Journal of Biomolecular NMR最新文献

{"title":"Protein resonance assignment by solid-state NMR based on 1H-detected 13C double-quantum spectroscopy at fast MAS","authors":"Alons Lends,&nbsp;Mélanie Berbon,&nbsp;Birgit Habenstein,&nbsp;Yusuke Nishiyama,&nbsp;Antoine Loquet","doi":"10.1007/s10858-021-00386-6","DOIUrl":"10.1007/s10858-021-00386-6","url":null,"abstract":"<div><p>Solid-state NMR spectroscopy is a powerful technique to study insoluble and non-crystalline proteins and protein complexes at atomic resolution. The development of proton (¹H) detection at fast magic-angle spinning (MAS) has considerably increased the analytical capabilities of the technique, enabling the acquisition of ¹H-detected fingerprint experiments in few hours. Here an approach based on double-quantum (DQ) ¹³C spectroscopy, detected on ¹H, is proposed for fast MAS regime (&gt; 60 kHz) to perform the sequential assignment of insoluble proteins of small size, without any specific deuteration requirement. By combining two three-dimensional ¹H detected experiments correlating a ¹³C DQ dimension respectively to its intra-residue and sequential ¹⁵ N-¹H pairs, a sequential walk through DQ (Ca + CO) resonance is obtained. The approach takes advantage of fast MAS to achieve an efficient sensitivity and the addition of a DQ dimension provides spectral features useful for the resonance assignment process.</p></div>","PeriodicalId":613,"journal":{"name":"Journal of Biomolecular NMR","volume":"75 10-12","pages":"417 - 427"},"PeriodicalIF":2.7,"publicationDate":"2021-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10858-021-00386-6.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4909078","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}

{"title":"Clustered sparsity and Poisson-gap sampling","authors":"Paweł Kasprzak,&nbsp;Mateusz Urbańczyk,&nbsp;Krzysztof Kazimierczuk","doi":"10.1007/s10858-021-00385-7","DOIUrl":"10.1007/s10858-021-00385-7","url":null,"abstract":"<div><p>Non-uniform sampling (NUS) is a popular way of reducing the amount of time taken by multidimensional NMR experiments. Among the various non-uniform sampling schemes that exist, the Poisson-gap (PG) schedules are particularly popular, especially when combined with compressed-sensing (CS) reconstruction of missing data points. However, the use of PG is based mainly on practical experience and has not, as yet, been explained in terms of CS theory. Moreover, an apparent contradiction exists between the reported effectiveness of PG and CS theory, which states that a “flat” pseudo-random generator is the best way to generate sampling schedules in order to reconstruct sparse spectra. In this paper we explain how, and in what situations, PG reveals its superior features in NMR spectroscopy. We support our theoretical considerations with simulations and analyses of experimental data from the Biological Magnetic Resonance Bank (BMRB). Our analyses reveal a previously unnoticed feature of many NMR spectra that explains the success of ”blue-noise” schedules, such as PG. We call this feature “clustered sparsity”. This refers to the fact that the peaks in NMR spectra are not just sparse but often form clusters in the indirect dimension, and PG is particularly suited to deal with such situations. Additionally, we discuss why denser sampling in the initial and final parts of the clustered signal may be useful.</p></div>","PeriodicalId":613,"journal":{"name":"Journal of Biomolecular NMR","volume":"75 10-12","pages":"401 - 416"},"PeriodicalIF":2.7,"publicationDate":"2021-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10858-021-00385-7.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4228439","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}

{"title":"Efficient solvent suppression with adiabatic inversion for 1H-detected solid-state NMR","authors":"Tatsuya Matsunaga,&nbsp;Ryotaro Okabe,&nbsp;Yoshitaka Ishii","doi":"10.1007/s10858-021-00384-8","DOIUrl":"10.1007/s10858-021-00384-8","url":null,"abstract":"<div><p>This study introduces a conceptually new solvent suppression scheme with adiabatic inversion pulses for ¹H-detected multidimensional solid-state NMR (SSNMR) of biomolecules and other systems, which is termed “Solvent suppression of Liquid signal with Adiabatic Pulse” (SLAP). ¹H-detected 2D ¹³C/¹H SSNMR data of uniformly ¹³C- and ¹⁵N-labeled GB1 sample using ultra-fast magic angle spinning at a spinning rate of 60 kHz demonstrated that the SLAP scheme showed up to 3.5-fold better solvent suppression performance over a traditional solvent-suppression scheme for SSNMR, MISSISSIPPI (Zhou and Rienstra, J Magn Reson 192:167–172, 2008) with 2/3 of the average RF power.</p></div>","PeriodicalId":613,"journal":{"name":"Journal of Biomolecular NMR","volume":"75 10-12","pages":"365 - 370"},"PeriodicalIF":2.7,"publicationDate":"2021-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4839561","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}

{"title":"Correction to: An automated iterative approach for protein structure refinement using pseudocontact shifts","authors":"Stefano Cucuzza,&nbsp;Peter Güntert,&nbsp;Andreas Plückthun,&nbsp;Oliver Zerbe","doi":"10.1007/s10858-021-00378-6","DOIUrl":"10.1007/s10858-021-00378-6","url":null,"abstract":"","PeriodicalId":613,"journal":{"name":"Journal of Biomolecular NMR","volume":"75 10-12","pages":"429 - 430"},"PeriodicalIF":2.7,"publicationDate":"2021-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10858-021-00378-6.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4558299","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}

{"title":"A simple and sensitive detection of the binding ligands by using the receptor aggregation and NMR spectroscopy: a test case of the maltose binding protein","authors":"Young Kee Chae,&nbsp;Yoonjin Um,&nbsp;Hakbeom Kim","doi":"10.1007/s10858-021-00381-x","DOIUrl":"10.1007/s10858-021-00381-x","url":null,"abstract":"<div><p>Protein-ligand interaction is one of the highlights of molecular recognition. The most popular application of this type of interaction is drug development which requires a high throughput screening of a ligand that binds to the target protein. Our goal was to find a binding ligand with a simple detection, and once this type of ligand was found, other methods could then be used to measure the detailed kinetic or thermodynamic parameters. We started with the idea that the ligand NMR signal would disappear if it was bound to the non-tumbling mass. In order to create the non-tumbling mass, we tried the aggregates of a target protein, which was fused to the elastin-like polypeptide. We chose the maltose binding proteinas a test case, and we tried it with several sugars, which included maltose, glucose, sucrose, lactose, galactose, maltotriose, and β-cyclodextrin. The maltose signal in the H-1 NMR spectrum disappeared completely as hoped around the protein to ligand ratio of 1:3 at 298 K where the proteins aggregated. The protein signals also disappeared upon aggregation except for the fast-moving part, which resulted in a cleaner background than the monomeric form. Since we only needed to look for a disappearing signal amongst those from the mixture, it should be useful in high throughput screening. Other types of sugars except for the maltotriose and β-cyclodextrin, which are siblings of the maltose, did not seem to bind at all. We believe that our system would be especially more effective when dealing with a smaller target protein, so both the protein and the bound ligand would lose their signals only when the aggregates formed. We hope that our proposed method would contribute to accelerating the development of the potent drug candidates by simultaneously identifying several binders directly from a mixture.</p></div>","PeriodicalId":613,"journal":{"name":"Journal of Biomolecular NMR","volume":"75 10-12","pages":"371 - 381"},"PeriodicalIF":2.7,"publicationDate":"2021-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10858-021-00381-x.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4631088","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}

{"title":"1H R1ρ relaxation dispersion experiments in aromatic side chains","authors":"Matthias Dreydoppel,&nbsp;Roman J. Lichtenecker,&nbsp;Mikael Akke,&nbsp;Ulrich Weininger","doi":"10.1007/s10858-021-00382-w","DOIUrl":"10.1007/s10858-021-00382-w","url":null,"abstract":"<div><p>Aromatic side chains are attractive probes of protein dynamic, since they are often key residues in enzyme active sites and protein binding sites. Dynamic processes on microsecond to millisecond timescales can be studied by relaxation dispersion experiments that attenuate conformational exchange contributions to the transverse relaxation rate by varying the refocusing frequency of applied radio-frequency fields implemented as either CPMG pulse trains or continuous spin-lock periods. Here we present an aromatic ¹H <i>R</i>_1<i>ρ</i> relaxation dispersion experiment enabling studies of two to three times faster exchange processes than achievable by existing experiments for aromatic side chains. We show that site-specific isotope labeling schemes generating isolated ¹H–¹³C spin pairs with vicinal ²H–¹²C moieties are necessary to avoid anomalous relaxation dispersion profiles caused by Hartmann–Hahn matching due to the ³<i>J</i>_HH couplings and limited chemical shift differences among ¹H spins in phenylalanine, tyrosine and the six-ring moiety of tryptophan. This labeling pattern is sufficient in that remote protons do not cause additional complications. We validated the approach by measuring ring-flip kinetics in the small protein GB1. The determined rate constants, <i>k</i>_flip, agree well with previous results from ¹³C <i>R</i>_1<i>ρ</i> relaxation dispersion experiments, and yield ¹H chemical shift differences between the two sides of the ring in good agreement with values measured under slow-exchange conditions. The aromatic¹H <i>R</i>_1<i>ρ</i> relaxation dispersion experiment in combination with the site-selective ¹H–¹³C/²H–¹²C labeling scheme enable measurement of exchange rates up to <i>k</i>_ex = 2<i>k</i>_flip = 80,000 s^–1, and serve as a useful complement to previously developed ¹³C-based methods.</p></div>","PeriodicalId":613,"journal":{"name":"Journal of Biomolecular NMR","volume":"75 10-12","pages":"383 - 392"},"PeriodicalIF":2.7,"publicationDate":"2021-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10858-021-00382-w.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4814138","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}

{"title":"CSI-LSTM: a web server to predict protein secondary structure using bidirectional long short term memory and NMR chemical shifts","authors":"Zhiwei Miao,&nbsp;Qianqian Wang,&nbsp;Xiongjie Xiao,&nbsp;Ghulam Mustafa Kamal,&nbsp;Linhong Song,&nbsp;Xu Zhang,&nbsp;Conggang Li,&nbsp;Xin Zhou,&nbsp;Bin Jiang,&nbsp;Maili Liu","doi":"10.1007/s10858-021-00383-9","DOIUrl":"10.1007/s10858-021-00383-9","url":null,"abstract":"<div><p>Protein secondary structure provides rich structural information, hence the description and understanding of protein structure relies heavily on it. Identification or prediction of secondary structures therefore plays an important role in protein research. In protein NMR studies, it is more convenient to predict secondary structures from chemical shifts as compared to the traditional determination methods based on inter-nuclear distances provided by NOESY experiment. In recent years, there was a significant improvement observed in deep neural networks, which had been applied in many research fields. Here we proposed a deep neural network based on bidirectional long short term memory (biLSTM) to predict protein 3-state secondary structure using NMR chemical shifts of backbone nuclei. While comparing with the existing methods the proposed method showed better prediction accuracy. Based on the proposed method, a web server has been built to provide protein secondary structure prediction service.</p></div>","PeriodicalId":613,"journal":{"name":"Journal of Biomolecular NMR","volume":"75 10-12","pages":"393 - 400"},"PeriodicalIF":2.7,"publicationDate":"2021-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4515765","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}

{"title":"Evaluation of the tert-butyl group as a probe for NMR studies of macromolecular complexes","authors":"Rashmi Voleti,&nbsp;Sofia Bali,&nbsp;Jaime Guerrero,&nbsp;Jared Smothers,&nbsp;Charis Springhower,&nbsp;Gerardo A. Acosta,&nbsp;Kyle D. Brewer,&nbsp;Fernando Albericio,&nbsp;Josep Rizo","doi":"10.1007/s10858-021-00380-y","DOIUrl":"10.1007/s10858-021-00380-y","url":null,"abstract":"<div><p>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.</p></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}

{"title":"TRACT revisited: an algebraic solution for determining overall rotational correlation times from cross-correlated relaxation rates","authors":"Scott A. Robson,&nbsp;Çağdaş Dağ,&nbsp;Hongwei Wu,&nbsp;Joshua J. Ziarek","doi":"10.1007/s10858-021-00379-5","DOIUrl":"10.1007/s10858-021-00379-5","url":null,"abstract":"<div><p>Accurate rotational correlation times (<span>({tau }_{text{c}})</span>) are critical for quantitative analysis of fast timescale NMR dynamics. As molecular weights increase, the classic derivation of <span>({tau }_{c})</span> 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 <span>({tau }_{text{c}})</span> estimation. These solutions enabled us to explore the boundaries of the Goldman relationship as a function of the H–N internuclear distance (<span>(r)</span>), difference of the two principal components of the axially-symmetric ¹⁵N CSA tensor (<span>(Delta {delta }_{N})</span>), and angle of the CSA tensor relative to the N–H bond vector (<span>(theta)</span>). We hope our algebraic solutions and analytical strategies will increase the accuracy and application of the TRACT experiment.</p></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}

{"title":"Off-resonance 13C–2H REDOR NMR for site-resolved studies of molecular motion","authors":"Martin D. Gelenter,&nbsp;Kelly J. Chen,&nbsp;Mei Hong","doi":"10.1007/s10858-021-00377-7","DOIUrl":"10.1007/s10858-021-00377-7","url":null,"abstract":"<div><p>We introduce a ¹³C–²H Rotational Echo DOuble Resonance (REDOR) technique that uses the difference between on-resonance and off-resonance ²H irradiation to detect dynamic segments in deuterated molecules. By selectively inverting specific regions of the ²H magic-angle spinning (MAS) sideband manifold to recouple some of the deuterons to nearby carbons, we distinguish dynamic and rigid residues in 1D and 2D ¹³C spectra. We demonstrate this approach on deuterated GB1, H/D exchanged GB1, and perdeuterated bacterial cellulose. Numerical simulations reproduce the measured mixing-time and ²H carrier-frequency dependence of the REDOR dephasing of bacterial cellulose. Combining numerical simulations with experiments thus allow the extraction of motionally averaged quadrupolar couplings from REDOR dephasing values.</p></div>","PeriodicalId":613,"journal":{"name":"Journal of Biomolecular NMR","volume":"75 8-9","pages":"335 - 345"},"PeriodicalIF":2.7,"publicationDate":"2021-08-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10858-021-00377-7.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4110760","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}