Magnetic resonance (Gottingen, Germany)最新文献_第4页

An improved, time-efficient approach to extract accurate distance restraints for NMR2 structure calculation 一种改进的、省时的NMR2结构精确距离约束提取方法

Magnetic resonance (Gottingen, Germany) Pub Date : 2022-08-01 DOI: 10.5194/mr-3-137-2022

Aditya Pokharna, Felix Torres, Harindranath Kadavath, J. Orts, R. Riek

{"title":"An improved, time-efficient approach to extract accurate distance restraints for NMR2 structure calculation","authors":"Aditya Pokharna, Felix Torres, Harindranath Kadavath, J. Orts, R. Riek","doi":"10.5194/mr-3-137-2022","DOIUrl":"https://doi.org/10.5194/mr-3-137-2022","url":null,"abstract":"Abstract. Exact nuclear Overhauser enhancement (eNOE) yields highly accurate, ensemble averaged 1H–1H distance restraints with an accuracy of up to 0.1 Å for the multi-state structure determination of proteins as well as for nuclear magnetic resonance molecular replacement (NMR2) to determine the structure of the protein–ligand interaction site in a time-efficient manner. However, in the latter application, the acquired eNOEs lack the obtainable precision of 0.1 Å because of the asymmetrical nature of the filtered nuclear Overhauser enhancement spectroscopy (NOESY) experiment used in NMR2. This error is further propagated to the eNOE equations used to fit and extract the distance restraints. In this work, a new analysis method is proposed to obtain inter-molecular distance restraints from the filtered NOESY spectrum more accurately and intuitively by dividing the NOE cross peak by the corresponding diagonal peak of the ligand. The method termed diagonal-normalised eNOEs was tested on the data acquired by Torres et al. (2020) on the complex of PIN1 and a small, weak-binding phenylimidazole fragment. NMR2 calculations performed using the distances derived from diagonal-normalised eNOEs yielded the right orientation of the fragment in the binding pocket and produced a structure that more closely resembles the benchmark X-ray structure (2XP6) (Potter et al., 2010) with an average heavy-atom root-mean-square deviation (RMSD) of 1.681 Å with respect to it, when compared to the one produced with traditional NMR2 with an average heavy atom RMSD of 3.628 Å. This is attributed to the higher precision of the evaluated distance restraints.\u0000","PeriodicalId":93333,"journal":{"name":"Magnetic resonance (Gottingen, Germany)","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44622216","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Magnetic expression in kerogen reveals impact on fluid transport. 干酪根中的磁性表达揭示了对流体输送的影响

Magnetic resonance (Gottingen, Germany) Pub Date : 2022-07-29 eCollection Date: 2022-01-01 DOI: 10.5194/mr-3-125-2022

Benjamin Nicot, Jean-Pierre Korb, Isabelle Jolivet, Hervé Vezin, Didier Gourier, Anne-Laure Rollet

{"title":"Magnetic expression in kerogen reveals impact on fluid transport.","authors":"Benjamin Nicot, Jean-Pierre Korb, Isabelle Jolivet, Hervé Vezin, Didier Gourier, Anne-Laure Rollet","doi":"10.5194/mr-3-125-2022","DOIUrl":"10.5194/mr-3-125-2022","url":null,"abstract":"How can the transport of fluids in a confined and complex mixed organic/inorganic matrix be far below the expected value from a topological aspect? A good example of this situation is oil shales. Oil and gas shales are source rocks in which organic matter has matured to form hydrocarbons. They exhibit a dual porous network formed by the intertwining of mineral and organic pores that leads to very low permeability. Still, the exact origin of this extremely low permeability remains somehow unclear. The present communication addresses this important question and provides novel insights on the mechanisms that strongly hinder fluid diffusion in such materials. By combining nuclear and electronic magnetic resonance techniques with SEM imaging, we show evidence that magnetic interaction occurs in kerogen. This results from a magnetic coupling between vanadyl present in porphyrins and the organic matrix. We demonstrate that such coupling retards fluid diffusion and is reversible. This key dynamical feature explains the extremely low mobility of oil in shale rocks. This phenomenon may be a more general feature occurring in several systems where fluids are confined in a complex hierarchical matrix that embeds both organic and inorganic radicals resulting from the aging process.","PeriodicalId":93333,"journal":{"name":"Magnetic resonance (Gottingen, Germany)","volume":" ","pages":"125-136"},"PeriodicalIF":0.0,"publicationDate":"2022-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10539839/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47494456","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Insight into the structure of black coatings of ancient Egyptian mummies by advanced electron magnetic resonance of vanadyl complexes. 通过钒基络合物的高级电子磁共振深入了解古埃及木乃伊黑色涂层的结构。

Magnetic resonance (Gottingen, Germany) Pub Date : 2022-07-13 eCollection Date: 2022-01-01 DOI: 10.5194/mr-3-111-2022

Charles E Dutoit, Laurent Binet, Hervé Vezin, Océane Anduze, Agnès Lattuati-Derieux, Didier Gourier

{"title":"Insight into the structure of black coatings of ancient Egyptian mummies by advanced electron magnetic resonance of vanadyl complexes.","authors":"Charles E Dutoit, Laurent Binet, Hervé Vezin, Océane Anduze, Agnès Lattuati-Derieux, Didier Gourier","doi":"10.5194/mr-3-111-2022","DOIUrl":"10.5194/mr-3-111-2022","url":null,"abstract":"Ancient Egyptian mummies from the Late Period to the Greco-Roman Period were covered by a black coating consisting of complex and heterogeneous mixtures of conifer resins, wax, fat and oil with variable amounts of bitumen. Natural bitumen always contains traces of vanadyl porphyrin complexes that we used here as internal probes to explore the nanoscale environment of V<math><msup><mi></mi><mrow><mn>4</mn><mo>+</mo></mrow></msup></math> ions in these black coatings by electron nuclear double resonance (ENDOR) and hyperfine sub-level correlation spectroscopy (HYSCORE). Four types of vanadyl porphyrin complexes were identified from the analysis of <math><msup><mi></mi><mn>14</mn></msup></math>N hyperfine interactions. Three types (referred to as VO-P1, VO-P2 and VO-P3) are present in natural bitumen from the Dead Sea, among which VO-P1 and VO-P2 are also present in black coatings of mummies. The absence of VO-P3 in mummies, which is replaced by another complex, VO-P4, may be due to its transformation during preparation of the black matter for embalming. Analysis of <math><msup><mi></mi><mn>1</mn></msup></math>H hyperfine interaction shows that bitumen and other natural substances are intimately mixed in these black coatings, with aggregate sizes of bitumen increasing with the bitumen content but not exceeding a few nanometres.","PeriodicalId":93333,"journal":{"name":"Magnetic resonance (Gottingen, Germany)","volume":"3 2","pages":"111-124"},"PeriodicalIF":0.0,"publicationDate":"2022-07-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10539842/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71415934","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

The effect of spin polarization on double electron-electron resonance (DEER) spectroscopy. 自旋极化对双电子共振（DEER）光谱的影响

Magnetic resonance (Gottingen, Germany) Pub Date : 2022-07-01 eCollection Date: 2022-01-01 DOI: 10.5194/mr-3-101-2022

Sarah R Sweger, Vasyl P Denysenkov, Lutz Maibaum, Thomas F Prisner, Stefan Stoll

引用次数: 0

Imatinib disassembles the regulatory core of Abelson kinase by binding to its ATP site and not by binding to its myristoyl pocket. 伊马替尼通过结合其ATP位点而不是通过结合其肉豆蔻醇口袋来分解Abelson激酶的调节核心。

Magnetic resonance (Gottingen, Germany) Pub Date : 2022-05-20 eCollection Date: 2022-01-01 DOI: 10.5194/mr-3-91-2022

Stephan Grzesiek, Johannes Paladini, Judith Habazettl, Rajesh Sonti

{"title":"Imatinib disassembles the regulatory core of Abelson kinase by binding to its ATP site and not by binding to its myristoyl pocket.","authors":"Stephan Grzesiek, Johannes Paladini, Judith Habazettl, Rajesh Sonti","doi":"10.5194/mr-3-91-2022","DOIUrl":"10.5194/mr-3-91-2022","url":null,"abstract":"It was recently reported (Xie et al., 2022) that the Abelson tyrosine kinase (Abl) ATP-site inhibitor imatinib also binds to Abl's myristoyl binding pocket, which is the target of allosteric Abl inhibitors. This was based on a crystal structure of a truncated Abl kinase domain construct in complex with imatinib bound to the allosteric site as well as further isothermal titration calorimetry (ITC), NMR, and kinase activity data. Although imatinib's affinity for the allosteric site is significantly weaker (10 <math><mrow><mi>µ</mi></mrow></math>M) than for the ATP site (10 nM), imatinib binding to the allosteric site may disassemble the regulatory core of Abl, thereby stimulating kinase activity, in particular for Abl mutants with reduced imatinib ATP-site affinity. It was argued that the previously observed imatinib-induced opening of the Abl regulatory core (Skora et al., 2013; Sonti et al., 2018) may be caused by the binding of imatinib to the allosteric site and not to the ATP site. We show here that this is not the case but that indeed imatinib binding to the ATP site induces the opening of the regulatory core at nanomolar concentrations. This agrees with findings that other type-II ATP-site inhibitors (nilotinib, ponatinib) disassemble the regulatory core despite demonstrated negligible binding to the allosteric site.","PeriodicalId":93333,"journal":{"name":"Magnetic resonance (Gottingen, Germany)","volume":"3 1","pages":"91-99"},"PeriodicalIF":0.0,"publicationDate":"2022-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10539847/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71415929","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A portable NMR platform with arbitrary phase control and temperature compensation. 具有任意相位控制和温度补偿的便携式核磁共振平台

Magnetic resonance (Gottingen, Germany) Pub Date : 2022-05-16 eCollection Date: 2022-01-01 DOI: 10.5194/mr-3-77-2022

Qing Yang, Jianyu Zhao, Frederik Dreyer, Daniel Krüger, Jens Anders

引用次数: 8

Localising nuclear spins by pseudocontact shifts from a single tagging site. 定位核自旋的伪接触移位从一个单一的标记点

Magnetic resonance (Gottingen, Germany) Pub Date : 2022-05-09 eCollection Date: 2022-01-01 DOI: 10.5194/mr-3-65-2022

Henry W Orton, Elwy H Abdelkader, Lydia Topping, Stephen J Butler, Gottfried Otting

{"title":"Localising nuclear spins by pseudocontact shifts from a single tagging site.","authors":"Henry W Orton, Elwy H Abdelkader, Lydia Topping, Stephen J Butler, Gottfried Otting","doi":"10.5194/mr-3-65-2022","DOIUrl":"10.5194/mr-3-65-2022","url":null,"abstract":"Ligating a protein at a specific site with a tag molecule containing a paramagnetic metal ion provides a versatile way of generating pseudocontact shifts (PCSs) in nuclear magnetic resonance (NMR) spectra. PCSs can be observed for nuclear spins far from the tagging site, and PCSs generated from multiple tagging sites have been shown to enable highly accurate structure determinations at specific sites of interest, even when using flexible tags, provided the fitted effective magnetic susceptibility anisotropy (<math><mrow><mi>Δ</mi><mi>χ</mi></mrow></math>) tensors accurately back-calculate the experimental PCSs measured in the immediate vicinity of the site of interest. The present work investigates the situation where only the local structure of a protein region or bound ligand is to be determined rather than the structure of the entire molecular system. In this case, the need for gathering structural information from tags deployed at multiple sites may be queried. Our study presents a computational simulation of the structural information available from samples produced with single tags attached at up to six different sites, up to six different tags attached to a single site, and in-between scenarios. The results indicate that the number of tags is more important than the number of tagging sites. This has important practical implications, as it is much easier to identify a single site that is suitable for tagging than multiple ones. In an initial experimental demonstration with the ubiquitin mutant S57C, PCSs generated with four different tags at a single site are shown to accurately pinpoint the location of amide protons in different segments of the protein.","PeriodicalId":93333,"journal":{"name":"Magnetic resonance (Gottingen, Germany)","volume":" ","pages":"65-76"},"PeriodicalIF":0.0,"publicationDate":"2022-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10539793/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45627325","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

SORDOR pulses: expansion of the Böhlen-Bodenhausen scheme for low-power broadband magnetic resonance. SORDOR脉冲：扩展用于低功率宽带磁共振的Böhlen-Bodenhausen方案。

Magnetic resonance (Gottingen, Germany) Pub Date : 2022-04-27 eCollection Date: 2022-01-01 DOI: 10.5194/mr-3-53-2022

Jens D Haller, David L Goodwin, Burkhard Luy

引用次数: 4

Radiation damping strongly perturbs remote resonances in the presence of homonuclear mixing. 在同核混合存在的情况下，辐射阻尼强烈地扰动了远共振

Magnetic resonance (Gottingen, Germany) Pub Date : 2022-02-24 eCollection Date: 2022-01-01 DOI: 10.5194/mr-3-43-2022

Philippe Pelupessy

引用次数: 2

Spin relaxation: is there anything new under the Sun? 旋转放松：太阳底下有什么新东西吗？

Magnetic resonance (Gottingen, Germany) Pub Date : 2022-02-09 eCollection Date: 2022-01-01 DOI: 10.5194/mr-3-27-2022

Bogdan A Rodin, Daniel Abergel

引用次数: 0