Biomolecular NMR Assignments最新文献_第5页

Backbone NMR resonance assignments for the VP1u N-terminal receptor-binding domain of the human parvovirus pathogen B19 人类副病毒病原体 B19 的 VP1u N 端受体结合域的骨架核磁共振共振分配。

IF 0.8 4区生物学

Biomolecular NMR Assignments Pub Date : 2024-06-21 DOI: 10.1007/s12104-024-10181-7

Maria Luiza Caldas Nogueira, Renuk Lakshmanan, Gwladys Rivière, Mario Mietzsch, Antonette Bennett, Robert McKenna, Joanna R. Long

{"title":"Backbone NMR resonance assignments for the VP1u N-terminal receptor-binding domain of the human parvovirus pathogen B19","authors":"Maria Luiza Caldas Nogueira, Renuk Lakshmanan, Gwladys Rivière, Mario Mietzsch, Antonette Bennett, Robert McKenna, Joanna R. Long","doi":"10.1007/s12104-024-10181-7","DOIUrl":"10.1007/s12104-024-10181-7","url":null,"abstract":"<div><p>Parvovirus B19 (B19V) is a human pathogen that is the causative agent of several diseases in infants and adults. Due to a lack of antivirals against this virus, treatment options are limited. The minor capsid protein of B19V has a unique N terminus, named VP1u, which is essential for infection. The VP1u encodes a receptor binding domain (RBD), necessary for host cell entry, and a phospholipase A2 (PLA<sub>2</sub>) domain, crucial for endosomal escape during cellular trafficking. Both domains are indispensable for infection, making the RBD a plausible drug target for inhibitors against B19V, as it is located on the exterior surface of the virus. To date, no experimental structural information has been available for the VP1u component for any Parvovirus. Here we report the backbone NMR resonance assignments for the RBD of B19V and demonstrate it forms a stable structure. The backbone chemical shifts are in good agreement with a structure predicted by AlphaFold, validating that the RBD contains three helices connected by tight turns. This RBD construct can now be used for further NMR studies, including assignment of full-length VP1u, determination of protein-protein interaction interfaces, and development of B19 antivirals specific to the RBD domain.</p></div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"18 2","pages":"147 - 152"},"PeriodicalIF":0.8,"publicationDate":"2024-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141431063","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 backbone resonance assignment of Cel45A from Phanerochaete chrysosporium 来自 Phanerochaete chrysosporium 的 Cel45A 的 1H、13C 和 15N 主干共振分配。

IF 0.8 4区生物学

Biomolecular NMR Assignments Pub Date : 2024-06-18 DOI: 10.1007/s12104-024-10182-6

Laura Okmane, Mats Sandgren, Jerry Ståhlberg, Gustav Nestor

引用次数: 0

Backbone triple resonance assignments of the dimerization domain of NF-kappaB p52 subunit NF-kappaB p52 亚基二聚化结构域的骨架三重共振分配。

IF 0.8 4区生物学

Biomolecular NMR Assignments Pub Date : 2024-06-10 DOI: 10.1007/s12104-024-10179-1

Sunirmala Sahoo, Nitin Dhaka, Sulakshana P. Mukherjee

引用次数: 0

Resonance assignments of cytochrome MtoD from the extracellular electron uptake pathway of sideroxydans lithotrophicus ES-1 细胞色素 MtoD 的共振赋值来自于纤毛虫 ES-1 的细胞外电子摄取途径。

IF 0.8 4区生物学

Biomolecular NMR Assignments Pub Date : 2024-06-07 DOI: 10.1007/s12104-024-10180-8

Anaísa Coelho, José M. Silva, Francesca Cantini, Mario Piccioli, Ricardo O. Louro, Catarina M. Paquete

{"title":"Resonance assignments of cytochrome MtoD from the extracellular electron uptake pathway of sideroxydans lithotrophicus ES-1","authors":"Anaísa Coelho, José M. Silva, Francesca Cantini, Mario Piccioli, Ricardo O. Louro, Catarina M. Paquete","doi":"10.1007/s12104-024-10180-8","DOIUrl":"10.1007/s12104-024-10180-8","url":null,"abstract":"<div><p>The contribution of Fe(II)-oxidizing bacteria to iron cycling in freshwater, groundwater, and marine environments has been widely recognized in recent years. These organisms perform extracellular electron transfer (EET), which constitutes the foundations of bioelectrochemical systems for the production of biofuels and bioenergy. It was proposed that the Gram-negative bacterium <i>Sideroxydans lithotrophicus</i> ES-1 oxidizes soluble ferrous Fe(II) at the surface of the cell and performs EET through the Mto redox pathway. This pathway is composed by the periplasmic monoheme cytochrome MtoD that is proposed to bridge electron transfer between the cell exterior and the cytoplasm. This makes its functional and structural characterization, as well as evaluating the interaction process with its physiological partners, essential for understanding the mechanisms underlying EET. Here, we report the complete assignment of the heme proton and carbon signals together with a near-complete assignment of <sup>1</sup>H, <sup>13</sup>C and <sup>15</sup>N backbone and side chain resonances for the reduced, diamagnetic form of the protein. These data pave the way to identify and structurally map the molecular interaction regions between the cytochrome MtoD and its physiological redox partners, to explore the EET processes of <i>S. lithotrophicus</i> ES-1.</p></div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"18 2","pages":"139 - 146"},"PeriodicalIF":0.8,"publicationDate":"2024-06-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11511738/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141282649","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

NMR chemical shift assignment of Drosophila odorant binding protein 44a in complex with 8(Z)-eicosenoic acid 果蝇气味结合蛋白 44a 与 8(Z)-eicosenoic acid 复合物的核磁共振化学位移分配。

IF 0.8 4区生物学

Biomolecular NMR Assignments Pub Date : 2024-06-01 DOI: 10.1007/s12104-024-10178-2

Myriam L. Cotten, Mary R. Starich, Yi He, Jun Yin, Quan Yuan, Nico Tjandra

{"title":"NMR chemical shift assignment of Drosophila odorant binding protein 44a in complex with 8(Z)-eicosenoic acid","authors":"Myriam L. Cotten, Mary R. Starich, Yi He, Jun Yin, Quan Yuan, Nico Tjandra","doi":"10.1007/s12104-024-10178-2","DOIUrl":"10.1007/s12104-024-10178-2","url":null,"abstract":"<div><p>The odorant binding protein, OBP44a is one of the most abundant proteins expressed in the brain of the developing fruit fly <i>Drosophila melanogaster</i>. Its cellular function has not yet been determined. The OBP family of proteins is well established to recognize hydrophobic molecules. In this study, NMR is employed to structurally characterize OBP44a. NMR chemical shift perturbation measurements confirm that OBP44a binds to fatty acids. Complete assignments of the backbone chemical shifts and secondary chemical shift analysis demonstrate that the apo state of OBP44a is comprised of six α-helices. Upon binding 8(Z)-eicosenoic acid (8(Z)-C20:1), the OBP44a C-terminal region undergoes a conformational change, from unstructured to α-helical. In addition to C-terminal restructuring upon ligand binding, some hydrophobic residues show dramatic chemical shift changes. Surprisingly, several charged residues are also strongly affected by lipid binding. Some of these residues could represent key structural features that OBP44a relies on to perform its cellular function. The NMR chemical shift assignment is the first step towards characterizing the structure of OBP44a and how specific residues might play a role in lipid binding and release. This information will be important in deciphering the biological function of OBP44a during fly brain development.</p></div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"18 2","pages":"129 - 134"},"PeriodicalIF":0.8,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11511771/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141185868","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 and methyl side-chain resonance assignments of the single chain Fab fragment of trastuzumab 曲妥珠单抗单链 Fab 片段的骨架和甲基侧链共振分配。

IF 0.8 4区生物学

Biomolecular NMR Assignments Pub Date : 2024-05-08 DOI: 10.1007/s12104-024-10177-3

Donald Gagné, James M. Aramini, Yves Aubin

引用次数: 0

1H, 13C, and 15N resonance assignments of the La Motif of the human La-related protein 1 人类 La 相关蛋白 1 的 La Motif 的 1H、13C 和 15N 共振赋值

IF 0.8 4区生物学

Biomolecular NMR Assignments Pub Date : 2024-05-01 DOI: 10.1007/s12104-024-10176-4

Benjamin C. Smith, Robert Silvers

引用次数: 0

1H, 15N and 13C resonance backbone and side-chain assignments and secondary structure determination of the BRCT domain of Mtb LigA Mtb LigA 的 BRCT 结构域的 1H、15N 和 13C 共振骨架和侧链分配及二级结构确定

IF 0.8 4区生物学

Biomolecular NMR Assignments Pub Date : 2024-04-30 DOI: 10.1007/s12104-024-10175-5

Jayanti Vaishnav, Ravi Sankar Ampapathi

{"title":"1H, 15N and 13C resonance backbone and side-chain assignments and secondary structure determination of the BRCT domain of Mtb LigA","authors":"Jayanti Vaishnav, Ravi Sankar Ampapathi","doi":"10.1007/s12104-024-10175-5","DOIUrl":"10.1007/s12104-024-10175-5","url":null,"abstract":"<div><p>The BRCA1 carboxyl-terminal (BRCT) domain, an evolutionarily conserved structural motif, is ubiquitous in a multitude of proteins spanning prokaryotic and eukaryotic organisms. In <i>Mycobacterium tuberculosis</i> (<i>Mtb</i>), BRCT domain plays a pivotal role in the catalytic activity of the NAD+-dependent DNA ligase (LigA). LigA is pivotal in DNA replication, catalyzing the formation of phosphodiester bonds in Okazaki fragments and repairing single-strand breaks in damaged DNA, essential for the survival of <i>Mtb</i>. Structural and functional aspects of LigA unveil its character as a highly modular protein, undergoing substantial conformational changes during its catalytic cycle. Although the BRCT domain of <i>Mtb</i> LigA plays an essential role in DNA binding and protein–protein interactions, the precise mechanism of action remains poorly understood. Unravelling the structure of the BRCT domain holds the promise of advancing our understanding of this pivotal domain. Additionally, it will facilitate further exploration of the protein–protein interactions and enhance our understanding of inter domain interactions within LigA, specifically between BRCT and the Adenylation domain. In this study, we demonstrate the overexpression of the BRCT domain of <i>Mtb</i> LigA and conduct its analysis using solution NMR spectroscopy, revealing a well-folded structure and we present the nearly complete chemical shift assignments of both backbone and sidechains. In addition, a secondary structure prediction by TALOS N predicts BRCT consisting of 3 <i>α</i>-helices and 4 <i>β</i>-sheets, closely resembling the typical structural topology of most BRCT domains.</p></div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"18 1","pages":"105 - 109"},"PeriodicalIF":0.8,"publicationDate":"2024-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140840748","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 assignment of dsRBD1 and dsRBD2 of Arabidopsis thaliana DRB3, an essential protein involved in RNAi-mediated antiviral defense 拟南芥 DRB3 的 dsRBD1 和 dsRBD2 的化学位移分配，DRB3 是参与 RNAi 介导的抗病毒防御的重要蛋白质。

IF 0.8 4区生物学

Biomolecular NMR Assignments Pub Date : 2024-04-26 DOI: 10.1007/s12104-024-10174-6

Jaydeep Paul, Mandar V. Deshmukh

引用次数: 0

1H, 13C, and 15N backbone and methyl group resonance assignments of ricin toxin A subunit 蓖麻毒素 A 亚基的 1H、13C 和 15N 骨架和甲基共振赋值

IF 0.8 4区生物学

Biomolecular NMR Assignments Pub Date : 2024-04-20 DOI: 10.1007/s12104-024-10172-8

Shibani Bhattacharya, Tassadite Dahmane, Michael J. Goger, Michael J. Rudolph, Nilgun E. Tumer

{"title":"1H, 13C, and 15N backbone and methyl group resonance assignments of ricin toxin A subunit","authors":"Shibani Bhattacharya, Tassadite Dahmane, Michael J. Goger, Michael J. Rudolph, Nilgun E. Tumer","doi":"10.1007/s12104-024-10172-8","DOIUrl":"10.1007/s12104-024-10172-8","url":null,"abstract":"<div><p>Ricin is a potent plant toxin that targets the eukaryotic ribosome by depurinating an adenine from the sarcin-ricin loop (SRL), a highly conserved stem-loop of the rRNA. As a category-B agent for bioterrorism it is a prime target for therapeutic intervention with antibodies and enzyme blocking inhibitors since no effective therapy exists for ricin. Ricin toxin A subunit (RTA) depurinates the SRL by binding to the P-stalk proteins at a remote site. Stimulation of the <i>N</i>-glycosidase activity of RTA by the P-stalk proteins has been studied extensively by biochemical methods and by X-ray crystallography. The current understanding of RTA’s depurination mechanism relies exclusively on X-ray structures of the enzyme in the free state and complexed with transition state analogues. To date we have sparse evidence of conformational dynamics and allosteric regulation of RTA activity that can be exploited in the rational design of inhibitors. Thus, our primary goal here is to apply solution NMR techniques to probe the residue specific structural and dynamic coupling active in RTA as a prerequisite to understand the functional implications of an allosteric network. In this report we present <i>de novo</i> sequence specific amide and sidechain methyl chemical shift assignments of the 267 residue RTA in the free state and in complex with an 11-residue peptide (P11) representing the identical C-terminal sequence of the ribosomal P-stalk proteins. These assignments will facilitate future studies detailing the propagation of binding induced conformational changes in RTA complexed with inhibitors, antibodies, and biologically relevant targets.</p></div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"18 1","pages":"85 - 91"},"PeriodicalIF":0.8,"publicationDate":"2024-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s12104-024-10172-8.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140624141","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