Journal of Biomolecular NMR最新文献

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Alpha-helices as alignment reporters in residual dipolar coupling analysis of proteins.
IF 1.3 3区 生物学
Journal of Biomolecular NMR Pub Date : 2024-12-11 DOI: 10.1007/s10858-024-00456-5
Yang Shen, Marshall J Smith, John M Louis, Ad Bax
{"title":"Alpha-helices as alignment reporters in residual dipolar coupling analysis of proteins.","authors":"Yang Shen, Marshall J Smith, John M Louis, Ad Bax","doi":"10.1007/s10858-024-00456-5","DOIUrl":"https://doi.org/10.1007/s10858-024-00456-5","url":null,"abstract":"<p><p>Inclusion of residual dipolar couplings (RDCs) during the early rounds of protein structure determination requires use of a floating alignment tensor or knowledge of the alignment tensor strength and rhombicity. For proteins with interdomain motion, such analysis can falsely hide the presence of domain dynamics. We demonstrate for three proteins, maltotriose-ligated maltose binding protein (MBP), Ca<sup>2+</sup>-ligated calmodulin, and a monomeric N-terminal deletion mutant of the SARS-CoV-2 Main Protease, MPro, that good alignment tensor estimates of their domains can be obtained from RDCs measured for residues that are identified as α-helical based on their chemical shifts. The program, Helix-Fit, fits the RDCs to idealized α-helical coordinates, often yielding a comparable or better alignment tensor estimate than fitting to the actual high-resolution X-ray helix coordinates. The 13 helices of ligated MBP all show very similar alignment tensors, indicative of a high degree of order relative to one another. By contrast, while for monomeric MPro the alignment strengths of the five helices in the C-terminal helical domain (residues 200-306) are very similar, pointing to a well-ordered domain, the single α-helix Y54-I59 in the N-terminal catalytic domain (residues 10-185) aligns considerably weaker. This result indicates the presence of large amplitude motions of either Y54-I59 or of the entire N-terminal domain relative to the C-terminal domain, contrasting with the high degree of order seen in the native homodimeric structure.</p>","PeriodicalId":613,"journal":{"name":"Journal of Biomolecular NMR","volume":" ","pages":""},"PeriodicalIF":1.3,"publicationDate":"2024-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142805914","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Using temperature coefficients to support resonance assignment of intrinsically disordered proteins.
IF 1.3 3区 生物学
Journal of Biomolecular NMR Pub Date : 2024-12-07 DOI: 10.1007/s10858-024-00452-9
Paulina Putko, Javier Agustin Romero, Christian F Pantoja, Markus Zweckstetter, Krzysztof Kazimierczuk, Anna Zawadzka-Kazimierczuk
{"title":"Using temperature coefficients to support resonance assignment of intrinsically disordered proteins.","authors":"Paulina Putko, Javier Agustin Romero, Christian F Pantoja, Markus Zweckstetter, Krzysztof Kazimierczuk, Anna Zawadzka-Kazimierczuk","doi":"10.1007/s10858-024-00452-9","DOIUrl":"https://doi.org/10.1007/s10858-024-00452-9","url":null,"abstract":"<p><p>The resonance assignment of large intrinsically disordered proteins (IDPs) is difficult due to the low dispersion of chemical shifts (CSs). Luckily, CSs are often specific for certain residue types, which makes the task easier. Our recent work showed that the CS-based spin-system classification can be improved by applying a linear discriminant analysis (LDA). In this paper, we extend a set of classification parameters by adding temperature coefficients (TCs), i.e., rates of change of chemical shifts with temperature. As demonstrated previously by other groups, the TCs in IDPs depend on a residue type, although the relation is often too complex to be predicted theoretically. Thus, we propose an approach based on experimental data; CSs and TCs values of residues assigned using conventional methods serve as a training set for LDA, which then classifies the remaining resonances. The method is demonstrated on a large fragment (1-239) of highly disordered protein Tau. We noticed that adding TCs to sets of chemical shifts significantly improves the recognition efficiency. For example, it allows distinguishing between lysine and glutamic acid, as well as valine and isoleucine residues based on <math> <msup><mrow><mtext>H</mtext></mrow> <mtext>N</mtext></msup> </math> , N, <math><msub><mtext>C</mtext> <mi>α</mi></msub> </math> and C <math><mmultiscripts><mrow></mrow> <mrow></mrow> <mo>'</mo></mmultiscripts> </math> data. Moreover, adding TCs to CSs of <math> <msup><mrow><mtext>H</mtext></mrow> <mtext>N</mtext></msup> </math> , N, <math><msub><mtext>C</mtext> <mi>α</mi></msub> </math> , and C <math><mmultiscripts><mrow></mrow> <mrow></mrow> <mo>'</mo></mmultiscripts> </math> is more beneficial than adding <math><msub><mtext>C</mtext> <mi>β</mi></msub> </math> CSs. Our program for LDA analysis is available at https://github.com/gugumatz/LDA-Temp-Coeff .</p>","PeriodicalId":613,"journal":{"name":"Journal of Biomolecular NMR","volume":" ","pages":""},"PeriodicalIF":1.3,"publicationDate":"2024-12-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142790829","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Perspective: on the importance of extensive, high-quality and reliable deposition of biomolecular NMR data in the age of artificial intelligence 视角:人工智能时代广泛、高质量和可靠地存储生物分子核磁共振数据的重要性。
IF 1.3 3区 生物学
Journal of Biomolecular NMR Pub Date : 2024-10-20 DOI: 10.1007/s10858-024-00451-w
Victoria A. Higman, Eliza Płoskoń, Gary S. Thompson, Geerten W. Vuister
{"title":"Perspective: on the importance of extensive, high-quality and reliable deposition of biomolecular NMR data in the age of artificial intelligence","authors":"Victoria A. Higman,&nbsp;Eliza Płoskoń,&nbsp;Gary S. Thompson,&nbsp;Geerten W. Vuister","doi":"10.1007/s10858-024-00451-w","DOIUrl":"10.1007/s10858-024-00451-w","url":null,"abstract":"<div><p>Artificial intelligence (AI) models are revolutionising scientific data analysis but are reliant on large training data sets. While artificial training data can be used in the context of NMR processing and data analysis methods, relating NMR parameters back to protein sequence and structure requires experimental data. In this perspective we examine what the biological NMR community needs to do, in order to store and share its data better so that we can make effective use of AI methods to further our understanding of biological molecules. We argue, first, that the community should be depositing much more of its experimental data. In particular, we should be depositing more spectra and dynamics data. Second, the NMR data deposited needs to capture the full information content required to be able to use and validate it adequately. The NMR Exchange Format (NEF) was designed several years ago to do this. The widespread adoption of NEF combined with a new proposal for dynamics data specifications come at the right time for the community to expand its deposition of data. Third, we highlight the importance of expanding and safeguarding our experimental data repository, the Biological Magnetic Resonance Data Bank (BMRB), not only in the interests of NMR spectroscopists, but biological scientists more widely. With this article we invite others in the biological NMR community to champion increased (possibly mandatory) data deposition, to get involved in designing new NEF specifications, and to advocate on behalf of the BMRB within the wider scientific community.</p></div>","PeriodicalId":613,"journal":{"name":"Journal of Biomolecular NMR","volume":"78 4","pages":"193 - 197"},"PeriodicalIF":1.3,"publicationDate":"2024-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10858-024-00451-w.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142455362","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
19F NMR relaxation of buried tryptophan side chains suggest anisotropic rotational diffusion of the protein RfaH 埋藏的色氨酸侧链的 19F NMR 驰豫表明,蛋白质 RfaH 存在各向异性的旋转扩散。
IF 1.3 3区 生物学
Journal of Biomolecular NMR Pub Date : 2024-10-16 DOI: 10.1007/s10858-024-00450-x
Md Khushnood Alam, R. Aishwarya Bhuvaneshwari, Ishita Sengupta
{"title":"19F NMR relaxation of buried tryptophan side chains suggest anisotropic rotational diffusion of the protein RfaH","authors":"Md Khushnood Alam,&nbsp;R. Aishwarya Bhuvaneshwari,&nbsp;Ishita Sengupta","doi":"10.1007/s10858-024-00450-x","DOIUrl":"10.1007/s10858-024-00450-x","url":null,"abstract":"<div><p>The recent application of <sup>19</sup>F NMR in the study of biomolecular structure and dynamics has made it a potentially attractive probe to complement traditional <sup>15</sup>N/<sup>13</sup>C labelled probes for backbone and sidechain dynamics, albeit with some complications. The utility of <sup>15</sup>N relaxation rates of rigid backbone amide groups to determine the rotational diffusion tensor of proteins is well established. Here we show that the measured <sup>19</sup>F relaxation rates of two buried and possibly immobile <sup>19</sup>F labelled tryptophan sidechains for the multidomain protein RfaH, in its closed conformation, are in reasonable agreement with the calculated values, only when anisotropic rotational diffusion of the protein is considered. While the sparsity of <sup>19</sup>F relaxation data from a limited number of probes precludes the experimental determination of the rotational diffusion tensor here, these results demonstrate the influence of rotational diffusion anisotropy of proteins on <sup>19</sup>F NMR relaxation of rigid tryptophan sidechains, while adding to the expanding literature of <sup>19</sup>F NMR relaxation data sets in biomolecules.</p></div>","PeriodicalId":613,"journal":{"name":"Journal of Biomolecular NMR","volume":"78 4","pages":"265 - 273"},"PeriodicalIF":1.3,"publicationDate":"2024-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142455361","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Pitfalls in measurements of R1 relaxation rates of protein backbone 15N nuclei. 蛋白质骨架 15N 核的 R1 弛豫速率测量中的陷阱。
IF 1.3 3区 生物学
Journal of Biomolecular NMR Pub Date : 2024-08-31 DOI: 10.1007/s10858-024-00449-4
Vladlena Kharchenko, Samah Al-Harthi, Andrzej Ejchart, Łukasz Jaremko
{"title":"Pitfalls in measurements of R<sub>1</sub> relaxation rates of protein backbone <sup>15</sup>N nuclei.","authors":"Vladlena Kharchenko, Samah Al-Harthi, Andrzej Ejchart, Łukasz Jaremko","doi":"10.1007/s10858-024-00449-4","DOIUrl":"https://doi.org/10.1007/s10858-024-00449-4","url":null,"abstract":"<p><p>The dynamics of the backbone and side-chains of protein are routinely studied by interpreting experimentally determined <sup>15</sup>N spin relaxation rates. R<sub>1</sub>(<sup>15</sup>N), the longitudinal relaxation rate, reports on fast motions and encodes, together with the transverse relaxation R<sub>2</sub>, structural information about the shape of the molecule and the orientation of the amide bond vectors in the internal diffusion frame. Determining error-free <sup>15</sup>N longitudinal relaxation rates remains a challenge for small, disordered, and medium-sized proteins. Here, we show that mono-exponential fitting is sufficient, with no statistical preference for bi-exponential fitting up to 800 MHz. A detailed comparison of the TROSY and HSQC techniques at medium and high fields showed no statistically significant differences. The least error-prone DD/CSA interference removal technique is the selective inversion of amide signals while avoiding water resonance. The exchange of amide with solvent deuterons appears to affect the rate R<sub>1</sub> of solvent-exposed amides in all fields tested and in each DD/CSA interference removal technique in a statistically significant manner. In summary, the most accurate R<sub>1</sub>(<sup>15</sup>N) rates in proteins are achieved by selective amide inversion, without the addition of D<sub>2</sub>O. Importantly, at high magnetic fields stronger than 800 MHz, when non-mono-exponential decay is involved, it is advisable to consider elimination of the shortest delays (typically up to 0.32 s) or bi-exponential fitting.</p>","PeriodicalId":613,"journal":{"name":"Journal of Biomolecular NMR","volume":" ","pages":""},"PeriodicalIF":1.3,"publicationDate":"2024-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142103198","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Towards cost-effective side-chain isotope labelling of proteins expressed in human cells 对人体细胞中表达的蛋白质进行具有成本效益的侧链同位素标记。
IF 1.3 3区 生物学
Journal of Biomolecular NMR Pub Date : 2024-08-22 DOI: 10.1007/s10858-024-00447-6
Martina Rosati, Letizia Barbieri, Matus Hlavac, Sarah Kratzwald, Roman J. Lichtenecker, Robert Konrat, Enrico Luchinat, Lucia Banci
{"title":"Towards cost-effective side-chain isotope labelling of proteins expressed in human cells","authors":"Martina Rosati,&nbsp;Letizia Barbieri,&nbsp;Matus Hlavac,&nbsp;Sarah Kratzwald,&nbsp;Roman J. Lichtenecker,&nbsp;Robert Konrat,&nbsp;Enrico Luchinat,&nbsp;Lucia Banci","doi":"10.1007/s10858-024-00447-6","DOIUrl":"10.1007/s10858-024-00447-6","url":null,"abstract":"<div><p>Side chain isotope labelling is a powerful tool to study protein structure and interactions by NMR spectroscopy. <sup>1</sup>H,<sup>13</sup>C labelling of side-chain methyl groups in a deuterated background allows studying large molecules, while side-chain aromatic groups are highly sensitive to the interaction with ligands, drugs, and other proteins. In <i>E. coli</i>, side chain labelling is performed by substituting amino acids with isotope-labelled precursors. However, proteins that can only be produced in mammalian cells require expensive isotope-labelled amino acids. Here we provide a simple and cost-effective method to label side chains in mammalian cells, which exploits the reversible reaction catalyzed by endogenous transaminases to convert isotope-labelled α-ketoacid precursors. We show by in-cell and in-lysate NMR spectroscopy that replacing an amino acid in the medium with its cognate precursor is sufficient to achieve selective labelling without scrambling, and how this approach allows monitoring conformational changes such as those arising from ligand binding.</p></div>","PeriodicalId":613,"journal":{"name":"Journal of Biomolecular NMR","volume":"78 4","pages":"237 - 247"},"PeriodicalIF":1.3,"publicationDate":"2024-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10858-024-00447-6.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142015955","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Optimising in-cell NMR acquisition for nucleic acids 优化核酸的细胞内 NMR 采集。
IF 1.3 3区 生物学
Journal of Biomolecular NMR Pub Date : 2024-08-20 DOI: 10.1007/s10858-024-00448-5
Henry T. P. Annecke, Reiner Eidelpes, Hannes Feyrer, Julian Ilgen, Cenk Onur Gürdap, Rubin Dasgupta, Katja Petzold
{"title":"Optimising in-cell NMR acquisition for nucleic acids","authors":"Henry T. P. Annecke,&nbsp;Reiner Eidelpes,&nbsp;Hannes Feyrer,&nbsp;Julian Ilgen,&nbsp;Cenk Onur Gürdap,&nbsp;Rubin Dasgupta,&nbsp;Katja Petzold","doi":"10.1007/s10858-024-00448-5","DOIUrl":"10.1007/s10858-024-00448-5","url":null,"abstract":"<div><p>Understanding the structure and function of nucleic acids in their native environment is crucial to structural biology and one focus of in-cell NMR spectroscopy. Many challenges hamper in-cell NMR in human cell lines, e.g. sample decay through cell death and RNA degradation. The resulting low signal intensities and broad line widths limit the use of more complex NMR experiments, reducing the possible structural and dynamic information that can be extracted. Here, we optimize the detection of imino proton signals, indicators of base-pairing and therefore secondary structure, of a double-stranded DNA oligonucleotide in HeLa cells, using selective excitation. We demonstrate the reproducible quantification of in-cell selective longitudinal relaxation times (selT<sub>1</sub>), which are reduced compared to the in vitro environment, as a result of interactions with the complex cellular environment. By measuring the intracellular selT<sub>1,</sub> we optimize the existing proton pulse sequences, and shorten measurement time whilst enhancing the signal gained per unit of time. This exemplifies an advantage of selective excitation over conventional methods like jump-return water suppression for in-cell NMR. Furthermore, important experimental controls are discussed, including intracellular quantification, supernatant control measurements, as well as the processing of lowly concentrated in-cell NMR samples. We expect that robust and fast in-cell NMR experiments of nucleic acids will facilitate the study of structure and dynamics and reveal their functional correlation.</p></div>","PeriodicalId":613,"journal":{"name":"Journal of Biomolecular NMR","volume":"78 4","pages":"249 - 264"},"PeriodicalIF":1.3,"publicationDate":"2024-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10858-024-00448-5.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142003309","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Transverse relaxation optimized spectroscopy of NH2 groups in glutamine and asparagine side chains of proteins 蛋白质谷氨酰胺和天冬酰胺侧链中 NH2 基团的横向弛豫优化光谱。
IF 1.3 3区 生物学
Journal of Biomolecular NMR Pub Date : 2024-07-31 DOI: 10.1007/s10858-024-00445-8
Vitali Tugarinov, Francesco Torricella, Jinfa Ying, G. Marius Clore
{"title":"Transverse relaxation optimized spectroscopy of NH2 groups in glutamine and asparagine side chains of proteins","authors":"Vitali Tugarinov,&nbsp;Francesco Torricella,&nbsp;Jinfa Ying,&nbsp;G. Marius Clore","doi":"10.1007/s10858-024-00445-8","DOIUrl":"10.1007/s10858-024-00445-8","url":null,"abstract":"<div><p>A transverse relaxation optimized spectroscopy (TROSY) approach is described for the optimal detection of NH<sub>2</sub> groups in asparagine and glutamine side chains of proteins. Specifically, we have developed NMR experiments for isolating the slow-relaxing <sup>15</sup>N and <sup>1</sup>H components of NH<sub>2</sub> multiplets. Although even modest sensitivity gains in 2D NH<sub>2</sub>-TROSY correlation maps compared to their decoupled NH<sub>2</sub>–HSQC counterparts can be achieved only occasionally, substantial improvements in resolution of the NMR spectra are demonstrated for asparagine and glutamine NH<sub>2</sub> sites of a buried cavity mutant, L99A, of T4 lysozyme at 5 ºC. The NH<sub>2</sub>-TROSY approach is applied to CPMG relaxation dispersion measurements at the side chain NH<sub>2</sub> positions of the L99A T4 lysozyme mutant — a model system for studies of the role of protein dynamics in ligand binding.</p></div>","PeriodicalId":613,"journal":{"name":"Journal of Biomolecular NMR","volume":"78 4","pages":"199 - 213"},"PeriodicalIF":1.3,"publicationDate":"2024-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10858-024-00445-8.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141854475","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Micromolar fluoride contamination arising from glass NMR tubes and a simple solution for biomolecular applications 玻璃 NMR 管产生的微摩尔氟污染以及生物分子应用的简单解决方案
IF 1.3 3区 生物学
Journal of Biomolecular NMR Pub Date : 2024-07-27 DOI: 10.1007/s10858-024-00442-x
Khushboo Matwani, Jasmine Cornish, Erika Alden DeBenedictis, Gabriella T. Heller
{"title":"Micromolar fluoride contamination arising from glass NMR tubes and a simple solution for biomolecular applications","authors":"Khushboo Matwani,&nbsp;Jasmine Cornish,&nbsp;Erika Alden DeBenedictis,&nbsp;Gabriella T. Heller","doi":"10.1007/s10858-024-00442-x","DOIUrl":"10.1007/s10858-024-00442-x","url":null,"abstract":"<div><p>Fluorine (<sup>19</sup>F) NMR is emerging as an invaluable analytical technique in chemistry, biochemistry, structural biology, material science, drug discovery, and medicine, especially due to the inherent rarity of naturally occurring fluorine in biological, organic, and inorganic compounds. Here, we revisit the under-reported problem of fluoride leaching from new and unused glass NMR tubes. We characterised the leaching of free fluoride from various types of new and unused glass NMR tubes over the course of several hours and quantify this contaminant to be at micromolar concentrations for typical NMR sample volumes across multiple glass types and brands. We find that this artefact is undetectable for samples prepared in quartz NMR tubes within the timeframes of our experiments. We also observed that pre-soaking new glass NMR tubes combined with rinsing removes this contamination below micromolar levels. Given the increasing popularity of <sup>19</sup>F NMR across a wide range of fields, increasing popularity of single-use screening tubes, the long collection times required for relaxation studies and samples of low concentrations, and the importance of avoiding contamination in all NMR experiments, we anticipate that our simple solution will be useful to biomolecular NMR spectroscopists.</p></div>","PeriodicalId":613,"journal":{"name":"Journal of Biomolecular NMR","volume":"78 3","pages":"161 - 167"},"PeriodicalIF":1.3,"publicationDate":"2024-07-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10858-024-00442-x.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141776891","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Quantitative analysis of the slow exchange process by 19F NMR in the presence of scalar and dipolar couplings: applications to the ribose 2′-19F probe in nucleic acids 在标量和偶极耦合作用下通过 19F NMR 对缓慢交换过程进行定量分析:核酸中核糖 2'-19F 探针的应用。
IF 1.3 3区 生物学
Journal of Biomolecular NMR Pub Date : 2024-06-25 DOI: 10.1007/s10858-024-00446-7
Yuki Toyama, Ichio Shimada
{"title":"Quantitative analysis of the slow exchange process by 19F NMR in the presence of scalar and dipolar couplings: applications to the ribose 2′-19F probe in nucleic acids","authors":"Yuki Toyama,&nbsp;Ichio Shimada","doi":"10.1007/s10858-024-00446-7","DOIUrl":"10.1007/s10858-024-00446-7","url":null,"abstract":"<div><p>Solution NMR spectroscopy is a particularly powerful technique for characterizing the functional dynamics of biomolecules, which is typically achieved through the quantitative characterization of chemical exchange processes via the measurement of spin relaxation rates. In addition to the conventional nuclei such as <sup>15</sup>N and <sup>13</sup>C, which are abundant in biomolecules, fluorine-19 (<sup>19</sup>F) has recently garnered attention and is being widely used as a site-specific spin probe. While <sup>19</sup>F offers the advantages of high sensitivity and low background, it can be susceptible to artifacts in quantitative relaxation analyses due to a multitude of dipolar and scalar coupling interactions with nearby <sup>1</sup>H spins. In this study, we focused on the ribose 2′-<sup>19</sup>F spin probe in nucleic acids and investigated the effects of <sup>1</sup>H-<sup>19</sup>F spin interactions on the quantitative characterization of slow exchange processes on the millisecond time scale. We demonstrated that the <sup>1</sup>H-<sup>19</sup>F dipolar coupling can significantly affect the interpretation of <sup>19</sup>F chemical exchange saturation transfer (CEST) experiments when <sup>1</sup>H decoupling is applied, while the <sup>1</sup>H-<sup>19</sup>F interactions have a lesser impact on Carr-Purcell-Meiboom-Gill relaxation dispersion applications. We also proposed a modified CEST scheme to alleviate these artifacts along with experimental verifications on self-complementary RNA systems. The theoretical framework presented in this study can be widely applied to various <sup>19</sup>F spin systems where <sup>1</sup>H-<sup>19</sup>F interactions are operative, further expanding the utility of <sup>19</sup>F relaxation-based NMR experiments.</p></div>","PeriodicalId":613,"journal":{"name":"Journal of Biomolecular NMR","volume":"78 4","pages":"215 - 235"},"PeriodicalIF":1.3,"publicationDate":"2024-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141449249","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
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