Biomolecular NMR Assignments最新文献_第6页

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>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 1H, 15N, and 13C 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.</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>KKT4 is a multi-domain kinetochore protein specific to kinetoplastids, such as Trypanosoma brucei. 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 1H, 13C and 15N resonance assignments for the BRCT domain of KKT4 (KKT4463–645) from T. brucei. 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 T. brucei 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.</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>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 HNF1B 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 HNF1B 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 POUS and POUHD 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 HNF1B 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.</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

NMR 1H, 13C, 15N backbone resonance assignments of wild-type human K-Ras and its oncogenic mutants G12D and G12C bound to GTP 野生型人K-Ras及其与GTP结合的致癌突变体G12D和G12C的NMR 1H、13C、15N骨架共振分配。

IF 0.8 4区生物学

Biomolecular NMR Assignments Pub Date : 2023-11-10 DOI: 10.1007/s12104-023-10162-2

Chunhua Yuan, Alexandar L. Hansen, Lei Bruschweiler-Li, Rafael Brüschweiler

引用次数: 0

13C and 15N resonance assignments of alpha synuclein fibrils amplified from Lewy Body Dementia tissue Lewy体痴呆组织中α-突触核蛋白原纤维的13C和15N共振定位

IF 0.9 4区生物学

Biomolecular NMR Assignments Pub Date : 2023-11-03 DOI: 10.1007/s12104-023-10156-0

Alexander M. Barclay, Dhruva D. Dhavale, Collin G. Borcik, Moses H. Milchberg, Paul T. Kotzbauer, Chad M. Rienstra

引用次数: 0

Chemical shift assignments of the catalytic domain of Staphylococcus aureus LytM 金黄色葡萄球菌LytM催化结构域的化学位移分配。

IF 0.8 4区生物学

Biomolecular NMR Assignments Pub Date : 2023-11-02 DOI: 10.1007/s12104-023-10161-3

Helena Tossavainen, Ilona Pitkänen, Lina Antenucci, Chandan Thapa, Perttu Permi

{"title":"Chemical shift assignments of the catalytic domain of Staphylococcus aureus LytM","authors":"Helena Tossavainen, Ilona Pitkänen, Lina Antenucci, Chandan Thapa, Perttu Permi","doi":"10.1007/s12104-023-10161-3","DOIUrl":"10.1007/s12104-023-10161-3","url":null,"abstract":"<div>S. aureus resistance to antibiotics has increased rapidly. MRSA strains can simultaneously be resistant to many different classes of antibiotics, including the so-called “last-resort” drugs. Resistance complicates treatment, increases mortality and substantially increases the cost of treatment. The need for new drugs against (multi)resistant S. aureus is high. M23B family peptidoglycan hydrolases, enzymes that can kill S. aureus by cleaving glycine-glycine peptide bonds in S. aureus cell wall are attractive targets for drug development because of their binding specificity and lytic activity. M23B enzymes lysostaphin, LytU and LytM have closely similar catalytic domain structures. They however differ in their lytic activities, which can arise from non-conserved residues in the catalytic groove and surrounding loops or differences in dynamics. We report here the near complete 1H/13C/15N resonance assignment of the catalytic domain of LytM, residues 185–316. The chemical shift data allow comparative structural and functional studies between the enzymes and is essential for understanding how these hydrolases degrade the cell wall.</div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"18 1","pages":"1 - 5"},"PeriodicalIF":0.8,"publicationDate":"2023-11-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11082022/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71419439","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

Correction to: NMR resonance assignments of 18.5 kDa complex of Arabidopsis thaliana DRB7.2:DRB4 interaction domains 更正：拟南芥DRB7.2的18.5kDa复合物的NMR共振分配：DRB4相互作用结构域。

IF 0.9 4区生物学

Biomolecular NMR Assignments Pub Date : 2023-11-01 DOI: 10.1007/s12104-023-10152-4

Sneha Paturi, Mandar V. Deshmukh

引用次数: 0

Backbone NMR resonance assignments for the C terminal domain of the Streptococcus mutans adhesin P1 变形链球菌粘附素P1的C末端结构域的骨干NMR共振归属。

IF 0.9 4区生物学

Biomolecular NMR Assignments Pub Date : 2023-10-21 DOI: 10.1007/s12104-023-10158-y

Emily-Qingqing Peng, M. Luiza Caldas Nogueira, Gwladys Rivière, L. Jeannine Brady, Joanna R. Long

{"title":"Backbone NMR resonance assignments for the C terminal domain of the Streptococcus mutans adhesin P1","authors":"Emily-Qingqing Peng, M. Luiza Caldas Nogueira, Gwladys Rivière, L. Jeannine Brady, Joanna R. Long","doi":"10.1007/s12104-023-10158-y","DOIUrl":"10.1007/s12104-023-10158-y","url":null,"abstract":"<div>Adhesin P1 (aka AgI/II) plays a pivotal role in mediating Streptococcus mutans attachment in the oral cavity, as well as in regulating biofilm development and maturation. P1’s naturally occurring truncation product, Antigen II (AgII), adopts both soluble, monomeric and insoluble, amyloidogenic forms within the bacterial life cycle. Monomers are involved in important quaternary interactions that promote cell adhesion and the functional amyloid form promotes detachment of mature biofilms. The heterologous, 51-kD C123 construct comprises most of AgII and was previously characterized by X-ray crystallography. C123 contains three structurally homologous domains, C1, C2, and C3. NMR samples made using the original C123 construct, or its C3 domain, yielded moderately resolved NMR spectra. Using Alphafold, we re-analyzed the P1 sequence to better identify domain boundaries for C123, and in particular the C3 domain. We then generated a more tractable construct for NMR studies of the monomeric form, including quaternary interactions with other proteins. The addition of seven amino acids at the C-terminus greatly improved the spectral dispersion for C3 relative to the prior construct. Here we report the backbone NMR resonance assignments for the new construct and characterize some of its quaternary interactions. These data are in good agreement with the structure predicted by Alphafold, which contains additional β-sheet secondary structure compared to the C3 domain in the C123 crystal structure for a construct lacking the seven C-terminal amino acids. Its quaternary interactions with known protein partners are in good agreement with prior competitive binding assays. This construct can be used for further NMR studies, including protein-protein interaction studies and assessing the impact of environmental conditions on C3 structure and dynamics within C123 as it transitions from monomer to amyloid form.</div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"17 2","pages":"293 - 299"},"PeriodicalIF":0.9,"publicationDate":"2023-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49672876","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 NMR assignments and structure for the dimeric kinesin neck domain 二聚驱动蛋白颈结构域的溶液NMR分配和结构。

IF 0.9 4区生物学

Biomolecular NMR Assignments Pub Date : 2023-10-20 DOI: 10.1007/s12104-023-10159-x

Diana Seo, Richard A. Kammerer, Andrei T. Alexandrescu

{"title":"Solution NMR assignments and structure for the dimeric kinesin neck domain","authors":"Diana Seo, Richard A. Kammerer, Andrei T. Alexandrescu","doi":"10.1007/s12104-023-10159-x","DOIUrl":"10.1007/s12104-023-10159-x","url":null,"abstract":"<div>Kinesin is a motor protein, comprised of two heavy and two light chains that transports cargo along the cytoskeletal microtubule filament network. The heavy chain has a neck domain connecting the ATPase motor head responsible for walking along microtubules, with the stalk and subsequent tail domains that bind cargo. The neck domain consists of a coiled coli homodimer with about five heptad repeats, preceded by a linker region that joins to the ATPase head. Here we report 1H, 15N, and 13C NMR assignments and a solution structure for the kinesin neck domain from rat isoform Kif5c. The calculation of the NMR structure of the homodimer was facilitated by unambiguously assigning sidechain NOEs between heptad a and d positions to interchain contacts, since these positions are too far apart to give sidechain contacts in the monomers. The dimeric coiled coil NMR structure is similar to the previously described X-ray structure, whereas the linker region is disordered in solution but contains a short segment with β-strand propensity— the β-linker. Only the coiled coil is protected from solvent exchange, with ∆G values for hydrogen exchange on the order of 4–6 kcal/mol. The high stability of the hydrogen-bonded α-helical structure makes it unlikely that unzippering of the coiled coil is involved in kinesin walking. Rather, the linker region serves as a flexible hinge between the kinesin head and neck.</div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"17 2","pages":"301 - 307"},"PeriodicalIF":0.9,"publicationDate":"2023-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49672877","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