Journal of Biomolecular NMR最新文献

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Solid state NMR spectral editing of histidine, arginine and lysine using Hadamard encoding.
IF 1.3 3区 生物学
Journal of Biomolecular NMR Pub Date : 2025-01-29 DOI: 10.1007/s10858-024-00455-6
Tata Gopinath, Alyssa Kraft, Kyungsoo Shin, Nicholas A Wood, Francesca M Marassi
{"title":"Solid state NMR spectral editing of histidine, arginine and lysine using Hadamard encoding.","authors":"Tata Gopinath, Alyssa Kraft, Kyungsoo Shin, Nicholas A Wood, Francesca M Marassi","doi":"10.1007/s10858-024-00455-6","DOIUrl":"https://doi.org/10.1007/s10858-024-00455-6","url":null,"abstract":"<p><p>The NMR signals from protein sidechains are rich in information about intra- and inter-molecular interactions, but their detection can be complicated due to spectral overlap as well as conformational and hydrogen exchange. In this work, we demonstrate a protocol for multi-dimensional solid-state NMR spectral editing of signals from basic sidechains based on Hadamard matrix encoding. The Hadamard method acquires multi-dimensional experiments in such a way that both the backbone and under-sampled sidechain signals can be decoded for unambiguous editing in the <sup>15</sup>N spectral frequency dimension. All multi-dimensional <sup>15</sup>N-edited solid-state NMR experiments can be acquired using this strategy, thereby accelerating the acquisition of spectra spanning broad frequency bandwidth. Application of these methods to the ferritin nanocage, reveals signals from N atoms from His, Arg, Lys and Trp sidechains, as well as their tightly bound, ordered water molecules. The Hadamard approach adds to the arsenal of spectroscopic approaches for protein NMR signal detection.</p>","PeriodicalId":613,"journal":{"name":"Journal of Biomolecular NMR","volume":" ","pages":""},"PeriodicalIF":1.3,"publicationDate":"2025-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143062996","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
15N-detected TROSY for 1H-15N heteronuclear correlation to study intrinsically disordered proteins: strategies to increase spectral quality. 15n检测TROSY用于1H-15N异核相关研究内在无序蛋白:提高光谱质量的策略。
IF 1.3 3区 生物学
Journal of Biomolecular NMR Pub Date : 2025-01-22 DOI: 10.1007/s10858-024-00453-8
Maria Anna Rodella, Robert Schneider, Rainer Kümmerle, Isabella C Felli, Roberta Pierattelli
{"title":"<sup>15</sup>N-detected TROSY for <sup>1</sup>H-<sup>15</sup>N heteronuclear correlation to study intrinsically disordered proteins: strategies to increase spectral quality.","authors":"Maria Anna Rodella, Robert Schneider, Rainer Kümmerle, Isabella C Felli, Roberta Pierattelli","doi":"10.1007/s10858-024-00453-8","DOIUrl":"https://doi.org/10.1007/s10858-024-00453-8","url":null,"abstract":"<p><p>Intrinsically disordered proteins and protein regions are central to many biological processes but difficult to characterize at atomic resolution. Nuclear magnetic resonance is particularly well-suited for providing structural and dynamical information on intrinsically disordered proteins, but existing NMR methodologies need to be constantly refined to provide greater sensitivity and resolution, particularly to capitalise on the potential of high magnetic fields to investigate large proteins. In this paper, we describe how <sup>15</sup>N-detected 2D NMR experiments can be optimised for better performance. We show that using selective aliphatic <sup>1</sup>H decoupling in N-TROSY type experiments results in significant increases in sensitivity and resolution for a prototypical intrinsically disordered protein, α-synuclein, as well as for a heterogeneous intrinsically disordered region of a large multidomain protein, CBP-ID4. We also investigated the performance of incorporating longitudinal relaxation enhancement in N-TROSY experiments, both with and without aliphatic <sup>1</sup>H decoupling, and discussed the findings in light of the available information for the two systems.</p>","PeriodicalId":613,"journal":{"name":"Journal of Biomolecular NMR","volume":" ","pages":""},"PeriodicalIF":1.3,"publicationDate":"2025-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142998175","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
Evaluation of TOCSY mixing for sensitivity-enhancement in solid-state NMR and application of 4D experiments for side-chain assignments of the full-length 30 kDa membrane protein GlpG. 固体核磁共振中TOCSY混合灵敏度增强的评价以及全长30kda膜蛋白GlpG侧链配位的4D实验应用。
IF 1.3 3区 生物学
Journal of Biomolecular NMR Pub Date : 2025-01-22 DOI: 10.1007/s10858-024-00454-7
Carl Öster, Veniamin Chevelkov, Adam Lange
{"title":"Evaluation of TOCSY mixing for sensitivity-enhancement in solid-state NMR and application of 4D experiments for side-chain assignments of the full-length 30 kDa membrane protein GlpG.","authors":"Carl Öster, Veniamin Chevelkov, Adam Lange","doi":"10.1007/s10858-024-00454-7","DOIUrl":"https://doi.org/10.1007/s10858-024-00454-7","url":null,"abstract":"<p><p>Chemical shift assignments of large membrane proteins by solid-state NMR experiments are challenging. Recent advancements in sensitivity-enhanced pulse sequences, have made it feasible to acquire <sup>1</sup>H-detected 4D spectra of these challenging protein samples within reasonable timeframes. However, obtaining unambiguous assignments remains difficult without access to side-chain chemical shifts. Drawing inspiration from sensitivity-enhanced TOCSY experiments in solution NMR, we have explored the potential of <sup>13</sup>C- <sup>13</sup>C TOCSY mixing as a viable option for triple sensitivity-enhanced 4D experiments aimed at side-chain assignments in solid-state NMR. Through simulations and experimental trials, we have identified optimal conditions to achieve uniform transfer efficiency for both transverse components and to minimize undesired cross-transfers. Our experiments, conducted on the 30 kDa membrane protein GlpG embedded in E. coli liposomes, have demonstrated enhanced sensitivity compared to the most effective dipolar and J-coupling-based <sup>13</sup>C- <sup>13</sup>C mixing sequences. Notably, a non-uniformly sampled 4D hCXCANH spectrum with exceptionally high sensitivity was obtained in just a few days using a 600 MHz spectrometer equipped with a 1.3 mm probe operating at a magic angle spinning rate of 55 kHz.</p>","PeriodicalId":613,"journal":{"name":"Journal of Biomolecular NMR","volume":" ","pages":""},"PeriodicalIF":1.3,"publicationDate":"2025-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142998176","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
Alpha-helices as alignment reporters in residual dipolar coupling analysis of proteins. α -螺旋作为残留偶极偶联分析蛋白的比对报告。
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. 使用温度系数来支持内在无序蛋白质的共振分配。
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
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