Biomolecular NMR Assignments最新文献_第4页

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

Solution NMR chemical shift assignment of apo and molybdate-bound ModA at two pHs 溶液核磁共振化学位移在两种 pH 值下的蛋白结合型和钼酸结合型 ModA 的分配

IF 0.8 4区生物学

Biomolecular NMR Assignments Pub Date : 2024-04-20 DOI: 10.1007/s12104-024-10173-7

Hiep LD Nguyen, Karin A. Crowhurst

{"title":"Solution NMR chemical shift assignment of apo and molybdate-bound ModA at two pHs","authors":"Hiep LD Nguyen, Karin A. Crowhurst","doi":"10.1007/s12104-024-10173-7","DOIUrl":"10.1007/s12104-024-10173-7","url":null,"abstract":"<div><p>ModA is a soluble periplasmic molybdate-binding protein found in most gram-negative bacteria. It is part of the ABC transporter complex ModABC that moves molybdenum into the cytoplasm, to be used by enzymes that carry out various redox reactions. Since there is no clear analog for ModA in humans, this protein could be a good target for antibacterial drug design. Backbone <sup>1</sup>H, <sup>13</sup>C and <sup>15</sup>N chemical shifts of apo and molybdate-bound ModA from <i>E. coli</i> were assigned at pHs 6.0 and 4.5. In addition, side chain atoms were assigned for apo ModA at pH 6.0. When comparing apo and molybdate-bound ModA at pH 6.0, large chemical shift perturbations are observed, not only in areas near the bound metal, but also in regions that are distant from the metal-binding site. Given the significant conformational change between apo and holo ModA, we might expect the large chemical shift changes to be more widespread; however, since they are limited to specific regions, the residues with large perturbations may reveal allosteric sites that could ultimately be important for the design of antibiotics that target ModA.</p></div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"18 1","pages":"93 - 98"},"PeriodicalIF":0.8,"publicationDate":"2024-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140624175","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

Backbone chemical shift and secondary structure assignments for mouse siderocalin 小鼠苷酸骨干化学位移和二级结构分配。

IF 0.8 4区生物学

Biomolecular NMR Assignments Pub Date : 2024-04-02 DOI: 10.1007/s12104-024-10171-9

Johanna Moeller, Nina G. Bozhanova, Markus Voehler, Jens Meiler, Clara T. Schoeder

{"title":"Backbone chemical shift and secondary structure assignments for mouse siderocalin","authors":"Johanna Moeller, Nina G. Bozhanova, Markus Voehler, Jens Meiler, Clara T. Schoeder","doi":"10.1007/s12104-024-10171-9","DOIUrl":"10.1007/s12104-024-10171-9","url":null,"abstract":"<div><p>\u0000 The lipocalin protein family is a structurally conserved group of proteins with a variety of biological functions defined by their ability to bind small molecule ligands and interact with partner proteins. One member of this family is siderocalin, a protein found in mammals. Its role is discussed in inflammatory processes, iron trafficking, protection against bacterial infections and oxidative stress, cell migration, induction of apoptosis, and cancer. Though it seems to be involved in numerous essential pathways, the exact mechanisms are often not fully understood. The NMR backbone assignments for the human siderocalin and its rat ortholog have been published before. In this work we describe the backbone NMR assignments of siderocalin for another important model organism, the mouse - data that might become important for structure-based drug discovery. Secondary structure elements were predicted based on the assigned backbone chemical shifts using TALOS-N and CSI 3.0, revealing a high content of beta strands and one prominent alpha helical region. Our findings correlate well with the known crystal structure and the overall conserved fold of the lipocalin family.</p></div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"18 1","pages":"79 - 84"},"PeriodicalIF":0.8,"publicationDate":"2024-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11081974/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140334185","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 resonance assignments and solution structure of the N-terminal divergent calponin homology (NN-CH) domain of human intraflagellar transport protein 54 人类鞘内转运蛋白 54 的 N 端分歧钙蛋白同源结构域（NN-CH）的 1H、13C 和 15N 共振赋值及溶液结构。

IF 0.8 4区生物学

Biomolecular NMR Assignments Pub Date : 2024-03-29 DOI: 10.1007/s12104-024-10170-w

Kanako Kuwasako, Weirong Dang, Fahu He, Mari Takahashi, Kengo Tsuda, Takashi Nagata, Akiko Tanaka, Naohiro Kobayashi, Takanori Kigawa, Peter Güntert, Mikako Shirouzu, Shigeyuki Yokoyama, Yutaka Muto

{"title":"1H, 13C, and 15N resonance assignments and solution structure of the N-terminal divergent calponin homology (NN-CH) domain of human intraflagellar transport protein 54","authors":"Kanako Kuwasako, Weirong Dang, Fahu He, Mari Takahashi, Kengo Tsuda, Takashi Nagata, Akiko Tanaka, Naohiro Kobayashi, Takanori Kigawa, Peter Güntert, Mikako Shirouzu, Shigeyuki Yokoyama, Yutaka Muto","doi":"10.1007/s12104-024-10170-w","DOIUrl":"10.1007/s12104-024-10170-w","url":null,"abstract":"<div><p>The intraflagellar transport (IFT) machinery plays a crucial role in the bidirectional trafficking of components necessary for ciliary signaling, such as the Hedgehog, Wnt/PCR, and cAMP/PKA systems. Defects in some components of the IFT machinery cause dysfunction, leading to a wide range of human diseases and developmental disorders termed ciliopathies, such as nephronophthisis. The IFT machinery comprises three sub-complexes: BBsome, IFT-A, and IFT-B. The IFT protein 54 (IFT54) is an important component of the IFT-B sub-complex. In anterograde movement, IFT54 binds to active kinesin-II, walking along the cilia microtubule axoneme and carrying the dynein-2 complex in an inactive state, which works for retrograde movement. Several mutations in IFT54 are known to cause Senior-Loken syndrome, a ciliopathy. IFT54 possesses a divergent Calponin Homology (CH) domain termed as NN-CH domain at its N-terminus. However, several aspects of the function of the NN-CH domain of IFT54 are still obscure. Here, we report the <sup>1</sup>H, <sup>15</sup>N, and <sup>13</sup>C resonance assignments of the NN-CH domain of human IFT54 and its solution structure. The NN-CH domain of human IFT54 adopts essentially the α1–α2–α3–α4–α5 topology as that of mouse IFT54, whose structure was determined by X-ray crystallographic study. The structural information and assignments obtained in this study shed light on the molecular function of the NN-CH domain in IFT54.</p></div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"18 1","pages":"71 - 78"},"PeriodicalIF":0.8,"publicationDate":"2024-03-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140326214","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 and side-chain resonance assignments of the human oncogenic protein NCYM 人类致癌蛋白 NCYM 的 1H、13C 和 15N 主干和侧链共振分配。

IF 0.8 4区生物学

Biomolecular NMR Assignments Pub Date : 2024-03-25 DOI: 10.1007/s12104-024-10169-3

Assia Mouhand, Kazuma Nakatani, Fumiaki Kono, Yoshitaka Hippo, Tatsuhito Matsuo, Philippe Barthe, Judith Peters, Yusuke Suenaga, Taro Tamada, Christian Roumestand

{"title":"1H, 13C and 15N backbone and side-chain resonance assignments of the human oncogenic protein NCYM","authors":"Assia Mouhand, Kazuma Nakatani, Fumiaki Kono, Yoshitaka Hippo, Tatsuhito Matsuo, Philippe Barthe, Judith Peters, Yusuke Suenaga, Taro Tamada, Christian Roumestand","doi":"10.1007/s12104-024-10169-3","DOIUrl":"10.1007/s12104-024-10169-3","url":null,"abstract":"<div><p>NCYM is a cis-antisense gene of MYCN oncogene and encodes an oncogenic protein that stabilizes MYCN via inhibition of GSK3b. High NCYM expression levels are associated with poor clinical outcomes in human neuroblastomas, and NCYM overexpression promotes distant metastasis in animal models of neuroblastoma. Using vacuum-ultraviolet circular dichroism and small-angle X-ray scattering, we previously showed that NCYM has high flexibility with partially folded structures; however, further structural characterization is required for the design of anti-cancer agents targeting NCYM. Here we report the <sup>1</sup>H, <sup>15</sup>N and <sup>13</sup>C nuclear magnetic resonance assignments of NCYM. Secondary structure prediction using Secondary Chemical Shifts and TALOS-N analysis demonstrates that the structure of NCYM is essentially disordered, even though residues in the central region of the peptide clearly present a propensity to adopt a dynamic helical structure. This preliminary study provides foundations for further analysis of interaction between NCYM and potential partners.</p></div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"18 1","pages":"65 - 70"},"PeriodicalIF":0.8,"publicationDate":"2024-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140287898","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