Biomolecular NMR Assignments最新文献_第2页

Backbone assignment of CcdB_G100T toxin from E.coli in complex with the toxin binding C-terminal domain of its cognate antitoxin CcdA 大肠杆菌 CcdB_G100T 毒素与其同源抗毒素 CcdA 的毒素结合 C 端结构域复合体的骨架分配

IF 0.8 4区生物学

Biomolecular NMR Assignments Pub Date : 2024-09-14 DOI: 10.1007/s12104-024-10201-6

Bahnikana Nanda, Jayantika Bhowmick, Raghavan Varadarajan, Siddhartha P. Sarma

{"title":"Backbone assignment of CcdB_G100T toxin from E.coli in complex with the toxin binding C-terminal domain of its cognate antitoxin CcdA","authors":"Bahnikana Nanda, Jayantika Bhowmick, Raghavan Varadarajan, Siddhartha P. Sarma","doi":"10.1007/s12104-024-10201-6","DOIUrl":"10.1007/s12104-024-10201-6","url":null,"abstract":"<div>The CcdAB system expressed in the E.coli cells is a prototypical example of the bacterial toxin-antitoxin (TA) systems that ensure the survival of the bacterial population under adverse environmental conditions. The solution and crystal structures of CcdA, CcdB and of CcdB in complex with the toxin-binding C-terminal domain of CcdA have been reported. Our interest lies in the dynamics of CcdB-CcdA complex formation. Solution NMR studies have shown that CcdB_G100T, in presence of saturating concentrations of CcdA-c, a truncated C-terminal fragment of CcdA exists in equilibrium between two major populations. Sequence specific backbone resonance assignments of both equilibrium forms of the ~ 27 kDa complex, have been obtained from a suite of triple resonance NMR experiments acquired on 2H, 13C, 15N enriched samples of CcdB_G100T. Analysis of 1H, 13Cα, 13Cβ secondary chemical shifts, shows that both equilibrium forms of CcdB_G100T have five beta-strands and one alpha-helix as the major secondary structural elements in the tertiary structure. The results of these studies are presented below.</div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"18 2","pages":"285 - 292"},"PeriodicalIF":0.8,"publicationDate":"2024-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142250472","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

The 1H, 15N, and 13C resonance assignments of a single-domain antibody against immunoglobulin G 抗免疫球蛋白 G 的单域抗体的 1H、15N 和 13C 共振赋值

IF 0.8 4区生物学

Biomolecular NMR Assignments Pub Date : 2024-09-13 DOI: 10.1007/s12104-024-10199-x

Vanessa Bezerra de Oliveira Leite, Rafael Alves de Andrade, Fabio Ceneviva Lacerda de Almeida, Claudia Jorge do Nascimento, Talita Stelling de Araujo, Marcius da Silva Almeida

{"title":"The 1H, 15N, and 13C resonance assignments of a single-domain antibody against immunoglobulin G","authors":"Vanessa Bezerra de Oliveira Leite, Rafael Alves de Andrade, Fabio Ceneviva Lacerda de Almeida, Claudia Jorge do Nascimento, Talita Stelling de Araujo, Marcius da Silva Almeida","doi":"10.1007/s12104-024-10199-x","DOIUrl":"10.1007/s12104-024-10199-x","url":null,"abstract":"<div>Research on camelid-derived single-domain antibodies (sdAbs) has demonstrated their significant utility in diverse biotechnological applications, including therapy and diagnostic. This is largely due to their relative simplicity as monomeric proteins, ranging from 12 to 15 kDa, in contrast to immunoglobulin G (IgG) antibodies, which are glycosylated heterotetramers of 150–160 kDa. Single-domain antibodies exhibit high conformational stability and adopt the typical immunoglobulin domain fold, consisting of a two-layer sandwich of 7–9 antiparallel beta-strands. They contain three loops, known as complementary-determining regions (CDRs), which are assembled on the sdAb surface and are responsible for antigen recognition. The single-domain antibody examined in this study, sdAb-mrh-IgG, was engineered to recognize IgG from rats, mice, but it also weakly recognizes IgG from humans (Pleiner et al. 2018). A search of the Protein Data Bank revealed only one NMR structure of a single-domain antibody, which is unrelated to sdAb-mrh-IgG. The NMR chemical shift assignments of sdAb-mrh-IgG will be utilized to study its molecular dynamics and interactions with antigens in solution, which is fundamental for the rational design of novel single-domain antibodies.</div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"18 2","pages":"269 - 274"},"PeriodicalIF":0.8,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142206233","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

The backbone NMR resonance assignments of the stabilized E. coli β clamp 稳定的大肠杆菌β钳夹的骨架核磁共振共振赋值

IF 0.8 4区生物学

Biomolecular NMR Assignments Pub Date : 2024-09-13 DOI: 10.1007/s12104-024-10202-5

Sam Mahdi, Socheata Lim, Irina Bezsonova, Penny J. Beuning, Dmitry M. Korzhnev

{"title":"The backbone NMR resonance assignments of the stabilized E. coli β clamp","authors":"Sam Mahdi, Socheata Lim, Irina Bezsonova, Penny J. Beuning, Dmitry M. Korzhnev","doi":"10.1007/s12104-024-10202-5","DOIUrl":"10.1007/s12104-024-10202-5","url":null,"abstract":"<div>The 81 kDa E. coli β clamp is a ring-shaped head-to-tail homodimer that encircles DNA and plays a central role in bacterial DNA replication by serving as a processivity factor for DNA polymerases and a binding platform for other DNA replication and repair proteins. Here we report the backbone 1H, 15N, and 13C NMR resonance assignments of the stabilized T45R/S107R β clamp variant obtained using standard TROSY-based triple-resonance experiments (BMRB 52548). The backbone assignments were aided by 13C and 15N edited NOESY experiments, allowing us to utilize our previously reported assignments of the β clamp ILV side-chain methyl groups (BMRB 51430, 51431). The backbone assignments of the T45R/S107R β clamp variant were transferred to the wild-type β clamp using a minimal set of TROSY-based 15N edited NOESY, NHCO and NHCA experiments (BMRB 52549). The reported backbone and previous ILV side-chain resonance assignments will enable NMR studies of the β clamp interactions and dynamics using amide and methyl groups as probes.</div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"18 2","pages":"293 - 297"},"PeriodicalIF":0.8,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142206232","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, 15N backbone resonance assignments of 14-3-3ζ binding region of human FOXO3a (residues 1-284) 人类 FOXO3a 的 14-3-3ζ 结合区（残基 1-284）的核磁共振 1H、13C 和 15N 骨架共振赋值

IF 0.8 4区生物学

Biomolecular NMR Assignments Pub Date : 2024-09-11 DOI: 10.1007/s12104-024-10200-7

Shota Enomoto, Shoichi Nakatsuka, Tomoya Kuwayama, Kosaku Kawatsu, Mariko Yokogawa, Masanori Osawa

{"title":"NMR 1H, 13C, 15N backbone resonance assignments of 14-3-3ζ binding region of human FOXO3a (residues 1-284)","authors":"Shota Enomoto, Shoichi Nakatsuka, Tomoya Kuwayama, Kosaku Kawatsu, Mariko Yokogawa, Masanori Osawa","doi":"10.1007/s12104-024-10200-7","DOIUrl":"10.1007/s12104-024-10200-7","url":null,"abstract":"<div>In tumors, mutation in Ras proteins stimulates a signaling cascade through phosphorylation. Downstream of the cascade, many transcription and translation factors are up- or down-regulated by phosphorylation, leading to cancer progression. This phosphorylation cascade is sustained by 14-3-3ζ protein. 14-3-3ζ binds to its client proteins that are Ser/Thr-phosphorylated and prevents their dephosphorylation. One of those transcription factors is FOXO3a, whose transcriptional activity is suppressed in the phosphorylation cascade. FOXO3a binds to specific DNA sequences and activates the transcription of apoptosis-related proteins. In cancer cells, however, FOXO3a is phosphorylated, bound to 14-3-3ζ, and dissociated from the DNA, resulting in FOXO3a inactivation. To elucidate the mechanism of FOXO3a inactivation by the 14-3-3ζ binding, we aim to perform NMR analysis of the interaction between 14-3-3ζ and di-phosphorylated FOXO3a residues 1-284 (dpFOXO3a). Here, we report the backbone resonance assignments of dpFOXO3a, which are transferred from those of the N-terminal domain (NTD) and the DNA-binding domain (DBD) of dpFOXO3a.</div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"18 2","pages":"275 - 283"},"PeriodicalIF":0.8,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s12104-024-10200-7.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142226381","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 assignment of the calcium-activated EndoU endoribonuclease 钙激活的 EndoU 内切核酸酶的 1H、13C 和 15N 主干共振分配。

IF 0.8 4区生物学

Biomolecular NMR Assignments Pub Date : 2024-09-09 DOI: 10.1007/s12104-024-10198-y

Florian Malard, Fedor V. Karginov, Sébastien Campagne

引用次数: 0

Solution NMR backbone assignment of the N-terminal tandem Zα1-Zα2 domains of Z-DNA binding protein 1 Z-DNA 结合蛋白 1 N 端串联 Zα1-Zα2 结构域的溶液核磁共振骨架分配。

IF 0.8 4区生物学

Biomolecular NMR Assignments Pub Date : 2024-08-31 DOI: 10.1007/s12104-024-10195-1

Lily G. Beck, Jeffrey B. Krall, Parker J. Nichols, Quentin Vicens, Morkos A. Henen, Beat Vögeli

引用次数: 0

NMR-based solution structure of the Caulobacter crescentus ProXp-ala trans-editing enzyme 基于核磁共振的新月杆菌 ProXp-ala 反式编辑酶溶液结构。

IF 0.8 4区生物学

Biomolecular NMR Assignments Pub Date : 2024-08-31 DOI: 10.1007/s12104-024-10193-3

Antonia D. Duran, Eric M. Danhart, Xiao Ma, Alexandra B. Kuzmishin Nagy, Karin Musier-Forsyth, Mark P. Foster

{"title":"NMR-based solution structure of the Caulobacter crescentus ProXp-ala trans-editing enzyme","authors":"Antonia D. Duran, Eric M. Danhart, Xiao Ma, Alexandra B. Kuzmishin Nagy, Karin Musier-Forsyth, Mark P. Foster","doi":"10.1007/s12104-024-10193-3","DOIUrl":"10.1007/s12104-024-10193-3","url":null,"abstract":"<div>ProXp-ala is a key component of the translational machinery in all three Domains of life. This enzyme helps to maintain the fidelity of proline codon translation through aminoacyl-tRNAPro proofreading. In the first step of tRNA aminoacylation, the cognate aminoacyl-tRNA synthetase (aaRS) binds and activates an amino acid in the enzyme’s synthetic active site. If a non-cognate amino acid passes this first selection step and is charged onto the tRNA, a distinct aaRS editing active site may recognize the mischarged tRNA and deacylate it. Alternatively, this editing reaction may be carried out by a separate enzyme that deacylates the mischarged tRNA in trans. ProXp-ala is responsible for editing Ala mischarged onto tRNAPro. Since trans-editing domains such as ProXp-ala bind their substrates after release from the synthetase, they must recognize not only the mischarged amino acid, but also the specific tRNA. Previous studies showed that Caulobacter crescentus (Cc) ProXp-ala distinguishes tRNAPro from tRNAAla, in part, based on the unique tRNAPro acceptor stem base pair C1:G72. Previous crystallographic and NMR data also revealed a role for conformational selection by the ProXp-ala α2 helix in Ala- versus Pro-tRNAPro substrate discrimination. The α2 helix makes lattice contacts in the crystal, which left some uncertainty as to its position in solution. We report resonance assignments for the substrate-free Cc ProXp-ala and the NMR-derived three-dimensional structure of the protein. These data reveal the position of the α2 helix in solution, with implications for substrate binding and recognition.</div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"18 2","pages":"233 - 238"},"PeriodicalIF":0.8,"publicationDate":"2024-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11511748/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142103133","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

Solution NMR backbone resonance assignment of the full-length resistance-related calcium-binding protein Sorcin 全长抗性相关钙结合蛋白 Sorcin 的溶液 NMR 主干共振分配。

IF 0.8 4区生物学

Biomolecular NMR Assignments Pub Date : 2024-08-31 DOI: 10.1007/s12104-024-10196-0

Kathleen Joyce Carillo, Yanan He, Qiushi Ye, Nicolas Delaeter, Yihong Chen, John Orban, Yanxin Liu

{"title":"Solution NMR backbone resonance assignment of the full-length resistance-related calcium-binding protein Sorcin","authors":"Kathleen Joyce Carillo, Yanan He, Qiushi Ye, Nicolas Delaeter, Yihong Chen, John Orban, Yanxin Liu","doi":"10.1007/s12104-024-10196-0","DOIUrl":"10.1007/s12104-024-10196-0","url":null,"abstract":"<div>Sorcin is a penta-EF hand calcium-binding protein that confers multidrug resistance in cancer cells. It regulates cellular Ca2+ homeostasis by interacting with calcium channels such as Ryanodine receptor 2 and Sarcoplasmic/endoplasmic reticulum Ca2+-ATPase in a calcium-dependent manner. The crystal structure of the Sorcin has been determined in both calcium-free and calcium-bound states to understand calcium-binding induced conformational change. However, due to its flexibility, most of the N-terminal domain is invisible in these crystal structures. Here we report the 1H, 13C, and 15N backbone resonance assignments of full-length Sorcin in the calcium-free state using solution NMR. The protein secondary structure was predicted based on the assigned backbone chemical shifts using TALOS+ and CSI 3.0. Our backbone resonance assignment of the full-length Sorcin provides a foundation for future NMR spectroscopic studies to uncover the mechanism of Ca2+ sensing by Sorcin.</div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"18 2","pages":"253 - 256"},"PeriodicalIF":0.8,"publicationDate":"2024-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142103135","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 α-actinin C-terminal EF-hand domain bound to a cytosolic C0 domain of GluN1 (residues 841–865) from the NMDA receptor α-肌动蛋白 C 端 EF-手结构域与 NMDA 受体 GluN1 的细胞膜 C0 结构域（残基 841-865）结合的化学位移分配。

IF 0.8 4区生物学

Biomolecular NMR Assignments Pub Date : 2024-08-29 DOI: 10.1007/s12104-024-10194-2

Aritra Bej, Johannes W. Hell, James B. Ames

引用次数: 0

1H, 15N and 13C resonance assignments of eggcase silk protein 3 蛋壳蚕丝蛋白 3 的 1H、15N 和 13C 共振分配。

IF 0.8 4区生物学

Biomolecular NMR Assignments Pub Date : 2024-08-24 DOI: 10.1007/s12104-024-10192-4

Shuixin Yu, Ruiqi Qin, Wensu Yuan, Zhi Lin

引用次数: 0