Journal of Biomolecular NMR最新文献_第7页

Journal of Biomolecular NMR: Editorial 生物分子核磁共振杂志:编辑

IF 2.7 3区生物学

Journal of Biomolecular NMR Pub Date : 2022-03-22 DOI: 10.1007/s10858-022-00391-3

Art Palmer

引用次数: 0

Optimization and validation of multi-state NMR protein structures using structural correlations 利用结构关联优化和验证多态核磁共振蛋白结构

IF 2.7 3区生物学

Journal of Biomolecular NMR Pub Date : 2022-03-19 DOI: 10.1007/s10858-022-00392-2

Dzmitry Ashkinadze, Harindranath Kadavath, Roland Riek, Peter Güntert

{"title":"Optimization and validation of multi-state NMR protein structures using structural correlations","authors":"Dzmitry Ashkinadze, Harindranath Kadavath, Roland Riek, Peter Güntert","doi":"10.1007/s10858-022-00392-2","DOIUrl":"10.1007/s10858-022-00392-2","url":null,"abstract":"<div><p>Recent advances in the field of protein structure determination using liquid-state NMR enable the elucidation of multi-state protein conformations that can provide insight into correlated and non-correlated protein dynamics at atomic resolution. So far, NMR-derived multi-state structures were typically evaluated by means of visual inspection of structure superpositions, target function values that quantify the violation of experimented restraints and root-mean-square deviations that quantify similarity between conformers. As an alternative or complementary approach, we present here the use of a recently introduced structural correlation measure, PDBcor, that quantifies the clustering of protein states as an additional measure for multi-state protein structure analysis. It can be used for various assays including the validation of experimental distance restraints, optimization of the number of protein states, estimation of protein state populations, identification of key distance restraints, NOE network analysis and semiquantitative analysis of the protein correlation network. We present applications for the final quality analysis stages of typical multi-state protein structure calculations.</p></div>","PeriodicalId":613,"journal":{"name":"Journal of Biomolecular NMR","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2022-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10858-022-00392-2.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4760162","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

Site-specific protein methyl deuterium quadrupolar patterns by proton-detected 3D 2H–13C–1H MAS NMR spectroscopy 质子检测3D 2H-13C-1H MAS NMR的位点特异性蛋白甲基氘四极性模式

IF 2.7 3区生物学

Journal of Biomolecular NMR Pub Date : 2022-01-08 DOI: 10.1007/s10858-021-00388-4

Ümit Akbey

引用次数: 3

Monitoring protein unfolding transitions by NMR-spectroscopy 核磁共振光谱监测蛋白质展开转变

IF 2.7 3区生物学

Journal of Biomolecular NMR Pub Date : 2022-01-04 DOI: 10.1007/s10858-021-00389-3

Matthias Dreydoppel, Jochen Balbach, Ulrich Weininger

{"title":"Monitoring protein unfolding transitions by NMR-spectroscopy","authors":"Matthias Dreydoppel, Jochen Balbach, Ulrich Weininger","doi":"10.1007/s10858-021-00389-3","DOIUrl":"10.1007/s10858-021-00389-3","url":null,"abstract":"<div><p>NMR-spectroscopy has certain unique advantages for recording unfolding transitions of proteins compared e.g. to optical methods. It enables per-residue monitoring and separate detection of the folded and unfolded state as well as possible equilibrium intermediates. This allows a detailed view on the state and cooperativity of folding of the protein of interest and the correct interpretation of subsequent experiments. Here we summarize in detail practical and theoretical aspects of such experiments. Certain pitfalls can be avoided, and meaningful simplification can be made during the analysis. Especially a good understanding of the NMR exchange regime and relaxation properties of the system of interest is beneficial. We show by a global analysis of signals of the folded and unfolded state of GB1 how accurate values of unfolding can be extracted and what limits different NMR detection and unfolding methods. E.g. commonly used exchangeable amides can lead to a systematic under determination of the thermodynamic protein stability. We give several perspectives of how to deal with more complex proteins and how the knowledge about protein stability at residue resolution helps to understand protein properties under crowding conditions, during phase separation and under high pressure.</p></div>","PeriodicalId":613,"journal":{"name":"Journal of Biomolecular NMR","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2022-01-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10858-021-00389-3.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4502881","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: 3

Glutamine-free mammalian expression of recombinant glycoproteins with uniform isotope labeling: an application for NMR analysis of pharmaceutically relevant Fc glycoforms of human immunoglobulin G1 用统一同位素标记的重组糖蛋白的无谷氨酰胺哺乳动物表达:用于人类免疫球蛋白G1药用相关Fc糖型的核磁共振分析的应用

IF 2.7 3区生物学

Journal of Biomolecular NMR Pub Date : 2022-01-03 DOI: 10.1007/s10858-021-00387-5

Saeko Yanaka, Hirokazu Yagi, Rina Yogo, Masayoshi Onitsuka, Koichi Kato

引用次数: 5

Protein resonance assignment by solid-state NMR based on 1H-detected 13C double-quantum spectroscopy at fast MAS 基于快速MAS下1h检测13C双量子光谱的固态核磁共振蛋白质共振配位

IF 2.7 3区生物学

Journal of Biomolecular NMR Pub Date : 2021-11-23 DOI: 10.1007/s10858-021-00386-6

Alons Lends, Mélanie Berbon, Birgit Habenstein, Yusuke Nishiyama, Antoine Loquet

{"title":"Protein resonance assignment by solid-state NMR based on 1H-detected 13C double-quantum spectroscopy at fast MAS","authors":"Alons Lends, Mélanie Berbon, Birgit Habenstein, Yusuke Nishiyama, 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 (<sup>1</sup>H) detection at fast magic-angle spinning (MAS) has considerably increased the analytical capabilities of the technique, enabling the acquisition of <sup>1</sup>H-detected fingerprint experiments in few hours. Here an approach based on double-quantum (DQ) <sup>13</sup>C spectroscopy, detected on <sup>1</sup>H, is proposed for fast MAS regime (> 60 kHz) to perform the sequential assignment of insoluble proteins of small size, without any specific deuteration requirement. By combining two three-dimensional <sup>1</sup>H detected experiments correlating a <sup>13</sup>C DQ dimension respectively to its intra-residue and sequential <sup>15</sup> N-<sup>1</sup>H 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":null,"pages":null},"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}

引用次数: 4

Clustered sparsity and Poisson-gap sampling 聚类稀疏性和泊松间隙抽样

IF 2.7 3区生物学

Journal of Biomolecular NMR Pub Date : 2021-11-05 DOI: 10.1007/s10858-021-00385-7

Paweł Kasprzak, Mateusz Urbańczyk, Krzysztof Kazimierczuk

{"title":"Clustered sparsity and Poisson-gap sampling","authors":"Paweł Kasprzak, Mateusz Urbańczyk, 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":null,"pages":null},"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}

引用次数: 9

Efficient solvent suppression with adiabatic inversion for 1H-detected solid-state NMR 高效溶剂抑制与绝热反演的1h检测固态核磁共振

IF 2.7 3区生物学

Journal of Biomolecular NMR Pub Date : 2021-10-21 DOI: 10.1007/s10858-021-00384-8

Tatsuya Matsunaga, Ryotaro Okabe, Yoshitaka Ishii

引用次数: 4

Correction to: An automated iterative approach for protein structure refinement using pseudocontact shifts 修正:一种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 : 2021-10-13 DOI: 10.1007/s10858-021-00378-6

Stefano Cucuzza, Peter Güntert, Andreas Plückthun, Oliver Zerbe

引用次数: 0

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 利用受体聚集和核磁共振光谱对结合配体进行简单灵敏的检测:麦芽糖结合蛋白的一个测试案例

IF 2.7 3区生物学

Journal of Biomolecular NMR Pub Date : 2021-09-15 DOI: 10.1007/s10858-021-00381-x

Young Kee Chae, Yoonjin Um, Hakbeom Kim

{"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, Yoonjin Um, 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":null,"pages":null},"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}

引用次数: 1