Biomolecular NMR Assignments最新文献_第6页

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

Assignment of the disordered, proline-rich N-terminal domain of the tumour suppressor p53 protein using 1HN and 1Hα-detected NMR measurements 使用1HN和1Hα检测的NMR测量对肿瘤抑制p53蛋白的无序、富含脯氨酸的N-末端结构域的分配

IF 0.9 4区生物学

Biomolecular NMR Assignments Pub Date : 2023-10-20 DOI: 10.1007/s12104-023-10160-4

Fanni Sebák, Péter Ecsédi, László Nyitray, Andrea Bodor

{"title":"Assignment of the disordered, proline-rich N-terminal domain of the tumour suppressor p53 protein using 1HN and 1Hα-detected NMR measurements","authors":"Fanni Sebák, Péter Ecsédi, László Nyitray, Andrea Bodor","doi":"10.1007/s12104-023-10160-4","DOIUrl":"10.1007/s12104-023-10160-4","url":null,"abstract":"<div>Protein p53 is mostly known for playing a key role in tumour suppression, and mutations in the p53 gene are amongst the most frequent genomic events accompanying oncogenic transformation. Continuous research is conducted to target disordered proteins/protein regions for cancer therapy, for which atomic level information is also necessary. The disordered N-terminal part of p53 contains the transactivation and the proline-rich domains—which besides being abundant in proline residues—contains repetitive Pro-Ala motifs. NMR assignment of such repetitive, proline-rich regions is challenging due to the lack of amide protons in the 1HN-detected approaches, as well as due to the small chemical shift dispersion. In the present study we perform the full assignment of the p531–100 region by applying a combination of 1HN- and 1Hα-detected NMR experiments. We also show the increased information content when using real-time homo- and heteronuclear decoupled acquisition schemes. On the other hand, we highlight the presence of minor proline species, and using Pro-selective experiments we determine the corresponding cis or trans conformation. Secondary chemical shifts for (Cα–Cβ) atoms indicate the disordered nature of this region, with expected helical tendency for the TAD1 region. As the role of the proline-rich domain is yet not well understood our results can contribute to further successful investigations.</div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"17 2","pages":"309 - 314"},"PeriodicalIF":0.9,"publicationDate":"2023-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71910051","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 resonance assignments for proteasome shuttle factor hHR23a 蛋白酶体穿梭因子hHR23a的1H，15N，13C共振分配

IF 0.9 4区生物学

Biomolecular NMR Assignments Pub Date : 2023-10-09 DOI: 10.1007/s12104-023-10157-z

Xiang Chen, Kylie J. Walters

引用次数: 0

Chemical shift assignments of wildtype human leptin 野生型人类瘦素的化学位移分配。

IF 0.9 4区生物学

Biomolecular NMR Assignments Pub Date : 2023-10-05 DOI: 10.1007/s12104-023-10153-3

Xiao Fan, Ruiqi Qin, Wensu Yuan, Jing-Song Fan, Zhi Lin

引用次数: 0

Solution-state NMR assignment and secondary structure analysis of the monomeric Pseudomonas biofilm-forming functional amyloid accessory protein FapA 单体假单胞菌生物膜形成功能性淀粉样蛋白辅助蛋白FapA的溶液态NMR定位和二级结构分析。

IF 0.9 4区生物学

Biomolecular NMR Assignments Pub Date : 2023-10-05 DOI: 10.1007/s12104-023-10155-1

Chang-Hyeock Byeon, Ümit Akbey

{"title":"Solution-state NMR assignment and secondary structure analysis of the monomeric Pseudomonas biofilm-forming functional amyloid accessory protein FapA","authors":"Chang-Hyeock Byeon, Ümit Akbey","doi":"10.1007/s12104-023-10155-1","DOIUrl":"10.1007/s12104-023-10155-1","url":null,"abstract":"<div>FapA is an accessory protein within the biofilm forming functional bacterial amyloid related fap-operon in Pseudomonas, and maybe a chaperone for FapC controlling its fibrillization. To allow further structural analysis, here we present a complete sequential assignment of 1Hamide, 13Cα, 13Cβ, and 15N NMR resonances for the functional form of the monomeric soluble FapA protein, comprising amino acids between 29 and 152. From these observed chemical shifts, the secondary structure propensities (SSPs) were determined. FapA predominantly adopts a random coil conformation, however, we also identified small propensities for α-helical and β-strand conformations. Notably, these observed SSPs are smaller compared to the ones we recently observed for the monomeric soluble FapC protein. These NMR results provide valuable insights into the activity of FapA in functional amyloid formation and regulation, that will also aid developing strategies targeting amyloid formation within biofilms and addressing chronic infections.</div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"17 2","pages":"275 - 280"},"PeriodicalIF":0.9,"publicationDate":"2023-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41094752","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: 1

Backbone 1H, 15N and 13C resonance assignments for an E2 ubiquitin conjugating enzyme-UBE2T E2泛素偶联酶UBE2T的骨架1H、15N和13C共振分配

IF 0.9 4区生物学

Biomolecular NMR Assignments Pub Date : 2023-09-29 DOI: 10.1007/s12104-023-10154-2

Qiwei Huang, Hui Qi Ng, Yong Yao Loh, Zhiyuan Ke, Wan Hsin Lim, CongBao Kang

引用次数: 0

1H, 13C, and 15N NMR chemical shift assignment of LytM N-terminal domain (residues 26–184) LytM N-末端结构域（残基26-184）的1H、13C和15N NMR化学位移分配

IF 0.9 4区生物学

Biomolecular NMR Assignments Pub Date : 2023-09-24 DOI: 10.1007/s12104-023-10151-5

Ilona Pitkänen, Helena Tossavainen, Perttu Permi

引用次数: 1

Backbone 1H, 15N and 13C resonance assignments of the 27kDa fluorescent protein mCherry 27kDa荧光蛋白mCherry的骨架1H、15N和13C共振定位

IF 0.9 4区生物学

Biomolecular NMR Assignments Pub Date : 2023-09-09 DOI: 10.1007/s12104-023-10149-z

Marco Sette, Laura Anne Johnson, Ralph Jimenez, Frans A.A. Mulder

引用次数: 0

NMR assignment and dynamics of the dimeric form of soluble C-terminal domain major ampullate spidroin 2 from Latrodectus hesperus 赤蛾壶腹蛛素2可溶性c端结构域二聚体的核磁共振分配和动力学研究。

IF 0.9 4区生物学

Biomolecular NMR Assignments Pub Date : 2023-09-05 DOI: 10.1007/s12104-023-10150-6

Nur Alia Oktaviani, Ali D. Malay, Mami Goto, Toshio Nagashima, Fumiaki Hayashi, Keiji Numata

引用次数: 0