Journal of Biomolecular NMR最新文献_第7页

The time-zero HSQC method improves the linear free energy relationship of a polypeptide chain through the accurate measurement of residue-specific equilibrium constants 时间零HSQC方法通过精确测量残基特定平衡常数，改善了多肽链的线性自由能关系

IF 2.7 3区生物学

Journal of Biomolecular NMR Pub Date : 2022-06-14 DOI: 10.1007/s10858-022-00396-y

Seiichiro Hayashi, Daisuke Kohda

{"title":"The time-zero HSQC method improves the linear free energy relationship of a polypeptide chain through the accurate measurement of residue-specific equilibrium constants","authors":"Seiichiro Hayashi, Daisuke Kohda","doi":"10.1007/s10858-022-00396-y","DOIUrl":"10.1007/s10858-022-00396-y","url":null,"abstract":"<div><p>EXSY (exchange spectroscopy) NMR provides the residue-specific equilibrium constants, <i>K</i>, and residue-specific kinetic rate constants, <i>k</i>, of a polypeptide chain in a two-state exchange in the slow exchange regime. A linear free energy relationship (LFER) discovered in a log <i>k</i> versus log <i>K</i> plot is considered to be a physicochemical basis for smooth folding and conformational changes of protein molecules. For accurate determination of the thermodynamic and kinetic parameters, the measurement bias arising from state-specific differences in the R<sub>1</sub> and R<sub>2</sub> relaxation rates of <sup>1</sup>H and other nuclei in HSQC and EXSY experiments must be minimized. Here, we showed that the time-zero HSQC acquisition scheme (HSQC0) is effective for this purpose, in combination with a special analytical method (Π analysis) for EXSY. As an example, we applied the HSQC0 + Π method to the two-state exchange of nukacin ISK-1 in an aqueous solution. Nukacin ISK-1 is a 27-residue lantibiotic peptide containing three mono-sulfide linkages. The resultant bias-free residue-based LFER provided valuable insights into the transition state of the topological interconversion of nukacin ISK-1. We found that two amino acid residues were exceptions in the residue-based LFER relationship. We inferred that the two residues could adopt special conformations in the transition state, to allow the threading of some side chains through a ring structure formed by one of the mono-sulfide linkages. In this context, the two residues are a useful target for the manipulation of the physicochemical properties and biological activities of nukacin ISK-1.</p></div>","PeriodicalId":613,"journal":{"name":"Journal of Biomolecular NMR","volume":"76 3","pages":"87 - 94"},"PeriodicalIF":2.7,"publicationDate":"2022-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4578155","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: 3

Towards autonomous analysis of chemical exchange saturation transfer experiments using deep neural networks 基于深度神经网络的化学交换饱和转移实验自主分析

IF 2.7 3区生物学

Journal of Biomolecular NMR Pub Date : 2022-05-27 DOI: 10.1007/s10858-022-00395-z

Gogulan Karunanithy, Tairan Yuwen, Lewis E. Kay, D. Flemming Hansen

{"title":"Towards autonomous analysis of chemical exchange saturation transfer experiments using deep neural networks","authors":"Gogulan Karunanithy, Tairan Yuwen, Lewis E. Kay, D. Flemming Hansen","doi":"10.1007/s10858-022-00395-z","DOIUrl":"10.1007/s10858-022-00395-z","url":null,"abstract":"<div><p>Macromolecules often exchange between functional states on timescales that can be accessed with NMR spectroscopy and many NMR tools have been developed to characterise the kinetics and thermodynamics of the exchange processes, as well as the structure of the conformers that are involved. However, analysis of the NMR data that report on exchanging macromolecules often hinges on complex least-squares fitting procedures as well as human experience and intuition, which, in some cases, limits the widespread use of the methods. The applications of deep neural networks (DNNs) and artificial intelligence have increased significantly in the sciences, and recently, specifically, within the field of biomolecular NMR, where DNNs are now available for tasks such as the reconstruction of sparsely sampled spectra, peak picking, and virtual decoupling. Here we present a DNN for the analysis of chemical exchange saturation transfer (CEST) data reporting on two- or three-site chemical exchange involving sparse state lifetimes of between approximately 3–60 ms, the range most frequently observed via experiment. The work presented here focuses on the <sup>1</sup>H CEST class of methods that are further complicated, in relation to applications to other nuclei, by anti-phase features. The developed DNNs accurately predict the chemical shifts of nuclei in the exchanging species directly from anti-phase <sup>1</sup>H<sup>N</sup> CEST profiles, along with an uncertainty associated with the predictions. The performance of the DNN was quantitatively assessed using both synthetic and experimental anti-phase CEST profiles. The assessments show that the DNN accurately determines chemical shifts and their associated uncertainties. The DNNs developed here do not contain any parameters for the end-user to adjust and the method therefore allows for autonomous analysis of complex NMR data that report on conformational exchange.</p></div>","PeriodicalId":613,"journal":{"name":"Journal of Biomolecular NMR","volume":"76 3","pages":"75 - 86"},"PeriodicalIF":2.7,"publicationDate":"2022-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10858-022-00395-z.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"5054696","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: 6

Ligand-induced structural transitions combined with paramagnetic ions facilitate unambiguous NMR assignments of methyl groups in large proteins 配体诱导的结构转变与顺磁离子结合，促进了大蛋白质中甲基的明确核磁共振分配

IF 2.7 3区生物学

Journal of Biomolecular NMR Pub Date : 2022-04-10 DOI: 10.1007/s10858-022-00394-0

Lars Mühlberg, Tuncay Alarcin, Thorben Maass, Robert Creutznacher, Richard Küchler, Alvaro Mallagaray

{"title":"Ligand-induced structural transitions combined with paramagnetic ions facilitate unambiguous NMR assignments of methyl groups in large proteins","authors":"Lars Mühlberg, Tuncay Alarcin, Thorben Maass, Robert Creutznacher, Richard Küchler, Alvaro Mallagaray","doi":"10.1007/s10858-022-00394-0","DOIUrl":"10.1007/s10858-022-00394-0","url":null,"abstract":"<div><p>NMR spectroscopy allows the study of biomolecules in close-to-native conditions. Structural information can be inferred from the NMR spectra when an assignment is available. Protein assignment is usually a time-consuming task, being specially challenging in the case of large, supramolecular systems. Here, we present an extension of existing state-of-the-art strategies for methyl group assignment that partially overcomes signal overlapping and other difficulties associated to isolated methyl groups. Our approach exploits the ability of proteins to populate two or more conformational states, allowing for unique NOE restraints in each protein conformer. The method is compatible with automated assignment algorithms, granting assignments beyond the limits of a single protein state. The approach also benefits from long-range structural restraints obtained from metal-induced pseudocontact shifts (PCS) and paramagnetic relaxation enhancements (PREs). We illustrate the method with the complete assignment of the 199 methyl groups of a MIL<sup>proS</sup>V<sup>proS</sup>AT methyl-labeled sample of the UDP-glucose pyrophosphorylase enzyme from <i>Leishmania major</i> (LmUGP). Protozoan parasites of the genus <i>Leishmania</i> causes Leishmaniasis, a neglected disease affecting over 12 million people worldwide. LmUGP is responsible for the de novo biosynthesis of uridine diphosphate-glucose, a precursor in the biosynthesis of the dense surface glycocalyx involved in parasite survival and infectivity. NMR experiments with LmUGP and related enzymes have the potential to unravel new insights in the host resistance mechanisms used by <i>Leishmania major</i>. Our efforts will help in the development of selective and efficient drugs against <i>Leishmania</i>.</p></div>","PeriodicalId":613,"journal":{"name":"Journal of Biomolecular NMR","volume":"76 3","pages":"59 - 74"},"PeriodicalIF":2.7,"publicationDate":"2022-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10858-022-00394-0.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4410929","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: 0

Fundamental and practical aspects of machine learning for the peak picking of biomolecular NMR spectra 生物分子核磁共振波谱峰拾取的机器学习的基本和实际方面

IF 2.7 3区生物学

Journal of Biomolecular NMR Pub Date : 2022-04-07 DOI: 10.1007/s10858-022-00393-1

Da-Wei Li, Alexandar L. Hansen, Lei Bruschweiler-Li, Chunhua Yuan, Rafael Brüschweiler

{"title":"Fundamental and practical aspects of machine learning for the peak picking of biomolecular NMR spectra","authors":"Da-Wei Li, Alexandar L. Hansen, Lei Bruschweiler-Li, Chunhua Yuan, Rafael Brüschweiler","doi":"10.1007/s10858-022-00393-1","DOIUrl":"10.1007/s10858-022-00393-1","url":null,"abstract":"<div><p>Rapid progress in machine learning offers new opportunities for the automated analysis of multidimensional NMR spectra ranging from protein NMR to metabolomics applications. Most recently, it has been demonstrated how deep neural networks (DNN) designed for spectral peak picking are capable of deconvoluting highly crowded NMR spectra rivaling the facilities of human experts. Superior DNN-based peak picking is one of a series of critical steps during NMR spectral processing, analysis, and interpretation where machine learning is expected to have a major impact. In this perspective, we lay out some of the unique strengths as well as challenges of machine learning approaches in this new era of automated NMR spectral analysis. Such a discussion seems timely and should help define common goals for the NMR community, the sharing of software tools, standardization of protocols, and calibrate expectations. It will also help prepare for an NMR future where machine learning and artificial intelligence tools will be common place.</p></div>","PeriodicalId":613,"journal":{"name":"Journal of Biomolecular NMR","volume":"76 3","pages":"49 - 57"},"PeriodicalIF":2.7,"publicationDate":"2022-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10858-022-00393-1.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4285376","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

77Se-13C based dipolar correlation experiments to map selenium sites in microcrystalline proteins 基于77Se-13C的偶极相关实验在微晶蛋白中定位硒位点

IF 2.7 3区生物学

Journal of Biomolecular NMR Pub Date : 2022-03-23 DOI: 10.1007/s10858-022-00390-4

Caitlin M. Quinn, Shiping Xu, Guangjin Hou, Qingqing Chen, Deepak Sail, R. Andrew Byrd, Sharon Rozovsky

{"title":"77Se-13C based dipolar correlation experiments to map selenium sites in microcrystalline proteins","authors":"Caitlin M. Quinn, Shiping Xu, Guangjin Hou, Qingqing Chen, Deepak Sail, R. Andrew Byrd, Sharon Rozovsky","doi":"10.1007/s10858-022-00390-4","DOIUrl":"10.1007/s10858-022-00390-4","url":null,"abstract":"<div><p>Sulfur-containing sites in proteins are of great importance for both protein structure and function, including enzymatic catalysis, signaling pathways, and recognition of ligands and protein partners. Selenium-77 is an NMR active spin-1/2 nucleus that shares many physiochemical properties with sulfur and can be readily introduced into proteins at sulfur sites without significant perturbations to the protein structure. The sulfur-containing amino acid methionine is commonly found at protein–protein or protein–ligand binding sites. Its selenium-containing counterpart, selenomethionine, has a broad chemical shift dispersion useful for NMR-based studies of complex systems. Methods such as (<sup>1</sup>H)-<sup>77</sup>Se-<sup>13</sup>C double cross polarization or {<sup>77</sup>Se}-<sup>13</sup>C REDOR could be valuable to map the local environment around selenium sites in proteins but have not been demonstrated to date. In this work, we explore these dipolar transfer mechanisms for structural characterization of the GB1 V39SeM variant of the model protein GB1 and demonstrate that <sup>77</sup>Se-<sup>13</sup>C based correlations can be used to map the local environment around selenium sites in proteins. We have found that the general detection limit is ~ 5 Å, but longer range distances up to ~ 7 Å can be observed as well. This study establishes a framework for the future characterization of selenium sites at protein–protein or protein–ligand binding interfaces.\u0000</p></div>","PeriodicalId":613,"journal":{"name":"Journal of Biomolecular NMR","volume":"76 1-2","pages":"29 - 37"},"PeriodicalIF":2.7,"publicationDate":"2022-03-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10858-022-00390-4.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4906123","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: 0

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":"76 1-2","pages":"39 - 47"},"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":"76 1-2","pages":"3 - 15"},"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