Biomolecular NMR Assignments最新文献_第6页

Solution NMR chemical shift assignment of apo and molybdate-bound ModA at two pHs 溶液核磁共振化学位移在两种 pH 值下的蛋白结合型和钼酸结合型 ModA 的分配

IF 0.8 4区生物学

Biomolecular NMR Assignments Pub Date : 2024-04-20 DOI: 10.1007/s12104-024-10173-7

Hiep LD Nguyen, Karin A. Crowhurst

{"title":"Solution NMR chemical shift assignment of apo and molybdate-bound ModA at two pHs","authors":"Hiep LD Nguyen, Karin A. Crowhurst","doi":"10.1007/s12104-024-10173-7","DOIUrl":"10.1007/s12104-024-10173-7","url":null,"abstract":"<div><p>ModA is a soluble periplasmic molybdate-binding protein found in most gram-negative bacteria. It is part of the ABC transporter complex ModABC that moves molybdenum into the cytoplasm, to be used by enzymes that carry out various redox reactions. Since there is no clear analog for ModA in humans, this protein could be a good target for antibacterial drug design. Backbone <sup>1</sup>H, <sup>13</sup>C and <sup>15</sup>N chemical shifts of apo and molybdate-bound ModA from <i>E. coli</i> were assigned at pHs 6.0 and 4.5. In addition, side chain atoms were assigned for apo ModA at pH 6.0. When comparing apo and molybdate-bound ModA at pH 6.0, large chemical shift perturbations are observed, not only in areas near the bound metal, but also in regions that are distant from the metal-binding site. Given the significant conformational change between apo and holo ModA, we might expect the large chemical shift changes to be more widespread; however, since they are limited to specific regions, the residues with large perturbations may reveal allosteric sites that could ultimately be important for the design of antibiotics that target ModA.</p></div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"18 1","pages":"93 - 98"},"PeriodicalIF":0.8,"publicationDate":"2024-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140624175","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 chemical shift and secondary structure assignments for mouse siderocalin 小鼠苷酸骨干化学位移和二级结构分配。

IF 0.8 4区生物学

Biomolecular NMR Assignments Pub Date : 2024-04-02 DOI: 10.1007/s12104-024-10171-9

Johanna Moeller, Nina G. Bozhanova, Markus Voehler, Jens Meiler, Clara T. Schoeder

{"title":"Backbone chemical shift and secondary structure assignments for mouse siderocalin","authors":"Johanna Moeller, Nina G. Bozhanova, Markus Voehler, Jens Meiler, Clara T. Schoeder","doi":"10.1007/s12104-024-10171-9","DOIUrl":"10.1007/s12104-024-10171-9","url":null,"abstract":"<div><p>\u0000 The lipocalin protein family is a structurally conserved group of proteins with a variety of biological functions defined by their ability to bind small molecule ligands and interact with partner proteins. One member of this family is siderocalin, a protein found in mammals. Its role is discussed in inflammatory processes, iron trafficking, protection against bacterial infections and oxidative stress, cell migration, induction of apoptosis, and cancer. Though it seems to be involved in numerous essential pathways, the exact mechanisms are often not fully understood. The NMR backbone assignments for the human siderocalin and its rat ortholog have been published before. In this work we describe the backbone NMR assignments of siderocalin for another important model organism, the mouse - data that might become important for structure-based drug discovery. Secondary structure elements were predicted based on the assigned backbone chemical shifts using TALOS-N and CSI 3.0, revealing a high content of beta strands and one prominent alpha helical region. Our findings correlate well with the known crystal structure and the overall conserved fold of the lipocalin family.</p></div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"18 1","pages":"79 - 84"},"PeriodicalIF":0.8,"publicationDate":"2024-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11081974/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140334185","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: 0

1H, 13C, and 15N resonance assignments and solution structure of the N-terminal divergent calponin homology (NN-CH) domain of human intraflagellar transport protein 54 人类鞘内转运蛋白 54 的 N 端分歧钙蛋白同源结构域（NN-CH）的 1H、13C 和 15N 共振赋值及溶液结构。

IF 0.8 4区生物学

Biomolecular NMR Assignments Pub Date : 2024-03-29 DOI: 10.1007/s12104-024-10170-w

Kanako Kuwasako, Weirong Dang, Fahu He, Mari Takahashi, Kengo Tsuda, Takashi Nagata, Akiko Tanaka, Naohiro Kobayashi, Takanori Kigawa, Peter Güntert, Mikako Shirouzu, Shigeyuki Yokoyama, Yutaka Muto

{"title":"1H, 13C, and 15N resonance assignments and solution structure of the N-terminal divergent calponin homology (NN-CH) domain of human intraflagellar transport protein 54","authors":"Kanako Kuwasako, Weirong Dang, Fahu He, Mari Takahashi, Kengo Tsuda, Takashi Nagata, Akiko Tanaka, Naohiro Kobayashi, Takanori Kigawa, Peter Güntert, Mikako Shirouzu, Shigeyuki Yokoyama, Yutaka Muto","doi":"10.1007/s12104-024-10170-w","DOIUrl":"10.1007/s12104-024-10170-w","url":null,"abstract":"<div><p>The intraflagellar transport (IFT) machinery plays a crucial role in the bidirectional trafficking of components necessary for ciliary signaling, such as the Hedgehog, Wnt/PCR, and cAMP/PKA systems. Defects in some components of the IFT machinery cause dysfunction, leading to a wide range of human diseases and developmental disorders termed ciliopathies, such as nephronophthisis. The IFT machinery comprises three sub-complexes: BBsome, IFT-A, and IFT-B. The IFT protein 54 (IFT54) is an important component of the IFT-B sub-complex. In anterograde movement, IFT54 binds to active kinesin-II, walking along the cilia microtubule axoneme and carrying the dynein-2 complex in an inactive state, which works for retrograde movement. Several mutations in IFT54 are known to cause Senior-Loken syndrome, a ciliopathy. IFT54 possesses a divergent Calponin Homology (CH) domain termed as NN-CH domain at its N-terminus. However, several aspects of the function of the NN-CH domain of IFT54 are still obscure. Here, we report the <sup>1</sup>H, <sup>15</sup>N, and <sup>13</sup>C resonance assignments of the NN-CH domain of human IFT54 and its solution structure. The NN-CH domain of human IFT54 adopts essentially the α1–α2–α3–α4–α5 topology as that of mouse IFT54, whose structure was determined by X-ray crystallographic study. The structural information and assignments obtained in this study shed light on the molecular function of the NN-CH domain in IFT54.</p></div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"18 1","pages":"71 - 78"},"PeriodicalIF":0.8,"publicationDate":"2024-03-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140326214","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 and side-chain resonance assignments of the human oncogenic protein NCYM 人类致癌蛋白 NCYM 的 1H、13C 和 15N 主干和侧链共振分配。

IF 0.8 4区生物学

Biomolecular NMR Assignments Pub Date : 2024-03-25 DOI: 10.1007/s12104-024-10169-3

Assia Mouhand, Kazuma Nakatani, Fumiaki Kono, Yoshitaka Hippo, Tatsuhito Matsuo, Philippe Barthe, Judith Peters, Yusuke Suenaga, Taro Tamada, Christian Roumestand

{"title":"1H, 13C and 15N backbone and side-chain resonance assignments of the human oncogenic protein NCYM","authors":"Assia Mouhand, Kazuma Nakatani, Fumiaki Kono, Yoshitaka Hippo, Tatsuhito Matsuo, Philippe Barthe, Judith Peters, Yusuke Suenaga, Taro Tamada, Christian Roumestand","doi":"10.1007/s12104-024-10169-3","DOIUrl":"10.1007/s12104-024-10169-3","url":null,"abstract":"<div><p>NCYM is a cis-antisense gene of MYCN oncogene and encodes an oncogenic protein that stabilizes MYCN via inhibition of GSK3b. High NCYM expression levels are associated with poor clinical outcomes in human neuroblastomas, and NCYM overexpression promotes distant metastasis in animal models of neuroblastoma. Using vacuum-ultraviolet circular dichroism and small-angle X-ray scattering, we previously showed that NCYM has high flexibility with partially folded structures; however, further structural characterization is required for the design of anti-cancer agents targeting NCYM. Here we report the <sup>1</sup>H, <sup>15</sup>N and <sup>13</sup>C nuclear magnetic resonance assignments of NCYM. Secondary structure prediction using Secondary Chemical Shifts and TALOS-N analysis demonstrates that the structure of NCYM is essentially disordered, even though residues in the central region of the peptide clearly present a propensity to adopt a dynamic helical structure. This preliminary study provides foundations for further analysis of interaction between NCYM and potential partners.</p></div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"18 1","pages":"65 - 70"},"PeriodicalIF":0.8,"publicationDate":"2024-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140287898","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 and13C resonance assignments of S2A mutant of human carbonic anhydrase II 人碳酸酐酶 II S2A 突变体的 1H、15N 和 13C 共振分配。

IF 0.8 4区生物学

Biomolecular NMR Assignments Pub Date : 2024-03-23 DOI: 10.1007/s12104-024-10166-6

Neelam, Himanshu Singh

引用次数: 0

Backbone 1H, 13C and 15N resonance assignment of the ubiquitin specific protease 7 catalytic domain (residues 208–554) in complex with a small molecule ligand 泛素特异性蛋白酶 7 催化结构域（残基 208-554）与小分子配体复合物的骨架 1H、13C 和 15N 共振赋值。

IF 0.8 4区生物学

Biomolecular NMR Assignments Pub Date : 2024-03-12 DOI: 10.1007/s12104-024-10165-7

Maya J. Pandya, Wojciech Augustyniak, Matthew J. Cliff, Ilka Lindner, Anne Stinn, Jan Kahmann, Koen Temmerman, Hugh R. W. Dannatt, Jonathan P. Waltho, Martin J. Watson

引用次数: 0

Backbone 1H, 13C, and 15N chemical shift assignments for human SERF2 人类 SERF2 的骨架 1H、13C 和 15N 化学位移分布图

IF 0.8 4区生物学

Biomolecular NMR Assignments Pub Date : 2024-03-11 DOI: 10.1007/s12104-024-10167-5

Bikash R. Sahoo, Vivekanandan Subramanian, James C.A. Bardwell

{"title":"Backbone 1H, 13C, and 15N chemical shift assignments for human SERF2","authors":"Bikash R. Sahoo, Vivekanandan Subramanian, James C.A. Bardwell","doi":"10.1007/s12104-024-10167-5","DOIUrl":"10.1007/s12104-024-10167-5","url":null,"abstract":"<div><p>Human small EDRK-rich factor protein SERF2 is a cellular driver of protein amyloid formation, a process that has been linked to neurodegenerative diseases including Alzheimer’s and Parkinson’s disease. SERF2 is a 59 amino acid protein, highly charged, and well conserved whose structure and physiological function is unclear. SERF family proteins including human SERF2 have shown a tendency to form fuzzy complexes with misfolded proteins such as α-Synuclein which has been linked to Parkinson’s disease. SERF family proteins have been recently identified to bind nucleic acids, but the binding mechanism(s) remain enigmatic. Here, using multidimensional solution NMR, we report the <sup>1</sup>H, <sup>15</sup>N, and <sup>13</sup>C chemical shift assignments (~ 86% of backbone resonance assignments) for human SERF2. TALOS-N predicted secondary structure of SERF2 showed three very short helices (3–4 residues long) in the N-terminal region of the protein and a long helix in the C-terminal region spanning residues 37–46 which is consistent with the helical content indicated by circular dichroism spectroscopy. Paramagnetic relaxation enhancement NMR analysis revealed that a short C-terminal region E53-K55 is in the proximity of the N-terminus. Having the backbone assignment of SERF2 allowed us to probe its interaction with α-Synuclein and to identify the residues in SERF2 binding interfaces that likely promote α-Synuclein aggregation.</p></div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"18 1","pages":"51 - 57"},"PeriodicalIF":0.8,"publicationDate":"2024-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140099982","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 study of the structure and dynamics of the BRCT domain from the kinetochore protein KKT4 来自动点核蛋白 KKT4 的 BRCT 结构域的核磁共振研究。

IF 0.8 4区生物学

Biomolecular NMR Assignments Pub Date : 2024-03-07 DOI: 10.1007/s12104-024-10163-9

Patryk Ludzia, Hanako Hayashi, Timothy Robinson, Bungo Akiyoshi, Christina Redfield

{"title":"NMR study of the structure and dynamics of the BRCT domain from the kinetochore protein KKT4","authors":"Patryk Ludzia, Hanako Hayashi, Timothy Robinson, Bungo Akiyoshi, Christina Redfield","doi":"10.1007/s12104-024-10163-9","DOIUrl":"10.1007/s12104-024-10163-9","url":null,"abstract":"<div><p>KKT4 is a multi-domain kinetochore protein specific to kinetoplastids, such as <i>Trypanosoma brucei</i>. It lacks significant sequence similarity to known kinetochore proteins in other eukaryotes. Our recent X-ray structure of the C-terminal region of KKT4 shows that it has a tandem BRCT (BRCA1 C Terminus) domain fold with a sulfate ion bound in a typical binding site for a phosphorylated serine or threonine. Here we present the <sup>1</sup>H, <sup>13</sup>C and <sup>15</sup>N resonance assignments for the BRCT domain of KKT4 (KKT4<sup>463–645</sup>) from <i>T. brucei</i>. We show that the BRCT domain can bind phosphate ions in solution using residues involved in sulfate ion binding in the X-ray structure. We have used these assignments to characterise the secondary structure and backbone dynamics of the BRCT domain in solution. Mutating the residues involved in phosphate ion binding in <i>T. brucei</i> KKT4 BRCT results in growth defects confirming the importance of the BRCT phosphopeptide-binding activity in vivo. These results may facilitate rational drug design efforts in the future to combat diseases caused by kinetoplastid parasites.</p></div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"18 1","pages":"15 - 25"},"PeriodicalIF":0.8,"publicationDate":"2024-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11081923/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140058298","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: 0

1H, 13C and 15N backbone resonance assignments of hepatocyte nuclear factor-1-beta (HNF1β) POUS and POUHD 肝细胞核因子-1-β（HNF1β）POUS 和 POUHD 的 1H、13C 和 15N 主干共振分配。

IF 0.8 4区生物学

Biomolecular NMR Assignments Pub Date : 2024-03-07 DOI: 10.1007/s12104-024-10168-4

Sayaka Hokazono, Eri Imagawa, Daishi Hirano, Takahisa Ikegami, Kimihiko Oishi, Tsuyoshi Konuma

{"title":"1H, 13C and 15N backbone resonance assignments of hepatocyte nuclear factor-1-beta (HNF1β) POUS and POUHD","authors":"Sayaka Hokazono, Eri Imagawa, Daishi Hirano, Takahisa Ikegami, Kimihiko Oishi, Tsuyoshi Konuma","doi":"10.1007/s12104-024-10168-4","DOIUrl":"10.1007/s12104-024-10168-4","url":null,"abstract":"<div><p>Hepatocyte nuclear factor 1β (HNF1β) is a transcription factor that plays a key role in the development and function of the liver, pancreas, and kidney. HNF1β plays a key role in early vertebrate development and the morphogenesis of these organs. In humans, heterozygous mutations in the <i>HNF1B</i> gene can result in organ dysplasia, making it the most common cause of developmental renal diseases, including renal cysts, renal malformations, and familial hypoplastic glomerular cystic kidney disease. Pathogenic variants in the <i>HNF1B</i> gene are known to cause various diseases, including maturity-onset diabetes of the young and developmental renal diseases. This study presents the backbone resonance assignments of HNF1β POU<sub>S</sub> and POU<sub>HD</sub> domains, which are highly conserved domains required for the recognition of double-stranded DNA. Our data will be useful for NMR studies to verify the altered structures and functions of mutant <i>HNF1B</i> proteins that can induce developmental renal diseases, including renal cysts, renal malformations, and familial hypoplastic glomerular cystic kidney disease. This study will provide the structural basis for future studies to elucidate the molecular mechanisms underlying how mutations in HNF1β cause diseases.</p></div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"18 1","pages":"59 - 63"},"PeriodicalIF":0.8,"publicationDate":"2024-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140048452","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 ACID domain of MED25, a subunit of the mediator complex in Arabidopsis thaliana 拟南芥介导复合体亚基 MED25 的 ACID 结构域的化学位移分配。

IF 0.8 4区生物学

Biomolecular NMR Assignments Pub Date : 2024-02-09 DOI: 10.1007/s12104-024-10164-8

Yue Xiong, Jiang Zhu, Rui Hu, Ying Li, Yunhuang Yang, Maili Liu

引用次数: 0