Journal of Biomolecular NMR最新文献_第9页

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

A simple approach for reconstruction of non-uniformly sampled pseudo-3D NMR data for accurate measurement of spin relaxation parameters 一种用于精确测量自旋弛豫参数的非均匀采样伪三维核磁共振数据重建的简单方法

IF 2.7 3区生物学

Journal of Biomolecular NMR Pub Date : 2021-05-07 DOI: 10.1007/s10858-021-00369-7

Kyle W. East, Frank Delaglio, George P. Lisi

{"title":"A simple approach for reconstruction of non-uniformly sampled pseudo-3D NMR data for accurate measurement of spin relaxation parameters","authors":"Kyle W. East, Frank Delaglio, George P. Lisi","doi":"10.1007/s10858-021-00369-7","DOIUrl":"10.1007/s10858-021-00369-7","url":null,"abstract":"<div>We explain how to conduct a pseudo-3D relaxation series NUS measurement so that it can be reconstructed by existing 3D NUS reconstruction methods to give accurate relaxation values. We demonstrate using reconstruction algorithms IST and SMILE that this 3D approach allows lower sampling densities than for independent 2D reconstructions. This is in keeping with the common finding that higher dimensionality increases signal sparsity, enabling lower sampling density. The approach treats the relaxation series as ordinary 3D time-domain data whose imaginary part in the pseudo-dimension is zero, and applies any suitably linear 3D NUS reconstruction method accordingly. Best results on measured and simulated data were achieved using acquisitions with 9 to 12 planes and exponential spacing in the pseudo-dimension out to ~ 2 times the inverse decay time. Given these criteria, in typical cases where 2D reconstructions require 50% sampling, the new 3D approach generates spectra reliably at sampling densities of 25%.</div>","PeriodicalId":613,"journal":{"name":"Journal of Biomolecular NMR","volume":"75 6-7","pages":"213 - 219"},"PeriodicalIF":2.7,"publicationDate":"2021-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10858-021-00369-7","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4311132","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

Quantifying the effects of long-range 13C-13C dipolar coupling on measured relaxation rates in RNA 定量长程13C-13C偶极偶联对RNA弛豫速率的影响

IF 2.7 3区生物学

Journal of Biomolecular NMR Pub Date : 2021-04-29 DOI: 10.1007/s10858-021-00368-8

Lukasz T. Olenginski, Theodore K. Dayie

{"title":"Quantifying the effects of long-range 13C-13C dipolar coupling on measured relaxation rates in RNA","authors":"Lukasz T. Olenginski, Theodore K. Dayie","doi":"10.1007/s10858-021-00368-8","DOIUrl":"https://doi.org/10.1007/s10858-021-00368-8","url":null,"abstract":"Selective stable isotope labeling has transformed structural and dynamics analysis of RNA by NMR spectroscopy. These methods can remove 13C-13C dipolar couplings that complicate 13C relaxation analyses. While these phenomena are well documented for sites with adjacent 13C nuclei (e.g. ribose C1′), less is known about so-called isolated sites (e.g. adenosine C2). To investigate and quantify the effects of long-range (>?2??) 13C-13C dipolar interactions on RNA dynamics, we simulated adenosine C2 relaxation rates in uniformly [U-13C/15N]-ATP or selectively [2-13C]-ATP labeled RNAs. Our simulations predict non-negligible 13C-13C dipolar contributions from adenosine C4, C5, and C6 to C2 longitudinal (R1) relaxation rates in [U-13C/15N]-ATP labeled RNAs. Moreover, these contributions increase at higher magnetic fields and molecular weights to introduce discrepancies that exceed 50%. This will become increasingly important at GHz fields. Experimental R1 measurements in the 61 nucleotide human hepatitis B virus encapsidation signal ε RNA labeled with [U-13C/15N]-ATP or [2-13C]-ATP corroborate these simulations. Thus, in the absence of selectively labeled samples, long-range 13C-13C dipolar contributions must be explicitly taken into account when interpreting adenosine C2 R1 rates in terms of motional models for large RNAs.","PeriodicalId":613,"journal":{"name":"Journal of Biomolecular NMR","volume":"75 4-5","pages":"203 - 211"},"PeriodicalIF":2.7,"publicationDate":"2021-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10858-021-00368-8","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"5589089","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

Spectral editing of alanine, serine, and threonine in uniformly labeled proteins based on frequency-selective homonuclear recoupling in solid-state NMR 基于固态核磁共振频率选择性同核重偶联的均匀标记蛋白质中丙氨酸、丝氨酸和苏氨酸的光谱编辑

IF 2.7 3区生物学

Journal of Biomolecular NMR Pub Date : 2021-04-22 DOI: 10.1007/s10858-021-00367-9

Hang Xiao, Zhengfeng Zhang, Yongxiang Zhao, Jun Yang

引用次数: 4