Qiwei Huang, Hui Qi Ng, Yong Yao Loh, Zhiyuan Ke, Wan Hsin Lim, CongBao Kang
{"title":"Backbone 1H, 15N and 13C resonance assignments for an E2 ubiquitin conjugating enzyme-UBE2T","authors":"Qiwei Huang, Hui Qi Ng, Yong Yao Loh, Zhiyuan Ke, Wan Hsin Lim, CongBao Kang","doi":"10.1007/s12104-023-10154-2","DOIUrl":"10.1007/s12104-023-10154-2","url":null,"abstract":"<div><p>Ubiquitin-conjugating enzyme E2 T (UBE2T) plays important roles in ubiquitination of proteins through participation in transferring ubiquitin to its substrate. Due to its importance in protein modifications, UBE2T associates with diverse diseases and serves as an important target for drug discovery and development. The crystal structure of UBE2T has been determined and the structure reveals the lack of a druggable pocket for binding to small molecules for clinical applications. Despite the challenge, effort has been made to develop UBE2T inhibitors. We obtained UBE2T constructs with and without the C-terminal region which is flexible in solution. Herein, we report the backbone resonance assignments for human UBE2T without the C-terminal region. The backbone dynamics of UBE2T was also explored. The available assignments will be helpful for hit identification, determining ligand binding site and understanding the mechanism of action of UBE2T inhibitors.</p></div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"17 2","pages":"269 - 274"},"PeriodicalIF":0.9,"publicationDate":"2023-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71910587","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 NMR chemical shift assignment of LytM N-terminal domain (residues 26–184)","authors":"Ilona Pitkänen, Helena Tossavainen, Perttu Permi","doi":"10.1007/s12104-023-10151-5","DOIUrl":"10.1007/s12104-023-10151-5","url":null,"abstract":"<div><p>Antibiotic resistance is a growing problem and a global threat for modern healthcare. New approaches complementing the traditional antibiotic drugs are urgently needed to secure the ability to treat bacterial infections also in the future. Among the promising alternatives are bacteriolytic enzymes, such as the cell wall degrading peptidoglycan hydrolases. <i>Staphylococcus aureus</i> LytM, a Zn<sup>2+</sup>-dependent glycyl-glycine endopeptidase of the M23 family, is one of the peptidoglycan hydrolases. It has a specificity towards staphylococcal peptidoglycan, making it an interesting target for antimicrobial studies. LytM hydrolyses the cell wall of <i>S. aureus</i>, a common pathogen with multi-resistant strains that are difficult to treat, such as the methicillin-resistant <i>S. aureus</i>, MRSA. Here we report the <sup>1</sup>H, <sup>15</sup>N and <sup>13</sup>C chemical shift assignments of <i>S. aureus</i> LytM N-terminal domain and linker region, residues 26–184. These resonance assignments can provide the basis for further studies such as elucidation of structure and interactions.</p></div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"17 2","pages":"257 - 263"},"PeriodicalIF":0.9,"publicationDate":"2023-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71910247","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}
Marco Sette, Laura Anne Johnson, Ralph Jimenez, Frans A.A. Mulder
{"title":"Backbone 1H, 15N and 13C resonance assignments of the 27kDa fluorescent protein mCherry","authors":"Marco Sette, Laura Anne Johnson, Ralph Jimenez, Frans A.A. Mulder","doi":"10.1007/s12104-023-10149-z","DOIUrl":"10.1007/s12104-023-10149-z","url":null,"abstract":"<div><p>mCherry is one of the most successfully applied monomeric red fluorescent proteins (RFPs) for in vivo and in vitro imaging. However, questions pertaining to the photostability of the RFPs remain and rational further engineering of their photostability requires information about the fluorescence quenching mechanism in solution. To this end, NMR spectroscopic investigations might be helpful, and we present the near-complete backbone NMR chemical shift assignment to aid in this pursuit.</p></div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"17 2","pages":"243 - 247"},"PeriodicalIF":0.9,"publicationDate":"2023-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71909583","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}
Nur Alia Oktaviani, Ali D. Malay, Mami Goto, Toshio Nagashima, Fumiaki Hayashi, Keiji Numata
{"title":"NMR assignment and dynamics of the dimeric form of soluble C-terminal domain major ampullate spidroin 2 from Latrodectus hesperus","authors":"Nur Alia Oktaviani, Ali D. Malay, Mami Goto, Toshio Nagashima, Fumiaki Hayashi, Keiji Numata","doi":"10.1007/s12104-023-10150-6","DOIUrl":"10.1007/s12104-023-10150-6","url":null,"abstract":"<div><p>Spider dragline silk has attracted great interest due to its outstanding mechanical properties, which exceed those of man-made synthetic materials. Dragline silk, which is composed of at least major ampullate spider silk protein 1 and 2 (MaSp1 and MaSp2), contains a long repetitive domain flanked by N-terminal and C-terminal domains (NTD and CTD). Despite the small size of the CTD, this domain plays a crucial role as a molecular switch that regulates and directs spider silk self-assembly. In this study, we report the <sup>1</sup>H, <sup>13</sup>C, and <sup>15</sup>N chemical shift assignments of the <i>Latrodectus hesperus</i> MaSp2 CTD in dimeric form at pH 7. Our solution NMR data demonstrated that this protein contains five helix regions connected by a flexible linker.</p></div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"17 2","pages":"249 - 255"},"PeriodicalIF":0.9,"publicationDate":"2023-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10146098","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}
Julia A. Brom, Sasiprapa Samsri, Ruta G. Petrikis, Stuart Parnham, Gary J. Pielak
{"title":"1H, 13C, 15N backbone resonance assignment of Escherichia coli adenylate kinase","authors":"Julia A. Brom, Sasiprapa Samsri, Ruta G. Petrikis, Stuart Parnham, Gary J. Pielak","doi":"10.1007/s12104-023-10147-1","DOIUrl":"10.1007/s12104-023-10147-1","url":null,"abstract":"<div><p>Adenylate kinase reversibly catalyzes the conversion of ATP plus AMP to two ADPs. This essential catalyst is present in every cell, and the <i>Escherichia coli</i> protein is often employed as a model enzyme. Our aim is to use the <i>E. coli</i> enzyme to understand dry protein structure and protection. Here, we report the expression, purification, steady-state assay, NMR conditions and <sup>1</sup>H, <sup>13</sup>C, <sup>15</sup>N backbone resonance NMR assignments of its C77S variant. These data will also help others utilize this prototypical enzyme.</p></div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"17 2","pages":"235 - 238"},"PeriodicalIF":0.9,"publicationDate":"2023-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71910623","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}
Carolina O. Matos, Glaucia M.S. Pinheiro, Carlos H. I. Ramos, Fabio C. L. Almeida
{"title":"Backbone and sidechain NMR assignments of residues 1–81 from yeast Sis1 in complex with an Hsp70 C-terminal EEVD peptide","authors":"Carolina O. Matos, Glaucia M.S. Pinheiro, Carlos H. I. Ramos, Fabio C. L. Almeida","doi":"10.1007/s12104-023-10148-0","DOIUrl":"10.1007/s12104-023-10148-0","url":null,"abstract":"<div><p>Molecular chaperones aid proteins to fold and assemble without modifying their final structure, requiring, in several folding processes, the interplay between members of the Hsp70 and Hsp40 families. Here, we report the NMR chemical shift assignments for <sup>1</sup> H, <sup>15</sup> N, and <sup>13</sup> C nuclei of the backbone and side chains of the J-domain of the class B Hsp40 from <i>Saccharomyces cerevisiae</i>, Sis1, complexed with the C-terminal EEVD motif of Hsp70. The data revealed information on the structure and backbone dynamics that add significantly to the understanding of the J-domain-Hsp70-EEVD mechanism of interaction.</p></div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"17 2","pages":"239 - 242"},"PeriodicalIF":0.9,"publicationDate":"2023-08-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10005545","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, 15N and 13C backbone and side chain solution NMR assignments of the TPM domain-containing protein of the thermophilic bacterium Rhodothermus marinus","authors":"Leonardo Pellizza, Lila Ramis, Ignacio Argañaraz Araoz, Martín Aran","doi":"10.1007/s12104-023-10146-2","DOIUrl":"10.1007/s12104-023-10146-2","url":null,"abstract":"<div><p>The InterPro family IPR007621 TPM_phosphatase is a widely conserved family of protein domains found in prokaryotes, plants and invertebrates. Despite similar predicted protein folding, members of this family are involved in different cellular processes. In recent years, the structural and biochemical characterization of evolutionarily divergent TPM domains has shown their ability to hydrolyze phosphate groups of different substrates. However, there are still inaccurate functional annotations and uncertain relationships between the structure and function of this domain family. We here report the <sup>1</sup>H, <sup>13</sup>C, and <sup>15</sup>N backbone and sidechain resonances of the TPM domain of a predicted TPM domain-containing protein of the thermophilic bacterium <i>Rhodothermus marinus</i>. These data will lay the groundwork for future NMR-based investigations, contributing to a thorough comprehension of the intricate aspects governing the interplay between structure and function of TPM domains. Additionally, they will unlock opportunities to explore dynamic structural changes, providing valuable insights into the molecular mechanisms underlying the evolutionary adaptations to extreme environmental conditions within this protein family.</p></div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"17 2","pages":"229 - 233"},"PeriodicalIF":0.9,"publicationDate":"2023-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71909141","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 and side chain NMR assignments and secondary structure calculation of the pheromone binding protein3 of Ostrinia nubilalis, an agricultural pest","authors":"Omar Al-Danoon, Smita Mohanty","doi":"10.1007/s12104-023-10145-3","DOIUrl":"10.1007/s12104-023-10145-3","url":null,"abstract":"<div><p><i>Ostrinia nubilalis</i>, also known as European Corn Borer (ECB), is a serious pest in Europe and North America, as well as in Central Asia and Northern Africa. It damages a variety of agricultural crops such as corn, oats, buckwheat, millet, and soybeans. causing annually at least one billion dollars in loss. The <i>Ostrinia nubilalis</i> pheromone-binding protein3 (OnubPBP3), preferentially expressed in the male moth antenna, has been implicated in the detection of the female-secreted pheromone blend during the mating process. Understanding the structure of and function of OnubPBP3, including the mechanism of pheromone binding and its release at the dendritic olfactory neuron (ORN), is essential if integrated pest management through sensory inhibition is to be achieved. We report here the backbone and side-chain resonance assignments of OnubPBP3 at pH 6.5 using various triple resonance NMR experiments on a <sup>13</sup>C, <sup>15</sup>N-labeled protein sample. The secondary structure of OnubPBP3 consists of six α-helices and an unstructured C-terminus based on backbone chemical shifts.</p></div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"17 2","pages":"223 - 227"},"PeriodicalIF":0.9,"publicationDate":"2023-07-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9879801","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}
Assia Mouhand, Joana Pissarra, Stéphane Delbecq, Christian Roumestand, Philippe Barthe
{"title":"1H, 13C and 15N backbone and side-chain resonance assignments of ∆∆BmSA1, the surface antigen of Babesia microti","authors":"Assia Mouhand, Joana Pissarra, Stéphane Delbecq, Christian Roumestand, Philippe Barthe","doi":"10.1007/s12104-023-10144-4","DOIUrl":"10.1007/s12104-023-10144-4","url":null,"abstract":"<div><p>Human babesiosis is a vector-borne zoonotic infection caused mostly by the Apicomplexan parasite <i>Babesia microti</i>, distributed worldwide. The infection can result in severe symptoms such as hemolytic anemia, especially in immunodeficient patients. Also, asymptomatic patients continue transmission as unscreened blood donors, and represent a risk for Public Health. Early host-parasite interactions are mediated by BmSA1, the major surface antigen of <i>Babesia microti</i>, crucial for invasion and immune escape. Hence, a structural and functional characterization of the BmSA1 protein constitutes a first strategic milestone toward the development of innovative tools to control infection. Knowledge of the 3D structure of such an important antigen is crucial for the development of vaccines or new diagnostic tests. Here, we report the <sup>1</sup>H, <sup>15</sup>N and <sup>13</sup>C NMR resonance assignment of ∆∆BmSA1, a truncated recombinant version of BmSA1 without the N-terminal signal peptide and the hydrophobic C-terminal GPI-anchor. Secondary structure prediction using CSI.3 and TALOS-N demonstrates a high content of alpha-helical structure. This preliminary study provides foundations for further structural characterization of BMSA1.</p></div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"17 2","pages":"217 - 221"},"PeriodicalIF":0.9,"publicationDate":"2023-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71909559","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}
Madison Rizzo, Eric Baggs, Abu Sayeed Chowdhury, Rajesh Nagarajan, Lisa Rose Warner
{"title":"Backbone 1H, 13C and 15N assignments of the apo-acyl carrier protein (ACP1) of Pseudomonas aeruginosa","authors":"Madison Rizzo, Eric Baggs, Abu Sayeed Chowdhury, Rajesh Nagarajan, Lisa Rose Warner","doi":"10.1007/s12104-023-10138-2","DOIUrl":"10.1007/s12104-023-10138-2","url":null,"abstract":"<div><p>The N-acyl-L-homoserine lactone (AHL) quorum sensing regulates virulence in the opportunistic pathogen, <i>Pseudomonas aeruginosa</i>. The LasI and RhlI AHL synthases use acyl carrier protein substrates to synthesize, respectively, the 3-oxododecanoyl-L-homoserine lactone (3-oxoC12-HSL) and butyryl-L-homoserine lactone (C4-HSL) QS signals for this bacterium. Although <i>P. aeruginosa</i> genome contains three open reading frames to encode three acyl carrier proteins, namely the ACP<sub>1</sub>, ACP<sub>2</sub> and ACP<sub>3</sub>, microarray and gene replacement studies show that only the ACP<sub>1</sub> carrier protein is under quorum sensing regulation. In this study, we isotopically enriched one of the acyl carrier proteins, ACP<sub>1</sub> from <i>P. aeruginosa</i> and describe the backbone resonance assignments for this protein to delineate the structural and molecular basis of ACP<sub>1</sub> recognition in <i>P. aeruginosa</i> AHL quorum sensing signal synthesis.</p></div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"17 2","pages":"183 - 188"},"PeriodicalIF":0.9,"publicationDate":"2023-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71909381","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}