Biomolecular NMR Assignments最新文献

{"title":"1HN, 13C, and 15N resonance assignments of Ca2+-calmodulin bound to a BP2 peptide derived from the sheep STRA6 vitamin A transporter (residues 625–656)","authors":"Mary E. Cook,&nbsp;Kristen M. Varney,&nbsp;Xinhao Zhuang,&nbsp;Aysenur Torun Yazici,&nbsp;Filippo Mancia,&nbsp;David J. Weber","doi":"10.1007/s12104-025-10258-x","DOIUrl":"10.1007/s12104-025-10258-x","url":null,"abstract":"<div><p>Vitamin A is essential for vision and many other biological processes required for human health and survival. Extracellular retinol binding protein (RBP) delivers vitamin A into the cell upon binding to the vitamin A transporter, STRA6. However, when retinol free RBP binds to STRA6, it induces vitamin A transport out of the cell. The bi-directionality of vitamin A transport is thought to be regulated further by an intracellular protein-protein interaction (PPI) between STRA6 and the EF-hand Ca²⁺-binding protein, calmodulin (CaM). Insights regarding how CaM regulates vitamin A transport were originally provided at atomic resolution by a cryoEM structure of the zebrafish STRA6-CaM complex. This cryoEM structure, together with NMR studies, confirmed that three STRA6 helices (i.e., BP0, BP1, and BP2) comprised the CaM-STRA6 binding interface, with BP2 providing the major set of interactions. NMR and other biophysical methods demonstrated that zebrafish BP2 peptide (zfBP2) binding to CaM involved a Ca²⁺-dependent type 2 binding and functional folding mechanism of action, which could influence structural, dynamic, and allosteric functions of STRA6. To expand our understanding of vitamin A transport to a mammalian STRA6 transporter, the backbone and sidechain ¹H^N, ¹³C, and ¹⁵N resonances were assigned here for ^CaCaM (148 residues) when bound to a sheep BP2 peptide (32 residues) (shBP2). Interestingly, the NMR data showed ^CaCaM resonances were affected differently upon binding shBP2 versus zfBP2. Such differences may be useful for distinguishing important features regarding ^CaCaM complexes with mammalian versus zebrafish STRA6.</p></div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"20 1","pages":""},"PeriodicalIF":0.6,"publicationDate":"2025-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s12104-025-10258-x.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145778589","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}

{"title":"Backbone NMR resonance assignments for the C2 domain of the Streptococcus mutans adhesin P1","authors":"Emily-Qingqing Peng,&nbsp;M. Luiza Caldas Nogueira,&nbsp;Chase Norton,&nbsp;L. Jeannine Brady,&nbsp;Joanna R. Long","doi":"10.1007/s12104-025-10251-4","DOIUrl":"10.1007/s12104-025-10251-4","url":null,"abstract":"<div><p>Adhesin P1 (aka AgI/II) is an extracellular protein regulating adherence and detachment of <i>Streptococcus mutans</i> in the oral cavity and thus plays a pivotal role in biofilm development and maturation. P1’s naturally occurring C-terminal truncation product, Antigen II (AgII), adopts both soluble, monomeric and insoluble, amyloidogenic forms during the bacterial life cycle. Monomeric AgII forms important quaternary interactions with P1’s A3VP1 segment that is projected from the bacterial cell surface to promote cell adhesion, while the functional amyloid form of AgII promotes detachment of mature biofilms. The heterologous recombinant 51-kD C123 construct, comprising most of AgII, has been characterized by X-ray crystallography and serves as a functional surrogate of AgII in studies of adhesion and biofilm regulation. C123 contains three structurally similar domains, C1, C2, and C3. Using Alphafold prediction and the C123 crystal structure, we identified domain boundaries within C123 to develop more tractable constructs for NMR studies, including quaternary interactions with other proteins. The C2 domain is of particular interest because it contains several unique helices in addition to the β-sheet fold it shares with the C1 and C3 domains. Here we report the backbone NMR resonance assignments for the C2 construct. Secondary structure predictions from NMR assignments are in good agreement with those anticipated by Alphafold and the observed crystal structure, except for some of the helices suggesting they are more dynamic. We then compare C2 chemical shift perturbations caused by quaternary interactions with recombinant A3VP1, as well as by a monoclonal antibody, MAb 6–8C, known to inhibit bacterial adherence and C123 binding to A3VP1. We note the C2 chemical shift perturbations are markedly different from previously observed interactions of C3 with A3VP1 and MAb 6–8C, providing further insight on how the individual domains of C123 may vary in their ability to mediate bacterial adhesion and formation of functional amyloid. The prior NMR assignment and characterization of C3 combined with the NMR assignment and characterization of C2 described here provide a foundation for further NMR studies, including assignment of C23 and C123 constructs, protein-protein interaction studies of C23 and C123, assessing the impact of environmental conditions on structure and dynamics within C123 as it transitions from monomer to amyloid form, and the functional relevance of having three successive domains with similar tertiary folds.</p></div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"20 1","pages":""},"PeriodicalIF":0.6,"publicationDate":"2025-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12701859/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145740205","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}

{"title":"1H, 13C, and 15N resonance assignments and solution structure of the CID domain of SR-related- and CTD-associated factor 8 (SCAF8)","authors":"Weirong Dang,&nbsp;Yutaka Muto,&nbsp;Fahu He,&nbsp;Mari Takahashi,&nbsp;Kengo Tsuda,&nbsp;Takashi Nagata,&nbsp;Akiko Tanaka,&nbsp;Naohiro Kobayashi,&nbsp;Takanori Kigawa,&nbsp;Peter Güntert,&nbsp;Mikako Shirouzu,&nbsp;Shigeyuki Yokoyama,&nbsp;Kanako Kuwasako","doi":"10.1007/s12104-025-10252-3","DOIUrl":"10.1007/s12104-025-10252-3","url":null,"abstract":"<div><p>Transcription mediated by RNA polymerase II (RNAPII) involves multiple stages, including initiation, promoter-proximal pausing for capping, elongation, and termination. The C-terminal domain of RNAPII (CTD) contains repetitions of the heptad consensus sequence, such as Y₁S₂P₃T₄S₅P₆S₇ with some variety, and the phosphorylated positions in the heptad sequences are altered according to the transcriptional stages. The interaction between several regulatory protein factors and the phosphorylated heptad sequence plays an important role in the accurate progress of transcription. A subset of these regulatory proteins possesses a CTD-interacting domain (CID) that specifically recognizes the phosphorylated CTD and mediates stage-specific transcriptional control. Among them, SCAF8 (RBM16), which also contains a CID, plays a key role in accurate transcriptional termination in conjunction with its paralog SCAF4. Despite their importance, the precise molecular mechanisms through which SCAF8 and SCAF4 coordinate transcriptional termination via their CID domains remain poorly understood. In this study, we report the ¹H, ¹⁵N, and ¹³C NMR resonance assignments and solution structure of the human SCAF8 CID domain. The structure exhibits an α1–α2–α3–α4–α5–α6–α7–α8 helical topology, consistent with the previously determined crystal structure. These assignments provide a valuable foundation for understanding how SCAF8 interacts with the RNAPII CTD and contributes to transcriptional elongation and termination.</p></div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"20 1","pages":""},"PeriodicalIF":0.6,"publicationDate":"2025-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145706897","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}

{"title":"NMR assignments of the human homodimeric mitochondrial ATP synthase inhibitor IF1","authors":"Julia Jerolamon,&nbsp;Nathan N. Alder,&nbsp;Andrei T. Alexandrescu","doi":"10.1007/s12104-025-10257-y","DOIUrl":"10.1007/s12104-025-10257-y","url":null,"abstract":"<div><p>ATPase inhibitory factor 1 (IF1) is the only known endogenous, proteinaceous inhibitor of mitochondrial ATP synthase in mammals. The inhibitor forms an antiparallel coiled-coil, which binds ATP synthase through an N-terminal α-helix extension that is disordered in the free protein. Because the IF1 dimer affects mitochondrial bioenergetics through its modulation of ATP synthase, it is a therapeutic target for cancer and cardiac disease. Here, we report ¹H, ¹³C and ¹⁵N NMR assignments for the mature dimeric form of human IF1. Secondary structure analyses based on chemical shifts and short-range NOE patterns indicate the N-terminal half of the 81-residue IF1 is intrinsically disordered, while the C-terminal half adopts a continuous α-helix. The chemical shift assignments for human IF1 provide a foundation for future mechanistic structure-function studies and NMR-based drug screening.</p></div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"20 1","pages":""},"PeriodicalIF":0.6,"publicationDate":"2025-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145612962","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}

{"title":"1H, 13C and 15N backbone resonance assignment of the lytic polysaccharide monooxygenase LsAA9A from Lentinus similis","authors":"Piera Wiesinger,&nbsp;Mats Sandgren,&nbsp;Gustav Nestor","doi":"10.1007/s12104-025-10256-z","DOIUrl":"10.1007/s12104-025-10256-z","url":null,"abstract":"<div><p>Lytic polysaccharide monooxygenases (LPMOs) are mono-copper binding enzymes involved in the degradation of carbohydrates. The 25 kDa sized LPMO <i>Ls</i>AA9A from the basidiomycete <i>Lentinus similis</i> is known to oxidate cellulose and cellooligomers at the C4 position and thus leading to a breakage of the glycosidic bond. <i>Ls</i>AA9A has been recombinantly expressed in <i>Escherichia coli</i> with ¹³C and ¹⁵N labelling. Here, we present the ¹H, ¹³C and ¹⁵N backbone resonance assignment of the <i>apo</i> form. The secondary structure was predicted using the TALOS-N software and it was overall in agreement with the crystal structure of <i>Ls</i>AA9A expressed in <i>E. coli</i>. A few shorter α-helices and β-sheets present in the crystal structure are missing in the NMR prediction and vice versa. <i>Ls</i>AA9A resembles the typical structural elements of LPMOs with a core β-sandwich.</p></div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"20 1","pages":""},"PeriodicalIF":0.6,"publicationDate":"2025-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s12104-025-10256-z.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145595409","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}

{"title":"Sequential backbone chemical shift assignments of a cancer-associated isoform of the HBx protein from human hepatitis B virus","authors":"Alexis Clavier,&nbsp;Toshinobu Shida,&nbsp;Maxim A. Droemer,&nbsp;Julian Holzinger,&nbsp;Anne K. Schütz","doi":"10.1007/s12104-025-10255-0","DOIUrl":"10.1007/s12104-025-10255-0","url":null,"abstract":"<div>\u0000 \u0000 <p>Chronic infections with hepatitis B virus (HBV) are a leading cause of liver cirrhosis and hepatocellular carcinoma worldwide. Among the four viral proteins encoded by HBV, the X protein (HBx) has remained resistant to atomic-level characterization. HBx is a small, non-structural protein that interacts with various human host proteins. It is essential for HBV replication and implicated in HBV-induced carcinogenesis. Here, we present the sequential backbone resonance assignments of a C-terminally truncated HBx isoform (residues 1–120), which is frequently found in chronically infected patients. Three-dimensional NMR experiments were recorded in the presence of residual urea (1 M), and the assignments of amide moieties were subsequently transferred to a low-urea condition (&lt; 0.2 M) compatible with HBx interaction studies. We compare manual assignments with automated predictions using the ARTINA software. These results reveal secondary structure propensities in the truncated HBx isoform and lay the groundwork for future NMR-based studies of HBx interactions in solution.</p>\u0000 </div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"20 1","pages":""},"PeriodicalIF":0.6,"publicationDate":"2025-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s12104-025-10255-0.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145456383","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}

{"title":"Backbone and Methyl resonance assignment of an active PETase","authors":"Jelena Grga,&nbsp;Emmanuelle Boll,&nbsp;Guy Lippens,&nbsp;Cyril Charlier","doi":"10.1007/s12104-025-10250-5","DOIUrl":"10.1007/s12104-025-10250-5","url":null,"abstract":"<div><p>LCC^ICCG, a bioengineered variant of a cutinase called LCC (Leaf-branch Compost Cutinase), is a high-performance, industrial-grade enzyme capable of efficiently degrading polyethylene terephthalate (PET). This engineered enzyme exhibits significantly enhanced thermal stability and PET hydrolysis activity compared to its predecessor and competing PETases. Here, we report the comprehensive resonance assignment of the polypeptide backbone and the side chain methyl groups of the active LCC^ICCG. Taking advantage of its exceptional thermostability all the experiments were conducted at 60 °C on a single, uniformly ¹⁵N-¹³C-labeled sample of this 27 kDa serine-hydrolase enzyme. LCC^ICCG represents a leap forward in enzymatic PET recycling, combining speed, efficiency, and scalability. The residue-specific information through both backbone and methyl side chain assignment represents a critical step toward detailed structural and dynamic NMR analyses.</p></div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"20 1","pages":""},"PeriodicalIF":0.6,"publicationDate":"2025-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145435782","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}

{"title":"1H, 13C, and 15N backbone resonance assignments of full-length and a SIM-SEP-containing fragment (101–266) of p47, a p97 adaptor protein","authors":"Rajivan Raseekan,&nbsp;Megan K. Black,&nbsp;Rui Huang","doi":"10.1007/s12104-025-10254-1","DOIUrl":"10.1007/s12104-025-10254-1","url":null,"abstract":"<div><p>p47/NSFL1C is a key adaptor protein of p97/VCP, a AAA+ ATPase that is involved in a diverse array of cellular functions. p47 directs p97 activity towards membrane remodelling and contributes to the regulation of cellular pathways such as NF-κB signalling and autophagy. p47 consists of three folded domains (UBA, SEP, UBX) connected by extended intrinsically disordered regions (IDRs). The dynamic and flexible nature of p47 has hindered high-resolution structural characterization of the full-length protein and its complex with p97 by X-ray crystallography or cryo-EM. Here, we report NMR backbone resonance assignments and secondary structure propensities of full-length p47, as well as of a truncated construct containing a SEP-interacting motif (SIM) and the SEP domain (residues 101–266). These findings provide the basis for future NMR studies aimed at elucidating the structural mechanisms by which p47 regulates p97 activity and for rational design of molecular binders to selectively target p47 and modulate specific p47-dependent pathways.</p></div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"20 1","pages":""},"PeriodicalIF":0.6,"publicationDate":"2025-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145435785","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}

{"title":"1H, 13C, and 15N resonance assignment of the C terminal region of the disordered postsynaptic scaffold protein GKAP","authors":"Eszter Nagy-Kanta,&nbsp;Anna Sánta,&nbsp;Zsófia E. Kálmán,&nbsp;Jessica Amy Li,&nbsp;Perttu Permi,&nbsp;Zoltán Gáspári,&nbsp;Bálint Péterfia","doi":"10.1007/s12104-025-10253-2","DOIUrl":"10.1007/s12104-025-10253-2","url":null,"abstract":"<div><p>Guanylate kinase-associated protein, GKAP, is a largely disordered scaffold protein with multiple interaction partners, playing a role in the organization of the postsynaptic protein network. Its C-terminus contains a binding motif for the PDZ domain of Shank proteins, another class of postsynaptic scaffolds. Based on predictions, this motif is preceded by a ~ 40-residue disordered segment with no known additional binding sites or established functional role. Here we report the expression, purification, and ¹H, ¹³C and ¹⁵N resonance assignment of the GKAP Ct43 construct containing the C-terminal 43 residues. This region is functionally intact, having a binding affinity to Shank1 PDZ in the micromolar range. Chemical shifts indicate that this region is indeed disordered but displays helical propensity in two regions. The short, slightly helical segment immediately before a PDZ-binding motif is somewhat comparable to the structural organization observed at the C-terminus of the E6 and RSK1 proteins, but its significance in GKAP is yet to be explored.</p></div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"20 1","pages":""},"PeriodicalIF":0.6,"publicationDate":"2025-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s12104-025-10253-2.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145435786","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}

{"title":"Resonance assignments of the human receptor interacting protein kinase 1 (RIPK1) in its fibrillar conformation","authors":"Paula Polonio,&nbsp;Miguel Mompeán","doi":"10.1007/s12104-025-10249-y","DOIUrl":"10.1007/s12104-025-10249-y","url":null,"abstract":"<div><p>Receptor-interacting protein kinase 1 (RIPK1) is a key regulator of necroptotic signalling that forms functional amyloid fibrils through its RIP Homotypic Interaction Motif (RHIM). Here, we report the solid-state NMR chemical shift assignments for the rigid amyloid core of human RIPK1 fibrils, encompassing residues 529–552 within the RHIM. Assignments were obtained from uniformly ¹³C,¹⁵N-labeled protein diluted with unlabeled protein and measured using cross-polarization magic angle spinning (CPMAS) experiments on a cryogenic probe. The dataset includes backbone and side-chain resonances for the ordered region and provides a basis for high-resolution structural and dynamics studies of RIPK1 and related RHIM-containing assemblies.</p></div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"19 2","pages":"299 - 304"},"PeriodicalIF":0.6,"publicationDate":"2025-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7618142/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145063164","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}