Chapter 6. Paramagnetic NMR Spectroscopy and Lowly Populated States

Schilder, Jesika T.; Hass, Mathias A. S.; Keizers, Peter H. J.; Ubbink, Marcellus

doi:10.1039/9781849735391-00130

Cited by 3 publications

(4 citation statements)

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“…Therefore, PREs are powerful tools for the detection of minor states or the characterization of ensembles of conformations, such as found in intrinsically disordered proteins or encounter complexes. 33,34,584 At the same time, the strong distance dependence of the PRE adds uncertainties to distance measurements of major conformations, when minor conformations or alternative interactions featuring short distances r IS contribute disproportionally to the observed PRE. Minor species populated as low as 0.1% can be manifested in the observed PRE in this way.…”

Section: Complications In Pre-to-distance Conversionmentioning

confidence: 99%

Paramagnetic Chemical Probes for Studying Biological Macromolecules

et al. 2022

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Paramagnetic chemical probes have been used in electron paramagnetic resonance (EPR) and nuclear magnetic resonance (NMR) spectroscopy for more than four decades. Recent years witnessed a great increase in the variety of probes for the study of biological macromolecules (proteins, nucleic acids, and oligosaccharides). This Review aims to provide a comprehensive overview of the existing paramagnetic chemical probes, including chemical synthetic approaches, functional properties, and selected applications. Recent developments have seen, in particular, a rapid expansion of the range of lanthanoid probes with anisotropic magnetic susceptibilities for the generation of structural restraints based on residual dipolar couplings and pseudocontact shifts in solution and solid state NMR spectroscopy, mostly for protein studies. Also many new isotropic paramagnetic probes, suitable for NMR measurements of paramagnetic relaxation enhancements, as well as EPR spectroscopic studies (in particular double resonance techniques) have been developed and employed to investigate biological macromolecules. Notwithstanding the large number of reported probes, only few have found broad application and further development of probes for dedicated applications is foreseen.

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Section: Complications In Pre-to-distance Conversionmentioning

confidence: 99%

Paramagnetic Chemical Probes for Studying Biological Macromolecules

et al. 2022

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“…We determined the conformer orientations for both MTSL and pyMTSL using intra-molecular PREs to see if a difference could be observed between these tags. 2 In order to account for potential differences in the most favourable SL orientations on free CcP compared to CcP in complex with Cc, all intramolecular PRE measurements were done in the presence of 300 mM nonisotopically labelled Cc (1 : 1 molar eq. ), which was the same concentration as used for the intermolecular PRE measurements.…”

Section: Experimental Optimization Of Sl Conformersmentioning

confidence: 99%

“…Various types of paramagnetic restraints can be used, such as pseudocontact shifts (PCS), residual dipolar couplings (RDC) induced by the alignment caused by the paramagnetic centre, or paramagnetic relaxation enhancement (PRE). 1,2 PRE is the most popular choice due to the simplicity of introducing relaxation centres to proteins, mainly in the form of sitespecific tags, of which spin labels (SLs) are the most common. SLs are small organic compounds that contain an unpaired electron in the form of a nitroxide radical and are generally quite stable under non-reducing conditions.…”

Section: Introductionmentioning

confidence: 99%

Protein docking using an ensemble of spin labels optimized by intra-molecular paramagnetic relaxation enhancement

Schilder

Liu

Kumar

et al. 2016

Phys. Chem. Chem. Phys.

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Paramagnetic NMR is a useful technique to study proteins and protein complexes and the use of paramagnetic relaxation enhancement (PRE) for this purpose has become wide-spread. PREs are commonly generated using paramagnetic spin labels (SLs) that contain an unpaired electron in the form of a nitroxide radical, with 1-oxyl-2,2,5,5-tetramethyl-2,5-dihydropyrrol-3-ylmethyl methane thiosulfonate (MTSL) being the most popular tag. The inherent flexibility of the SL causes sampling of several conformations in solution, which can be problematic as over- or underestimation of the spatial distribution of the unpaired electron in structural calculations will lead to errors in the distance restraints. We investigated the effect of this mobility on the accuracy of protein-protein docking calculations using intermolecular PRE data by comparing MTSL and the less mobile 3-methanesulfonilthiomethyl-4-(pyridin-3-yl)-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-1-yloxyl (pyMTSL) on the dynamic complex of cytochrome c and cytochrome c peroxidase. No significant differences were found between the two SLs. Docking was performed using either single or multiple conformers and either fixed or flexible SLs. It was found that mobility of the SLs is the limiting factor for obtaining accurate solutions. Optimization of SL conformer orientations using intra-molecular PRE improves the accuracy of docking.

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“…In spite of the limited number of papers dealing with NMR of single-domain magnets, it is becoming increasingly apparent that NMR is a powerful tool for their fine characterization and rational design: in NMR-spectroscopic terms, Single Ion Magnets are systems with large and axial magnetic susceptibility anisotropies and fast electron relaxation times at room temperature, making them ideal candidates for an NMR investigation (vide infra). At the same time, the high magnetic susceptibility anisotropies of SIMs are expected to make them suited for NMR applications: a large magnetic anisotropy can provide robust experimental data for the determination of structure and dynamics in biological systems [27][28][29][30] and improved contrast agents for Magnetic Resonance Imaging [31,32]. In this review, we will focus on the NMR properties of single-domain magnets, in particular, of lanthanoid Single Ion Magnets (Ln-SIMs) [11,33].…”

Section: Introductionmentioning

confidence: 99%

NMR for Single Ion Magnets

et al. 2021

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Nuclear Magnetic Resonance is particularly sensitive to the electronic structure of matter and is thus a powerful tool to characterize in-depth the magnetic properties of a system. NMR is indeed increasingly recognized as an ideal tool to add precious structural information for the development of Single Ion Magnets, small complexes that are recently gaining much popularity due to their quantum computing and spintronics applications. In this review, we recall the theoretical principles of paramagnetic NMR, with particular attention to lanthanoids, and we give an overview of the recent advances in this field.

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Chapter 6. Paramagnetic NMR Spectroscopy and Lowly Populated States

Cited by 3 publications

References 0 publications

Paramagnetic Chemical Probes for Studying Biological Macromolecules

Paramagnetic Chemical Probes for Studying Biological Macromolecules

Protein docking using an ensemble of spin labels optimized by intra-molecular paramagnetic relaxation enhancement

NMR for Single Ion Magnets

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