-10050-7.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4879791","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}

{"title":"Correction to: Resonance assignments for the tandem PWWP-ARID domains of human RBBP1","authors":"Weibin Gong,&nbsp;Xingzhe Yao,&nbsp;Qihui Liang,&nbsp;Yufeng Tong,&nbsp;Sarah Perrett,&nbsp;Yingang Feng","doi":"10.1007/s12104-021-10051-6","DOIUrl":"10.1007/s12104-021-10051-6","url":null,"abstract":"","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"16 1","pages":"179 - 179"},"PeriodicalIF":0.9,"publicationDate":"2021-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4556746","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}

{"title":"1H, 13C and 15N assignment of stem-loop SL1 from the 5'-UTR of SARS-CoV-2","authors":"Christian Richter,&nbsp;Katharina F. Hohmann,&nbsp;Sabrina Toews,&nbsp;Daniel Mathieu,&nbsp;Nadide Altincekic,&nbsp;Jasleen Kaur Bains,&nbsp;Oliver Binas,&nbsp;Betül Ceylan,&nbsp;Elke Duchardt-Ferner,&nbsp;Jan Ferner,&nbsp;Boris Fürtig,&nbsp;J. Tassilo Grün,&nbsp;Martin Hengesbach,&nbsp;Daniel Hymon,&nbsp;Hendrik R. A. Jonker,&nbsp;Bozana Knezic,&nbsp;Sophie M. Korn,&nbsp;Tom Landgraf,&nbsp;Frank Löhr,&nbsp;Stephen A. Peter,&nbsp;Dennis J. Pyper,&nbsp;Nusrat S. Qureshi,&nbsp;Andreas Schlundt,&nbsp;Robbin Schnieders,&nbsp;Elke Stirnal,&nbsp;Alexey Sudakov,&nbsp;Jennifer Vögele,&nbsp;Julia E. Weigand,&nbsp;Julia Wirmer-Bartoschek,&nbsp;Kerstin Witt,&nbsp;Jens Wöhnert,&nbsp;Harald Schwalbe,&nbsp;Anna Wacker","doi":"10.1007/s12104-021-10047-2","DOIUrl":"10.1007/s12104-021-10047-2","url":null,"abstract":"<div><p>The stem-loop (SL1) is the 5'-terminal structural element within the single-stranded SARS-CoV-2 RNA genome. It is formed by nucleotides 7–33 and consists of two short helical segments interrupted by an asymmetric internal loop. This architecture is conserved among Betacoronaviruses. SL1 is present in genomic SARS-CoV-2 RNA as well as in all subgenomic mRNA species produced by the virus during replication, thus representing a ubiquitous <i>cis</i>-regulatory RNA with potential functions at all stages of the viral life cycle. We present here the ¹H, ¹³C and ¹⁵N chemical shift assignment of the 29 nucleotides-RNA construct 5_SL1, which denotes the native 27mer SL1 stabilized by an additional terminal G-C base-pair.</p></div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"15 2","pages":"467 - 474"},"PeriodicalIF":0.9,"publicationDate":"2021-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s12104-021-10047-2","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"5071177","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}

{"title":"NMR chemical shift assignments of RNA oligonucleotides to expand the RNA chemical shift database","authors":"Yaping Liu,&nbsp;Anita Kotar,&nbsp;Tracy L. Hodges,&nbsp;Kyrillos Abdallah,&nbsp;Mallak H. Taleb,&nbsp;Brayden A. Bitterman,&nbsp;Sara Jaime,&nbsp;Kyle J. Schaubroeck,&nbsp;Ethan Mathew,&nbsp;Nicholas W. Morgenstern,&nbsp;Anthony Lohmeier,&nbsp;Jordan L. Page,&nbsp;Matt Ratanapanichkich,&nbsp;Grace Arhin,&nbsp;Breanna L. Johnson,&nbsp;Stanislav Cherepanov,&nbsp;Stephen C. Moss,&nbsp;Gisselle Zuniga,&nbsp;Nicholas J. Tilson,&nbsp;Zoe C. Yeoh,&nbsp;Bruce A. Johnson,&nbsp;Sarah C. Keane","doi":"10.1007/s12104-021-10049-0","DOIUrl":"10.1007/s12104-021-10049-0","url":null,"abstract":"<div><p>RNAs play myriad functional and regulatory roles in the cell. Despite their significance, three-dimensional structure elucidation of RNA molecules lags significantly behind that of proteins. NMR-based studies are often rate-limited by the assignment of chemical shifts. Automation of the chemical shift assignment process can greatly facilitate structural studies, however, accurate chemical shift predictions rely on a robust and complete chemical shift database for training. We searched the Biological Magnetic Resonance Data Bank (BMRB) to identify sequences that had no (or limited) chemical shift information. Here, we report the chemical shift assignments for 12 RNA hairpins designed specifically to help populate the BMRB.</p></div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"15 2","pages":"479 - 490"},"PeriodicalIF":0.9,"publicationDate":"2021-08-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s12104-021-10049-0","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"5029373","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}

{"title":"The 1H, 15N and 13C resonance assignments of the C-terminal domain of Serpine mRNA binding protein 1 (SERBP1)","authors":"Antoine Baudin,&nbsp;Xiaoping Xu,&nbsp;David S. Libich","doi":"10.1007/s12104-021-10046-3","DOIUrl":"10.1007/s12104-021-10046-3","url":null,"abstract":"<div><p>SERBP1 is a multifunctional mRNA-binding protein that has been shown to play a regulatory role in a number of biological processes such as thrombosis, DNA damage repair, and the cellular response to nutrient deprivation. Additionally, SERBP1 is upregulated in glioblastoma, leukemia as well as liver, prostrate and ovarian cancers where it has been implicated in metastatic disease and poor patient outcomes. SERBP1 binds target mRNA, stabilizing and regulating the post-translational expression of the transcript. Since SERBP1 lacks canonical RNA-binding motifs such as RRM domains or zinc fingers, its target recognition and binding mechanisms are not well understood. Recent reports suggest that it is capable of recognizing both RNA sequence motifs and structured domains. Here we report the production and purification of the intrinsically disordered C-terminal domain of SERBP1, the assignment of the ¹H, ¹³C, ¹⁵N backbone resonances of the protein by solution-state NMR, and secondary structure predictions. We show that the protein is not entirely disordered and identify an α-helix that was stable under the experimental conditions. This work is the first step toward understanding the structural basis underpinning the molecular mechanisms of SERBP1 functions, particularly interactions with mRNA targets.</p></div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"15 2","pages":"461 - 466"},"PeriodicalIF":0.9,"publicationDate":"2021-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s12104-021-10046-3.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4997105","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}

{"title":"1H, 15N and 13C resonance assignments of a repetitive domain of tubuliform spidroin 2","authors":"Tiantian Fan,&nbsp;Yan Zhang,&nbsp;Jing-Song Fan,&nbsp;Wensu Yuan,&nbsp;Zhi Lin","doi":"10.1007/s12104-021-10048-1","DOIUrl":"10.1007/s12104-021-10048-1","url":null,"abstract":"<div><p>Spider silk is renowned for its excellent mechanical properties. Among six types of silk and one silk glue produced by different abdominal glands for various purposes, tubuliform (eggcase) silk is unique due to its high serine and low glycine content. Eggcase silk is spun from at least two spidroins, tubuliform spidroin 1 (TuSp1) and TuSp2. TuSp1 and TuSp2 were identified as the major and the minor components in tubuliform glands, respectively. TuSp2 consists of multiple repetitive (RP) domains with short terminal tails and shares very limited homology to all known spidroins. Here we report backbone and side chain resonance assignments of TuSp2-RP as a basis for structural and functional studies on eggcase silk formation.</p></div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"15 2","pages":"475 - 477"},"PeriodicalIF":0.9,"publicationDate":"2021-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4997109","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}