Journal of Biomolecular NMR最新文献_第9页

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":null,"pages":null},"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

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":null,"pages":null},"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

FID-Net: A versatile deep neural network architecture for NMR spectral reconstruction and virtual decoupling FID-Net:用于核磁共振光谱重建和虚拟解耦的通用深度神经网络架构

IF 2.7 3区生物学

Journal of Biomolecular NMR Pub Date : 2021-04-19 DOI: 10.1007/s10858-021-00366-w

Gogulan Karunanithy, D. Flemming Hansen

{"title":"FID-Net: A versatile deep neural network architecture for NMR spectral reconstruction and virtual decoupling","authors":"Gogulan Karunanithy, D. Flemming Hansen","doi":"10.1007/s10858-021-00366-w","DOIUrl":"https://doi.org/10.1007/s10858-021-00366-w","url":null,"abstract":"In recent years, the transformative potential of deep neural networks (DNNs) for analysing and interpreting NMR data has clearly been recognised. However, most applications of DNNs in NMR to date either struggle to outperform existing methodologies or are limited in scope to a narrow range of data that closely resemble the data that the network was trained on. These limitations have prevented a widescale uptake of DNNs in NMR. Addressing this, we introduce FID-Net, a deep neural network architecture inspired by WaveNet, for performing analyses on time domain NMR data. We first demonstrate the effectiveness of this architecture in reconstructing non-uniformly sampled (NUS) biomolecular NMR spectra. It is shown that a single network is able to reconstruct a diverse range of 2D NUS spectra that have been obtained with arbitrary sampling schedules, with a range of sweep widths, and a variety of other acquisition parameters. The performance of the trained FID-Net in this case exceeds or matches existing methods currently used for the reconstruction of NUS NMR spectra. Secondly, we present a network based on the FID-Net architecture that can efficiently virtually decouple 13Cα-13Cβ couplings in HNCA protein NMR spectra in a single shot analysis, while at the same time leaving glycine residues unmodulated. The ability for these DNNs to work effectively in a wide range of scenarios, without retraining, paves the way for their widespread usage in analysing NMR data.","PeriodicalId":613,"journal":{"name":"Journal of Biomolecular NMR","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2021-04-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10858-021-00366-w","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4739617","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: 26

A COVID moonshot: assessment of ligand binding to the SARS-CoV-2 main protease by saturation transfer difference NMR spectroscopy COVID登月计划:利用饱和转移差核磁共振光谱评估配体与SARS-CoV-2主要蛋白酶的结合

IF 2.7 3区生物学

Journal of Biomolecular NMR Pub Date : 2021-04-15 DOI: 10.1007/s10858-021-00365-x

Anastassia L. Kantsadi, Emma Cattermole, Minos-Timotheos Matsoukas, Georgios A. Spyroulias, Ioannis Vakonakis

{"title":"A COVID moonshot: assessment of ligand binding to the SARS-CoV-2 main protease by saturation transfer difference NMR spectroscopy","authors":"Anastassia L. Kantsadi, Emma Cattermole, Minos-Timotheos Matsoukas, Georgios A. Spyroulias, Ioannis Vakonakis","doi":"10.1007/s10858-021-00365-x","DOIUrl":"https://doi.org/10.1007/s10858-021-00365-x","url":null,"abstract":"Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiological cause of the coronavirus disease 2019, for which no effective antiviral therapeutics are available. The SARS-CoV-2 main protease (Mpro) is essential for viral replication and constitutes a promising therapeutic target. Many efforts aimed at deriving effective Mpro inhibitors are currently underway, including an international open-science discovery project, codenamed COVID Moonshot. As part of COVID Moonshot, we used saturation transfer difference nuclear magnetic resonance (STD-NMR) spectroscopy to assess the binding of putative Mpro ligands to the viral protease, including molecules identified by crystallographic fragment screening and novel compounds designed as Mpro inhibitors. In this manner, we aimed to complement enzymatic activity assays of Mpro performed by other groups with information on ligand affinity. We have made the Mpro STD-NMR data publicly available. Here, we provide detailed information on the NMR protocols used and challenges faced, thereby placing these data into context. Our goal is to assist the interpretation of Mpro STD-NMR data, thereby accelerating ongoing drug design efforts.","PeriodicalId":613,"journal":{"name":"Journal of Biomolecular NMR","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2021-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10858-021-00365-x","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4598986","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

Comparative analysis of 13C chemical shifts of β-sheet amyloid proteins and outer membrane proteins β-片淀粉样蛋白与外膜蛋白13C化学位移的比较分析

IF 2.7 3区生物学

Journal of Biomolecular NMR Pub Date : 2021-04-12 DOI: 10.1007/s10858-021-00364-y

Noah H. Somberg, Martin D. Gelenter, Mei Hong

{"title":"Comparative analysis of 13C chemical shifts of β-sheet amyloid proteins and outer membrane proteins","authors":"Noah H. Somberg, Martin D. Gelenter, Mei Hong","doi":"10.1007/s10858-021-00364-y","DOIUrl":"https://doi.org/10.1007/s10858-021-00364-y","url":null,"abstract":"Cross-β amyloid fibrils and membrane-bound β-barrels are two important classes of β-sheet proteins. To investigate whether there are systematic differences in the backbone and sidechain conformations of these two families of proteins, here we analyze the 13C chemical shifts of 17 amyloid proteins and 7 β-barrel membrane proteins whose high-resolution structures have been determined by NMR. These 24 proteins contain 373 β-sheet residues in amyloid fibrils and 521 β-sheet residues in β-barrel membrane proteins. The 13C chemical shifts are shown in 2D 13C–13C correlation maps, and the amino acid residues are categorized by two criteria: (1) whether they occur in β-strand segments or in loops and turns; (2) whether they are water-exposed or dry, facing other residues or lipids. We also examine the abundance of each amino acid in amyloid proteins and β-barrels and compare the sidechain rotameric populations. The 13C chemical shifts indicate that hydrophobic methyl-rich residues and aromatic residues exhibit larger static sidechain conformational disorder in amyloid fibrils than in β-barrels. In comparison, hydroxyl- and amide-containing polar residues have more ordered sidechains and more ordered backbones in amyloid fibrils than in β-barrels. These trends can be explained by steric zipper interactions between β-sheet planes in cross-β fibrils, and by the interactions of β-barrel residues with lipid and water in the membrane. These conformational trends should be useful for structural analysis of amyloid fibrils and β-barrels based principally on NMR chemical shifts.","PeriodicalId":613,"journal":{"name":"Journal of Biomolecular NMR","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2021-04-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10858-021-00364-y","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4481541","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

NMR refinement and peptide folding using the GROMACS software 使用GROMACS软件进行核磁共振细化和肽折叠

IF 2.7 3区生物学

Journal of Biomolecular NMR Pub Date : 2021-03-28 DOI: 10.1007/s10858-021-00363-z

Anna Sinelnikova, David van der Spoel

引用次数: 8

How wide is the window opened by high-resolution relaxometry on the internal dynamics of proteins in solution? 高分辨率弛豫测量法对溶液中蛋白质内部动力学的影响有多大?

IF 2.7 3区生物学

Journal of Biomolecular NMR Pub Date : 2021-03-23 DOI: 10.1007/s10858-021-00361-1

Albert A. Smith, Nicolas Bolik-Coulon, Matthias Ernst, Beat H. Meier, Fabien Ferrage

{"title":"How wide is the window opened by high-resolution relaxometry on the internal dynamics of proteins in solution?","authors":"Albert A. Smith, Nicolas Bolik-Coulon, Matthias Ernst, Beat H. Meier, Fabien Ferrage","doi":"10.1007/s10858-021-00361-1","DOIUrl":"https://doi.org/10.1007/s10858-021-00361-1","url":null,"abstract":"The dynamics of molecules in solution is usually quantified by the determination of timescale-specific amplitudes of motions. High-resolution nuclear magnetic resonance (NMR) relaxometry experiments—where the sample is transferred to low fields for longitudinal (T1) relaxation, and back to high field for detection with residue-specific resolution—seeks to increase the ability to distinguish the contributions from motion on timescales slower than a few nanoseconds. However, tumbling of a molecule in solution masks some of these motions. Therefore, we investigate to what extent relaxometry improves timescale resolution, using the “detector” analysis of dynamics. Here, we demonstrate improvements in the characterization of internal dynamics of methyl-bearing side chains by carbon-13 relaxometry in the small protein ubiquitin. We show that relaxometry data leads to better information about nanosecond motions as compared to high-field relaxation data only. Our calculations show that gains from relaxometry are greater with increasing correlation time of rotational diffusion.","PeriodicalId":613,"journal":{"name":"Journal of Biomolecular NMR","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2021-03-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10858-021-00361-1","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4904961","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: 8