Biomolecular NMR Assignments最新文献

NMR resonance assignment of a ligand-binding domain of ephrin receptor A2.

IF 0.8 4区生物学

Biomolecular NMR Assignments Pub Date : 2024-12-19 DOI: 10.1007/s12104-024-10211-4

Konstantin S Mineev, Santosh L Gande, Verena Linhard, Sattar Khashkhashi Moghaddam, Harald Schwalbe

引用次数: 0

Backbone resonance assignments of the C-terminal thioesterase domain of tyrocidine synthetase C.

IF 0.8 4区生物学

Biomolecular NMR Assignments Pub Date : 2024-12-11 DOI: 10.1007/s12104-024-10210-5

Mitsuhiro Takeda, Rino Saito, Sho Konno, Takayuki Nagae, Hiroshi Aoyama, Sosuke Yoshinaga, Hiroaki Terasawa, Akihiro Taguchi, Atsuhiko Taniguchi, Yoshio Hayashi, Masaki Mishima

{"title":"Backbone resonance assignments of the C-terminal thioesterase domain of tyrocidine synthetase C.","authors":"Mitsuhiro Takeda, Rino Saito, Sho Konno, Takayuki Nagae, Hiroshi Aoyama, Sosuke Yoshinaga, Hiroaki Terasawa, Akihiro Taguchi, Atsuhiko Taniguchi, Yoshio Hayashi, Masaki Mishima","doi":"10.1007/s12104-024-10210-5","DOIUrl":"https://doi.org/10.1007/s12104-024-10210-5","url":null,"abstract":"Natural macrocyclic peptides produced by microorganisms serve as valuable resources for therapeutic compounds, including antibiotics, anticancer agents, and immune suppressive agents. Nonribosomal peptide synthetases (NRPSs) are responsible for the biosynthesis of macrocyclic peptides. NRPSs are large multimodular enzymes, and each module recognizes and incorporates one specific amino acid into the polypeptide product. In the final biosynthetic step, the mature linear peptide precursor is subject to head-to-tail cyclization by the thioesterase (TE) domain in the C-terminal module. Since the TE domains can autonomously catalyze the cyclization of diverse linear peptide substrates, isolated TE domains can be used to produce natural product derivatives. To understand the mechanism of TE domains in NRPSs as a base for therapeutic applications, we investigated the TE domain (residues 6236-6486) of tyrocidine synthetase TycC by NMR. Tyrocidine is a cyclic decapeptide with antibiotic activity, and TycC-TE catalyzes the cyclization of the linear decapeptide precursor. Here, we report the backbone resonance assignments of TycC-TE. The assignments of TycC-TE provide the basis for NMR investigations of the structure and substrate-recognition mode of the TE domain in NRPS.","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":" ","pages":""},"PeriodicalIF":0.8,"publicationDate":"2024-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142805711","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, ¹³C, and ¹⁵N resonance assignments of the amyloidogenic peptide SEM2(49-107) by NMR spectroscopy.

IF 0.8 4区生物学

Biomolecular NMR Assignments Pub Date : 2024-11-29 DOI: 10.1007/s12104-024-10209-y

Anastasia A Troshkina, Vladimir V Klochkov, Aydar G Bikmullin, Evelina A Klochkova, Dmitriy S Blokhin

{"title":"1H, 13C, and 15N resonance assignments of the amyloidogenic peptide SEM2(49-107) by NMR spectroscopy.","authors":"Anastasia A Troshkina, Vladimir V Klochkov, Aydar G Bikmullin, Evelina A Klochkova, Dmitriy S Blokhin","doi":"10.1007/s12104-024-10209-y","DOIUrl":"https://doi.org/10.1007/s12104-024-10209-y","url":null,"abstract":"It has been shown that human seminal fluid is a major factor in enhancing HIV activity. The SEM2(49-107) peptide is a product of cleavage after ejaculation by internal prostheses of the semenogelin 2 protein, expressed in seminal vesicles. It is established that the peptide SEM2(49-107) forms amyloid fibrils, which increase probability of contracting HIV infection. In this nuclear magnetic resonance (NMR) study, we present almost complete (86%) resonance assignments for the 1H 15N and 13C atoms of the backbone and side-chain of the SEM2(49-107) peptide (BioMagResBank accession number 52356). The secondary structure of SEM2(49-107) peptide was estimated by using two approaches, secondary chemical shifts analysis (CSI) and TALOS-N prediction. Analysis of the secondary structure of the SEM2(49-107) peptide using both methods revealed that the peptide contains helical segments at the C-terminus. Also in this work, we used phase-sensitive 2D HSQC 1H- 15N experiments measuring longitudinal T1 and transverse T2 NMR relaxation times to report predicted secondary structure and backbone dynamics of the SEM2(49-107) peptide. This resonance assignment will form the basis of future NMR research, contributing to a better understanding of the peptide structure and internal dynamics of the molecule.","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":" ","pages":""},"PeriodicalIF":0.8,"publicationDate":"2024-11-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142749710","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 backbone resonance assignment of the N-terminal region of Zika virus NS4B protein in detergent micelles. 寨卡病毒 NS4B 蛋白 N 端区域在洗涤剂胶束中的 1H、15N 和 13C 骨架共振分配。

IF 0.8 4区生物学

Biomolecular NMR Assignments Pub Date : 2024-11-07 DOI: 10.1007/s12104-024-10208-z

Yan Li, Ying Ru Loh, Qingxin Li, Dahai Luo, CongBao Kang

引用次数: 0

Backbone 1H, 15N, and 13C resonance assignments of the FF1 domain from P190A RhoGAP in 5 and 8 M urea P190A RhoGAP 的 FF1 结构域在 5 M 和 8 M 尿素中的 1H、15N 和 13C 骨架共振赋值。

IF 0.8 4区生物学

Biomolecular NMR Assignments Pub Date : 2024-10-14 DOI: 10.1007/s12104-024-10197-z

Aarão Camilo-Ramos, Dmitry M. Korzhnev, Ramon Pinheiro-Aguiar, Fabio C. L. Almeida

引用次数: 0

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