Journal of Biomolecular NMR最新文献_第10页

Evaluation of the tert-butyl group as a probe for NMR studies of macromolecular complexes 叔丁基作为大分子配合物核磁共振研究探针的评价

IF 2.7 3区生物学

Journal of Biomolecular NMR Pub Date : 2021-09-09 DOI: 10.1007/s10858-021-00380-y

Rashmi Voleti, Sofia Bali, Jaime Guerrero, Jared Smothers, Charis Springhower, Gerardo A. Acosta, Kyle D. Brewer, Fernando Albericio, Josep Rizo

{"title":"Evaluation of the tert-butyl group as a probe for NMR studies of macromolecular complexes","authors":"Rashmi Voleti, Sofia Bali, Jaime Guerrero, Jared Smothers, Charis Springhower, Gerardo A. Acosta, Kyle D. Brewer, Fernando Albericio, Josep Rizo","doi":"10.1007/s10858-021-00380-y","DOIUrl":"10.1007/s10858-021-00380-y","url":null,"abstract":"<div>The development of methyl transverse relaxation optimized spectroscopy has greatly facilitated the study of macromolecular assemblies by solution NMR spectroscopy. However, limited sample solubility and stability has hindered application of this technique to ongoing studies of complexes formed on membranes by the neuronal SNAREs that mediate neurotransmitter release and synaptotagmin-1, the Ca2+ sensor that triggers release. Since the 1H NMR signal of a tBu group attached to a large protein or complex can be observed with high sensitivity if the group retains high mobility, we have explored the use of this strategy to analyze presynaptic complexes involved in neurotransmitter release. For this purpose, we attached tBu groups at single cysteines of fragments of synaptotagmin-1, complexin-1 and the neuronal SNAREs by reaction with 5-(tert-butyldisulfaneyl)-2-nitrobenzoic acid (BDSNB), tBu iodoacetamide or tBu acrylate. The tBu resonances of the tagged proteins were generally sharp and intense, although tBu groups attached with BDSNB had a tendency to exhibit somewhat broader resonances that likely result because of the shorter linkage between the tBu and the tagged cysteine. Incorporation of the tagged proteins into complexes on nanodiscs led to severe broadening of the tBu resonances in some cases. However, sharp tBu resonances could readily be observed for some complexes of more than 200 kDa at low micromolar concentrations. Our results show that tagging of proteins with tBu groups provides a powerful approach to study large biomolecular assemblies of limited stability and/or solubility that may be applicable even at nanomolar concentrations.</div>","PeriodicalId":613,"journal":{"name":"Journal of Biomolecular NMR","volume":"75 8-9","pages":"347 - 363"},"PeriodicalIF":2.7,"publicationDate":"2021-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10858-021-00380-y.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4713517","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: 4

TRACT revisited: an algebraic solution for determining overall rotational correlation times from cross-correlated relaxation rates 重新审视:从交叉相关弛豫率确定总体旋转相关时间的代数解决方案

IF 2.7 3区生物学

Journal of Biomolecular NMR Pub Date : 2021-09-03 DOI: 10.1007/s10858-021-00379-5

Scott A. Robson, Çağdaş Dağ, Hongwei Wu, Joshua J. Ziarek

{"title":"TRACT revisited: an algebraic solution for determining overall rotational correlation times from cross-correlated relaxation rates","authors":"Scott A. Robson, Çağdaş Dağ, Hongwei Wu, Joshua J. Ziarek","doi":"10.1007/s10858-021-00379-5","DOIUrl":"10.1007/s10858-021-00379-5","url":null,"abstract":"<div>Accurate rotational correlation times (({tau }_{text{c}})) are critical for quantitative analysis of fast timescale NMR dynamics. As molecular weights increase, the classic derivation of ({tau }_{c}) using transverse and longitudinal relaxation rates becomes increasingly unsuitable due to the non-trivial contribution of remote dipole–dipole interactions to longitudinal relaxation. Derivations using cross-correlated relaxation experiments, such as TRACT, overcome these limitations but are erroneously calculated in 65% of the citing literature. Herein, we developed an algebraic solutions to the Goldman relationship that facilitate rapid, point-by-point calculations for straightforward identification of appropriate spectral regions where global tumbling is likely to be dominant. The rigid-body approximation of the Goldman relationship has been previously shown to underestimate TRACT-based rotational correlation time estimates. This motivated us to develop a second algebraic solution that employs a simplified model-free spectral density function including an order parameter term that could, in principle, be set to an average backbone S2 ≈ 0.9 to further improve the accuracy of ({tau }_{text{c}}) estimation. These solutions enabled us to explore the boundaries of the Goldman relationship as a function of the H–N internuclear distance ((r)), difference of the two principal components of the axially-symmetric 15N CSA tensor ((Delta {delta }_{N})), and angle of the CSA tensor relative to the N–H bond vector ((theta)). We hope our algebraic solutions and analytical strategies will increase the accuracy and application of the TRACT experiment.</div>","PeriodicalId":613,"journal":{"name":"Journal of Biomolecular NMR","volume":"75 8-9","pages":"293 - 302"},"PeriodicalIF":2.7,"publicationDate":"2021-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10858-021-00379-5.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4143933","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: 5

Off-resonance 13C–2H REDOR NMR for site-resolved studies of molecular motion 非共振13C-2H REDOR核磁共振用于分子运动的位点分辨研究

IF 2.7 3区生物学

Journal of Biomolecular NMR Pub Date : 2021-08-03 DOI: 10.1007/s10858-021-00377-7

Martin D. Gelenter, Kelly J. Chen, Mei Hong

引用次数: 2

An automated iterative approach for protein structure refinement using pseudocontact shifts 使用伪接触位移的蛋白质结构优化的自动迭代方法

IF 2.7 3区生物学

Journal of Biomolecular NMR Pub Date : 2021-08-02 DOI: 10.1007/s10858-021-00376-8

Stefano Cucuzza, Peter Güntert, Andreas Plückthun, Oliver Zerbe

{"title":"An automated iterative approach for protein structure refinement using pseudocontact shifts","authors":"Stefano Cucuzza, Peter Güntert, Andreas Plückthun, Oliver Zerbe","doi":"10.1007/s10858-021-00376-8","DOIUrl":"10.1007/s10858-021-00376-8","url":null,"abstract":"<div>NMR structure calculation using NOE-derived distance restraints requires a considerable number of assignments of both backbone and sidechains resonances, often difficult or impossible to get for large or complex proteins. Pseudocontact shifts (PCSs) also play a well-established role in NMR protein structure calculation, usually to augment existing structural, mostly NOE-derived, information. Existing refinement protocols using PCSs usually either require a sizeable number of sidechain assignments or are complemented by other experimental restraints. Here, we present an automated iterative procedure to perform backbone protein structure refinements requiring only a limited amount of backbone amide PCSs. Already known structural features from a starting homology model, in this case modules of repeat proteins, are framed into a scaffold that is subsequently refined by experimental PCSs. The method produces reliable indicators that can be monitored to judge about the performance. We applied it to a system in which sidechain assignments are hardly possible, designed Armadillo repeat proteins (dArmRPs), and we calculated the solution NMR structure of YM4A, a dArmRP containing four sequence-identical internal modules, obtaining high convergence to a single structure. We suggest that this approach is particularly useful when approximate folds are known from other techniques, such as X-ray crystallography, while avoiding inherent artefacts due to, for instance, crystal packing.</div>","PeriodicalId":613,"journal":{"name":"Journal of Biomolecular NMR","volume":"75 8-9","pages":"319 - 334"},"PeriodicalIF":2.7,"publicationDate":"2021-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10858-021-00376-8","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4071154","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: 5

Toho-1 β-lactamase: backbone chemical shift assignments and changes in dynamics upon binding with avibactam Toho-1 β-内酰胺酶:与阿维巴坦结合后的主干化学位移分配和动力学变化

IF 2.7 3区生物学

Journal of Biomolecular NMR Pub Date : 2021-07-04 DOI: 10.1007/s10858-021-00375-9

Varun V. Sakhrani, Rittik K. Ghosh, Eduardo Hilario, Kevin L. Weiss, Leighton Coates, Leonard J. Mueller

{"title":"Toho-1 β-lactamase: backbone chemical shift assignments and changes in dynamics upon binding with avibactam","authors":"Varun V. Sakhrani, Rittik K. Ghosh, Eduardo Hilario, Kevin L. Weiss, Leighton Coates, Leonard J. Mueller","doi":"10.1007/s10858-021-00375-9","DOIUrl":"10.1007/s10858-021-00375-9","url":null,"abstract":"<div>Backbone chemical shift assignments for the Toho-1 β-lactamase (263 amino acids, 28.9 kDa) are reported based on triple resonance solution-state NMR experiments performed on a uniformly 2H,13C,15N-labeled sample. These assignments allow for subsequent site-specific characterization at the chemical, structural, and dynamical levels. At the chemical level, titration with the non-β-lactam β-lactamase inhibitor avibactam is found to give chemical shift perturbations indicative of tight covalent binding that allow for mapping of the inhibitor binding site. At the structural level, protein secondary structure is predicted based on the backbone chemical shifts and protein residue sequence using TALOS-N and found to agree well with structural characterization from X-ray crystallography. At the dynamical level, model-free analysis of 15N relaxation data at a single field of 16.4 T reveals well-ordered structures for the ligand-free and avibactam-bound enzymes with generalized order parameters of ~ 0.85. Complementary relaxation dispersion experiments indicate that there is an escalation in motions on the millisecond timescale in the vicinity of the active site upon substrate binding. The combination of high rigidity on short timescales and active site flexibility on longer timescales is consistent with hypotheses for achieving both high catalytic efficiency and broad substrate specificity: the induced active site dynamics allows variously sized substrates to be accommodated and increases the probability that the optimal conformation for catalysis will be sampled.</div>","PeriodicalId":613,"journal":{"name":"Journal of Biomolecular NMR","volume":"75 8-9","pages":"303 - 318"},"PeriodicalIF":2.7,"publicationDate":"2021-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10858-021-00375-9","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4164701","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: 1

Antipsychotic phenothiazine drugs bind to KRAS in vitro 抗精神病吩噻嗪类药物与KRAS的体外结合

IF 2.7 3区生物学

Journal of Biomolecular NMR Pub Date : 2021-06-26 DOI: 10.1007/s10858-021-00371-z

Xu Wang, Alemayehu A. Gorfe, John A. Putkey

引用次数: 1

Biomolecular solid-state NMR spectroscopy at 1200 MHz: the gain in resolution 生物分子固态核磁共振光谱在1200兆赫:在分辨率增益

IF 2.7 3区生物学

Journal of Biomolecular NMR Pub Date : 2021-06-25 DOI: 10.1007/s10858-021-00373-x

Morgane Callon, Alexander A. Malär, Sara Pfister, Václav Římal, Marco E. Weber, Thomas Wiegand, Johannes Zehnder, Matías Chávez, Riccardo Cadalbert, Rajdeep Deb, Alexander Däpp, Marie-Laure Fogeron, Andreas Hunkeler, Lauriane Lecoq, Anahit Torosyan, Dawid Zyla, Rudolf Glockshuber, Stefanie Jonas, Michael Nassal, Matthias Ernst, Anja Böckmann, Beat H. Meier

{"title":"Biomolecular solid-state NMR spectroscopy at 1200 MHz: the gain in resolution","authors":"Morgane Callon, Alexander A. Malär, Sara Pfister, Václav Římal, Marco E. Weber, Thomas Wiegand, Johannes Zehnder, Matías Chávez, Riccardo Cadalbert, Rajdeep Deb, Alexander Däpp, Marie-Laure Fogeron, Andreas Hunkeler, Lauriane Lecoq, Anahit Torosyan, Dawid Zyla, Rudolf Glockshuber, Stefanie Jonas, Michael Nassal, Matthias Ernst, Anja Böckmann, Beat H. Meier","doi":"10.1007/s10858-021-00373-x","DOIUrl":"10.1007/s10858-021-00373-x","url":null,"abstract":"<div>Progress in NMR in general and in biomolecular applications in particular is driven by increasing magnetic-field strengths leading to improved resolution and sensitivity of the NMR spectra. Recently, persistent superconducting magnets at a magnetic field strength (magnetic induction) of 28.2 T corresponding to 1200 MHz proton resonance frequency became commercially available. We present here a collection of high-field NMR spectra of a variety of proteins, including molecular machines, membrane proteins, viral capsids, fibrils and large molecular assemblies. We show this large panel in order to provide an overview over a range of representative systems under study, rather than a single best performing model system. We discuss both carbon-13 and proton-detected experiments, and show that in 13C spectra substantially higher numbers of peaks can be resolved compared to 850 MHz while for 1H spectra the most impressive increase in resolution is observed for aliphatic side-chain resonances.</div>","PeriodicalId":613,"journal":{"name":"Journal of Biomolecular NMR","volume":"75 6-7","pages":"255 - 272"},"PeriodicalIF":2.7,"publicationDate":"2021-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10858-021-00373-x","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4976076","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: 32

Extensively sparse 13C labeling to simplify solid-state NMR 13C spectra of membrane proteins 广泛稀疏13C标记，以简化膜蛋白的固态核磁共振13C光谱

IF 2.7 3区生物学

Journal of Biomolecular NMR Pub Date : 2021-06-20 DOI: 10.1007/s10858-021-00372-y

Qiong Tong, Huan Tan, Jianping Li, Huayong Xie, Yongxiang Zhao, Yanke Chen, Jun Yang

{"title":"Extensively sparse 13C labeling to simplify solid-state NMR 13C spectra of membrane proteins","authors":"Qiong Tong, Huan Tan, Jianping Li, Huayong Xie, Yongxiang Zhao, Yanke Chen, Jun Yang","doi":"10.1007/s10858-021-00372-y","DOIUrl":"10.1007/s10858-021-00372-y","url":null,"abstract":"<div>Solid-state Nuclear Magnetic Resonance (ssNMR) is an emerging technique to investigate the structures and dynamics of membrane proteins in an artificial or native membrane environment. However, the structural studies of proteins by ssNMR are usually prolonged or impeded by signal assignments, especially the assignments of signals for collection of distance restraints, because of serious overlapping of signals in 2D 13C–13C spectra. Sparse labeling of 13C spins is an effective approach to simplify the 13C spectra and facilitate the extractions of distance restraints. Here, we propose a new reverse labeling combination of six types of amino acid residues (Ile, Leu, Phe, Trp, Tyr and Lys), and show a clean reverse labeling effect on a model membrane protein E. coli aquaporin Z (AqpZ). We further combine this reverse labeling combination and alternate 13C–12C labeling, and demonstrate an enhanced dilution effect in 13C–13C spectra. In addition, the influences of reverse labeling on the labeling of the other types of residues are quantitatively analyzed in the two strategies (1, reverse labeling and 2, reverse labeling combining alternate 13C–12C labeling). The signal intensities of some other types of residues in 2D 13C–13C spectra are observed to be 20–50% weaker because of the unwanted reverse labeling. The extensively sparse 13C labeling proposed in this study is expected to be useful in the collection of distance restraints using 2D 13C–13C spectra of membrane proteins.</div>","PeriodicalId":613,"journal":{"name":"Journal of Biomolecular NMR","volume":"75 6-7","pages":"245 - 254"},"PeriodicalIF":2.7,"publicationDate":"2021-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10858-021-00372-y","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4793191","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: 1

CheSPI: chemical shift secondary structure population inference CheSPI:化学位移二级结构种群推断

IF 2.7 3区生物学

Journal of Biomolecular NMR Pub Date : 2021-06-19 DOI: 10.1007/s10858-021-00374-w

Jakob Toudahl Nielsen, Frans A. A. Mulder

引用次数: 12

Optimized precursor to simplify assignment transfer between backbone resonances and stereospecifically labelled valine and leucine methyl groups: application to human Hsp90 N-terminal domain 优化前体以简化主链共振与立体特异标记的缬氨酸和亮氨酸甲基之间的分配转移:在人Hsp90 n端结构域的应用

IF 2.7 3区生物学

Journal of Biomolecular NMR Pub Date : 2021-05-27 DOI: 10.1007/s10858-021-00370-0

Faustine Henot, Rime Kerfah, Ricarda Törner, Pavel Macek, Elodie Crublet, Pierre Gans, Matthias Frech, Olivier Hamelin, Jerome Boisbouvier

{"title":"Optimized precursor to simplify assignment transfer between backbone resonances and stereospecifically labelled valine and leucine methyl groups: application to human Hsp90 N-terminal domain","authors":"Faustine Henot, Rime Kerfah, Ricarda Törner, Pavel Macek, Elodie Crublet, Pierre Gans, Matthias Frech, Olivier Hamelin, Jerome Boisbouvier","doi":"10.1007/s10858-021-00370-0","DOIUrl":"10.1007/s10858-021-00370-0","url":null,"abstract":"<div>Methyl moieties are highly valuable probes for quantitative NMR studies of large proteins. Hence, their assignment is of the utmost interest to obtain information on both interactions and dynamics of proteins in solution. Here, we present the synthesis of a new precursor that allows connection of leucine and valine pro-S methyl moieties to backbone atoms by linear 13C-chains. This optimized 2H/13C-labelled acetolactate precursor can be combined with existing 13C/2H-alanine and isoleucine precursors in order to directly transfer backbone assignment to the corresponding methyl groups. Using this simple approach leucine and valine pro-S methyl groups can be assigned using a single sample without requiring correction of 1H/2H isotopic shifts on 13C resonances. The approach was demonstrated on the N-terminal domain of human HSP90, for which complete assignment of Ala-β, Ile-δ1, Leu-δ2, Met-ε, Thr-γ and Val-γ2 methyl groups was obtained.</div>","PeriodicalId":613,"journal":{"name":"Journal of Biomolecular NMR","volume":"75 6-7","pages":"221 - 232"},"PeriodicalIF":2.7,"publicationDate":"2021-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10858-021-00370-0","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"5054641","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: 4