Biomolecular NMR Assignments最新文献_第2页

NMR assignment of the conserved bacterial DNA replication protein DnaA domain IV 保守细菌 DNA 复制蛋白 DnaA 结构域 IV 的核磁共振分配。

IF 0.8 4区生物学

Biomolecular NMR Assignments Pub Date : 2024-10-04 DOI: 10.1007/s12104-024-10206-1

Alexander Nguyen Abrams, Geoff Kelly, Julia Hubbard

引用次数: 0

Imino chemical shift assignments of tRNAAsp, tRNAVal and tRNAPhe from Escherichia coli 大肠杆菌 tRNAAsp、tRNAVal 和 tRNAPhe 的氨基化学位移分布。

IF 0.8 4区生物学

Biomolecular NMR Assignments Pub Date : 2024-10-04 DOI: 10.1007/s12104-024-10207-0

Marcel-Joseph Yared, Carine Chagneau, Pierre Barraud

{"title":"Imino chemical shift assignments of tRNAAsp, tRNAVal and tRNAPhe from Escherichia coli","authors":"Marcel-Joseph Yared, Carine Chagneau, Pierre Barraud","doi":"10.1007/s12104-024-10207-0","DOIUrl":"10.1007/s12104-024-10207-0","url":null,"abstract":"<div>Transfer RNAs (tRNAs) are an essential component of the protein synthesis machinery. In order to accomplish their cellular functions, tRNAs go through a highly controlled biogenesis process leading to the production of correctly folded tRNAs. tRNAs in solution adopt the characteristic L-shape form, a stable tertiary conformation imperative for the cellular stability of tRNAs, their thermotolerance, their interaction with protein and RNA complexes and their activity in the translation process. The introduction of post-transcriptional modifications by modification enzymes, the global conformation of tRNAs, and their cellular stability are highly interconnected. We aim to further investigate this existing link by monitoring the maturation of bacterial tRNAs in E. coli extracts using NMR. Here, we report on the 1H, 15N chemical shift assignment of the imino groups and some amino groups of unmodified and modified E. coli tRNAAsp, tRNAVal and tRNAPhe, which are essential for characterizing their maturation process using NMR spectroscopy.</div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"18 2","pages":"323 - 331"},"PeriodicalIF":0.8,"publicationDate":"2024-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11511762/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142370573","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

Backbone assignments of the biotin carboxyl carrier protein domain of Propionyl CoA carboxylase of Leishmania major and its interaction with its cognate Biotin protein ligase 大利什曼原虫丙酰 CoA 羧化酶生物素羧基载体蛋白结构域的骨架分配及其与同源生物素蛋白连接酶的相互作用。

IF 0.8 4区生物学

Biomolecular NMR Assignments Pub Date : 2024-09-23 DOI: 10.1007/s12104-024-10205-2

Sonika Bhatnagar, Debodyuti Sadhukhan, Monica Sundd

{"title":"Backbone assignments of the biotin carboxyl carrier protein domain of Propionyl CoA carboxylase of Leishmania major and its interaction with its cognate Biotin protein ligase","authors":"Sonika Bhatnagar, Debodyuti Sadhukhan, Monica Sundd","doi":"10.1007/s12104-024-10205-2","DOIUrl":"10.1007/s12104-024-10205-2","url":null,"abstract":"<div>Propionyl CoA carboxylase (PCC) is a multimeric enzyme composed of two types of subunits, α and β arranged in α6β6 stoichiometry. The α-subunit consists of an N-terminal carboxylase domain, a carboxyl transferase domains, and a C-terminal biotin carboxyl carrier protein domain (BCCP). The β-subunit is made up of an N- and a C- carboxyl transferase domain. During PCC catalysis, the BCCP domain plays a central role by transporting a carboxyl group from the α-subunit to the β-subunit, and finally to propionyl CoA carboxylase, resulting in the formation of methyl malonyl CoA. A point mutation in any of the subunits interferes with multimer assembly and function. Due to the association of this enzyme with propionic acidemia, a genetic metabolic disorder found in humans, PCC has become an enzyme of wide spread interest. Interestingly, unicellular eukaryotes like Leishmania also possess a PCC in their mitochondria that displays high sequence conservation with the human enzyme. Thus, to understand the function of this enzyme at the molecular level, we have initiated studies on Leishmania major PCC (LmPCC). Here we report chemical shift assignments of LmPCC BCCP domain using NMR. Conformational changes in LmPCC BCCP domain upon biotinylation, as well as upon interaction with its cognate biotinylating enzyme (Biotin protein ligase from L. major) have also been reported. Our studies disclose residues important for LmPCC BCCP interaction and function.</div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"18 2","pages":"309 - 314"},"PeriodicalIF":0.8,"publicationDate":"2024-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142306875","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 and 13C resonance assignments of the S2A and H64A double mutant of human carbonic anhydrase II 人类碳酸酐酶 II 的 S2A 和 H64A 双突变体的 1H、15N 和 13C 共振分配。

IF 0.8 4区生物学

Biomolecular NMR Assignments Pub Date : 2024-09-21 DOI: 10.1007/s12104-024-10203-4

Neelam, Mandar Bopardikar, Himanshu Singh

{"title":"1H, 15N and 13C resonance assignments of the S2A and H64A double mutant of human carbonic anhydrase II","authors":"Neelam, Mandar Bopardikar, Himanshu Singh","doi":"10.1007/s12104-024-10203-4","DOIUrl":"10.1007/s12104-024-10203-4","url":null,"abstract":"<div>Protein-water interactions profoundly influence protein structure and dynamics. Consequently, the function of many biomacromolecules is directly related to the presence and exchange of water molecules. While structural water molecules can be readily identified through X-ray crystallography, the dynamics within functional protein-water networks remain largely elusive. Therefore, to understand the role of biological water in protein dynamics and function, we have introduced S2A and H64A mutations in human Carbonic Anhydrase II (hCAII), a model system to study protein-water interactions. The mutations of serine to alanine at position 2 and histidine to alanine at position 64 cause an increase in hydrophobicity in the N-terminus and active site loop thereby restricting water entry and disrupting the water network in the Zn2+-binding pocket. To pave the way for a detailed investigation into the structural, functional, and mechanistic aspects of the Ser2Ala/His64Ala double mutant of hCAII, we present here almost complete sequence-specific resonance assignments for 1H, 15N, and 13C. These assignments serve as the basis for comprehensive studies on the dynamics of the protein-water network within the Zn2+-binding pocket and its role in catalysis.</div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"18 2","pages":"299 - 304"},"PeriodicalIF":0.8,"publicationDate":"2024-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142278433","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 PA2072 CHASE4 domain PA2072 CHASE4 结构域的化学位移分配。

IF 0.8 4区生物学

Biomolecular NMR Assignments Pub Date : 2024-09-21 DOI: 10.1007/s12104-024-10204-3

Yajing Duan, Wensu Yuan, Zhi Lin, Yan Zhang

引用次数: 0

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