Biomolecular NMR Assignments最新文献_第4页

1H, 15N, and 13C resonance assignment of human heat shock protein 10 人热休克蛋白的1H， 15N和13C共振分配

IF 0.6 4区生物学

Biomolecular NMR Assignments Pub Date : 2025-09-13 DOI: 10.1007/s12104-025-10247-0

Abigail Page, Wyatt Hendricks, Marielle A. Wälti

{"title":"1H, 15N, and 13C resonance assignment of human heat shock protein 10","authors":"Abigail Page, Wyatt Hendricks, Marielle A. Wälti","doi":"10.1007/s12104-025-10247-0","DOIUrl":"10.1007/s12104-025-10247-0","url":null,"abstract":"<div><p>The human chaperonin system, Hsp60/Hsp10, is essential for maintaining protein homeostasis and is found mainly in mitochondria. Hsp60 forms a bowl-shaped structure that provides an enclosed environment for protein folding, while its co-chaperone, Hsp10, acts as a cap to seal the barrel. This coordinated process is crucial for the proper folding of many unfolded or misfolded proteins, making the Hsp60/Hsp10 complex an indispensable chaperone system. Changes in their expression levels have been linked to diseases such as neurodegenerative disorders and cancer. Although Hsp60 has gained increasing attention, its co-chaperone Hsp10 remains relatively underexplored and has often been assumed to play a passive role. However, emerging studies challenge this view, suggesting that Hsp10 alone may exert regulatory functions within the chaperonin cycle. Here, we present the near-complete NMR backbone assignment of the 102-residue human Hsp10, laying the groundwork for future investigations into its structure, interactions, and roles in facilitating protein folding and preventing aggregation.</p></div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"19 2","pages":"287 - 292"},"PeriodicalIF":0.6,"publicationDate":"2025-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s12104-025-10247-0.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145051580","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 RNA binding motif 39 (RBM39) tandem RNA recognition motifs (RRM1−2) RNA结合基序39 （RBM39）串联RNA识别基序（RRM1-2）的1H， 13C和15N骨干共振分配。

IF 0.6 4区生物学

Biomolecular NMR Assignments Pub Date : 2025-09-13 DOI: 10.1007/s12104-025-10248-z

Florian Malard, Léa Bouton, Sébastien Campagne

引用次数: 0

Resonance assignments of asymmetric tetrameric platelet factor 4 (PF4) 不对称四聚体血小板因子4 （PF4）的共振赋值。

IF 0.6 4区生物学

Biomolecular NMR Assignments Pub Date : 2025-09-08 DOI: 10.1007/s12104-025-10246-1

Qiulin Ma, Jinfeng Huang, Stephen Boulton, Ellen Mak, Madoka Akimoto, Estefanía López Giraldo, Mikayla Truong, Mercy Daka, Angela Huynh, Sarah Kwok, Rumi Clare, Ishac Nazy, Woonghee Lee, Giuseppe Melacini

{"title":"Resonance assignments of asymmetric tetrameric platelet factor 4 (PF4)","authors":"Qiulin Ma, Jinfeng Huang, Stephen Boulton, Ellen Mak, Madoka Akimoto, Estefanía López Giraldo, Mikayla Truong, Mercy Daka, Angela Huynh, Sarah Kwok, Rumi Clare, Ishac Nazy, Woonghee Lee, Giuseppe Melacini","doi":"10.1007/s12104-025-10246-1","DOIUrl":"10.1007/s12104-025-10246-1","url":null,"abstract":"<div><p>Platelet Factor 4 (PF4), also known as CXCL4, is a CXC chemokine crucial for hemostasis, inflammation, and immune responses. Under physiological conditions PF4 assembles into asymmetric tetramers (31.2 kDa) that are dimers of dimers with highly flexible N-terminal regions. PF4 tetramers play a central role in prothrombotic autoimmune conditions, such as heparin-induced thrombocytopenia (HIT), as well as vaccine-induced immune thrombocytopenia and thrombosis (VITT). Here, we report the resonance assignments of <sup>1</sup>H, <sup>15</sup>N, and <sup>13</sup>C nuclei for wild-type asymmetric PF4 tetramers using TROSY-based triple resonance NMR experiments. We also used N<sub>z</sub>-exchange spectroscopy to identify peaks split by slow-exchange between two distinct conformational states caused by the asymmetry of PF4 tetramers. Our NMR assignments establish a foundation for future investigations into the structural dynamics and functional mechanisms of PF4 as well as its pathological role in anti-PF4 disorders.</p></div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"19 2","pages":"281 - 286"},"PeriodicalIF":0.6,"publicationDate":"2025-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145022595","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 assignments of flap endonuclease from Plasmodium falciparum 恶性疟原虫皮瓣内切酶的1H， 15N和13C骨干共振定位。

IF 0.6 4区生物学

Biomolecular NMR Assignments Pub Date : 2025-08-09 DOI: 10.1007/s12104-025-10241-6

Rodolpho do Aido-Machado, Nicola J. Baxter, Michelle L. Rowe, Manoj B. Pohare, Srdjan Vitovski, Jon R. Sayers, Jonathan P. Waltho

{"title":"1H, 15N and 13C backbone resonance assignments of flap endonuclease from Plasmodium falciparum","authors":"Rodolpho do Aido-Machado, Nicola J. Baxter, Michelle L. Rowe, Manoj B. Pohare, Srdjan Vitovski, Jon R. Sayers, Jonathan P. Waltho","doi":"10.1007/s12104-025-10241-6","DOIUrl":"10.1007/s12104-025-10241-6","url":null,"abstract":"<div><p>Flap endonuclease (FEN) enzymes are a group of metallonucleases that have essential roles in DNA repair and the maintenance of genomic resilience. They catalyse hydrolytic cleavage of a phosphodiester bond to remove 5′-flaps present on double-stranded DNA molecules formed during DNA replication. FEN locates a target scissile bond through the structural recognition of a pronounced bend in the double-stranded DNA substrate along with the presence of both a 5′-flap and a 1-nucleotide 3′-flap. FEN enzymes share a common structural architecture and are functionally conserved across all living organisms. In this work, we report the <sup>1</sup>H, <sup>15</sup>N and <sup>13</sup>C backbone resonance assignments of residues 2–349 of FEN from <i>Plasmodium falciparum</i> (<i>Pf</i>FEN349) in its substrate-free state. Using heteronuclear multidimensional NMR spectroscopy, 90% of all backbone resonances of <i>Pf</i>FEN349 were assigned, with 298 backbone amide resonances out of 337 theoretically-detectible resonances (which exclude 10 prolines and the N-terminal glycine) identified in the <sup>1</sup>H–<sup>15</sup> N TROSY spectrum. Prediction of solution secondary structure content from a chemical shift analysis using the TALOS-N webserver is mostly in good agreement with an AlphaFold model of <i>Pf</i>FEN349. The reported assignments provide a pathway for drug discovery as <i>Pf</i>FEN349 is a potential target for the development of new inhibitors that could be utilised to control the incidence of malaria across the globe.</p></div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"19 2","pages":"235 - 243"},"PeriodicalIF":0.6,"publicationDate":"2025-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s12104-025-10241-6.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144803192","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 chemical shift assignment for stem-loop 5a from the 5‘UTR of HCoV-229E 从HCoV-229E的5'UTR中，茎环5a的1H， 13C和15N化学位移分配。

IF 0.6 4区生物学

Biomolecular NMR Assignments Pub Date : 2025-07-31 DOI: 10.1007/s12104-025-10243-4

Nina M. Krause, Anna Wacker, Christian Richter, Boris Fürtig, Ramakanth Madhugiri, John Ziebuhr, Harald Schwalbe

{"title":"1H, 13C and 15N chemical shift assignment for stem-loop 5a from the 5‘UTR of HCoV-229E","authors":"Nina M. Krause, Anna Wacker, Christian Richter, Boris Fürtig, Ramakanth Madhugiri, John Ziebuhr, Harald Schwalbe","doi":"10.1007/s12104-025-10243-4","DOIUrl":"10.1007/s12104-025-10243-4","url":null,"abstract":"<div><p>Due to the emergence of the SARS-CoV-2 virus, research on coronaviruses has been massively accelerated. In addition to SARS-CoV-2, there are other human coronaviruses, including HCoV-229E. In all coronaviruses, secondary structure predictions indicate the presence of conserved structural elements in the 5’-untranslated region (5’-UTR). These conserved elements play crucial roles in RNA translation and replication. Stem-loop 5 (SL5), consisting of three substructures (5a, 5b, 5c), is highly conserved and harbours the start codon for translation. SL5 has repetitive structural motifs (RSMs), 5’-UUYYGU-3’, which are conserved in many alpha- and betacoronaviruses. In the following, we present the <sup>1</sup>H, <sup>13</sup>C and <sup>15</sup>N NMR resonance assignment of the SL5a RNA element from HCoV-229E and variations in the RSMs to show the effect of loop mutations on the structure of the hexaloop, revealing the different impact of each loop nucleotide on RNA dynamics.</p></div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"19 2","pages":"255 - 265"},"PeriodicalIF":0.6,"publicationDate":"2025-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s12104-025-10243-4.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144751962","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 NMR assignments of the essential oxidoreductase tryparedoxin from the human pathogenic parasite Trypanosoma cruzi 人类致病性克氏锥虫必需氧化还原酶tryparedoxin的核磁共振骨架分配。

IF 0.6 4区生物学

Biomolecular NMR Assignments Pub Date : 2025-07-28 DOI: 10.1007/s12104-025-10244-3

Eric Schwegler, Ute A. Hellmich

{"title":"Backbone NMR assignments of the essential oxidoreductase tryparedoxin from the human pathogenic parasite Trypanosoma cruzi","authors":"Eric Schwegler, Ute A. Hellmich","doi":"10.1007/s12104-025-10244-3","DOIUrl":"10.1007/s12104-025-10244-3","url":null,"abstract":"<div><p>Over 7 million people worldwide are affected with Chagas disease, a lifelong debilitating and potentially fatal Neglected Tropical Disease caused by the single cell protozoan parasite <i>Trypanosoma cruzi</i>. To maintain viability and to reproduce under the harsh conditions within a host organism, pathogens express a variety of protecting enzymes and virulence factors that can serve as potential drug targets. To protect itself from redox stress, <i>T. cruzi</i> takes advantage of a unique thiol metabolism. For instance, a cytosolic peroxide clearance cascade is centered on the conserved oxidoreductase Tryparedoxin (Tpx). Tpx efficiently distributes reducing equivalents across the parasitic cell through the promiscuous yet selective binding of numerous up- and downstream clients. However, the exact structure and binding interfaces of this central protein binding hub remain unknown. To study the redox-dependent structural dynamics of <i>T. cruzi</i> Tpx, and its interactions with binding partners, we determined the <sup>1</sup>H, <sup>13</sup>C, <sup>15</sup>N-backbone NMR assignments of the enzyme in the reduced and oxidized state. In agreement with earlier NMR studies on Tpx from related protozoans, we report redox-dependent changes in the enzyme’s dithiol active site that could play a crucial role in the recognition of physiological substrates and should be considered in the rational design of small molecule inhibitors.</p></div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"19 2","pages":"267 - 273"},"PeriodicalIF":0.6,"publicationDate":"2025-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s12104-025-10244-3.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144726342","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, 15N backbone chemical shift assignment of P18ink4c from Danio rerio (zebrafish) using solution-state NMR spectroscopy 利用溶液态核磁共振光谱分析斑马鱼P18ink4c的1H， 13C， 15N主链化学位移。

IF 0.6 4区生物学

Biomolecular NMR Assignments Pub Date : 2025-07-28 DOI: 10.1007/s12104-025-10245-2

Aakriti Sethi, Pierre de Cordovez, Biswaranjan Mohanty, Vanessa K. Morris, Christoph Göbl

引用次数: 0

Backbone assignment of a 28.5 kDa class A extended spectrum β-lactamase by high-field, carbon-detected solid-state NMR 一个28.5 kDa的a类扩展光谱β-内酰胺酶的高场碳检测固体核磁共振骨架分配。

IF 0.6 4区生物学

Biomolecular NMR Assignments Pub Date : 2025-07-27 DOI: 10.1007/s12104-025-10242-5

Christopher G. Williams, Songlin Wang, Alexander F. Thome, Owen A. Warmuth, Varun Sakhrani, Leighton Coates, Chad M. Rienstra, Leonard J. Mueller

引用次数: 0

NMR chemical shift assignment of UEV domain of ubiquitin-conjugating enzyme E2 variant 3 lactate dehydrogenase (UEVLD) 泛素偶联酶E2变体3乳酸脱氢酶（UEVLD） UEV结构域的NMR化学位移赋值。

IF 0.6 4区生物学

Biomolecular NMR Assignments Pub Date : 2025-06-26 DOI: 10.1007/s12104-025-10240-7

Jose G. Vazquez, David A. Nyenhuis, Marie-Paule Strub, Nico Tjandra

{"title":"NMR chemical shift assignment of UEV domain of ubiquitin-conjugating enzyme E2 variant 3 lactate dehydrogenase (UEVLD)","authors":"Jose G. Vazquez, David A. Nyenhuis, Marie-Paule Strub, Nico Tjandra","doi":"10.1007/s12104-025-10240-7","DOIUrl":"10.1007/s12104-025-10240-7","url":null,"abstract":"<div><p>UEV domains are catalytically dead variants of the E2 enzymes which play an intermediate role in ubiquitin signaling. UEV domain containing proteins, like the ESCRT-I factor Tsg101 often play critical roles in trafficking of ubiquitylated cargos or in modulating ubiquitin processivity, or in determining the type of signal that is transferred to a target protein. Ubiquitin-conjugating enzyme E2 variant (UEV) and lactate/malate dehydrogenase (UEVLD), also known as UEV3, is a human paralogue of Tsg101 with apparent associations to cancer, innate immunity, NF-κB signaling, and autophagy. It contains an N-terminal UEV domain with 56% identity to that of Tsg101 and a C-terminal lactate dehydrogenase domain. Here, we show the backbone assignments of the UEV domain from UEVLD and find that its Cα shifts are consistent with a UEV domain composition. Further experiments suggest that it may have regions corresponding to the known binding pockets of Tsg101, but further structural and functional work will be required to uncover critical determinants of UEV domain function, and the role of these domains in Ubiquitin signaling as a whole.</p></div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"19 2","pages":"227 - 233"},"PeriodicalIF":0.6,"publicationDate":"2025-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s12104-025-10240-7.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144504408","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

Resonance assignment of the intrinsically disordered actin-binding region of Drebrin 德雷布林内在无序动作蛋白结合区的共振分配。

IF 0.6 4区生物学

Biomolecular NMR Assignments Pub Date : 2025-06-14 DOI: 10.1007/s12104-025-10239-0

Soma Varga, Julie Maibøll Kaasen, Zoltán Gáspári, Bálint Ferenc Péterfia, Frans A. A. Mulder

{"title":"Resonance assignment of the intrinsically disordered actin-binding region of Drebrin","authors":"Soma Varga, Julie Maibøll Kaasen, Zoltán Gáspári, Bálint Ferenc Péterfia, Frans A. A. Mulder","doi":"10.1007/s12104-025-10239-0","DOIUrl":"10.1007/s12104-025-10239-0","url":null,"abstract":"<div><p>Drebrin (developmentally regulated brain protein) is a vital component of the Postsynaptic Density (PSD). It performs important biological roles as it interacts with the postsynaptic protein Homer and anchors the complete protein network to the cellular skeleton through actin filaments. Drebrin contains unique structural elements including an evolutionarily unconventional actin-depolymerizing factor homology (ADFH) domain that has lost its strong actin-binding ability, and a Single Alpha-Helix (SAH) motif harbored by long flexible regions. In vivo studies have suggested that a disordered segment in Drebrin plays a key role in binding filamentous actin, yet the atomic-level characterization of the binding interface between these proteins has not been reported. To bridge this gap, we designed the intrinsically disordered construct D233 and employed 3D (HN)CO(CO)NH NMR spectroscopy to accomplish a near-complete backbone resonance assignment. This work serves as an essential step toward a detailed structural and functional investigation of the interaction between Drebrin and F-Actin.</p></div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"19 2","pages":"221 - 225"},"PeriodicalIF":0.6,"publicationDate":"2025-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s12104-025-10239-0.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144293164","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