Paramagnetic-iterative relaxation matrix approach: extracting PRE-restraints from NOESY spectra for 3D structure elucidation of biomolecules

Cetiner, Erhan Can; Jonker, Hendrik R. A.; Helmling, Christina; Gophane, Dnyaneshwar B.; Grünewald, Christian; Sigurdsson, Snorri Th.; Schwalbe, Harald

doi:10.1007/s10858-019-00282-0

Cited by 10 publications

(5 citation statements)

References 31 publications

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“…The synthetic incorporation of Ç and Çm into DNA and RNA was recently improved to circumvent partial reduction during oligonucleotide synthesis . Both labels deliver accurate distances in DNA and RNA and have been used in numerous applications. − Recently, the tetraethyl nitroxide versions EÇ and EÇm have been developed and incorporated into DNA and RNA . They are more inert toward reduction by ascorbate and thus potentially allow in-cell EPR measurements, as recently demonstrated for E Im Um …”

Section: General Overview Of Natural and Chemically Generated Paramag...mentioning

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: General Overview Of Natural and Chemically Generated Paramag...mentioning

confidence: 99%

Paramagnetic Chemical Probes for Studying Biological Macromolecules

et al. 2022

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“…In consequence, NMR solution structures of paramagnetic macromolecules have required a combination of classical structural constraints (NOE, residual dipolar couplings and secondary structure predictions) and paramagnetism-based constraints (cross-correlation, pseudocontact shifts and paramagnetic relaxation enhancements) [13][14][15][16] . High resolution NMR structures were obtained for paramagnetic metalloproteins [17][18][19][20][21] and for proteins containing paramagnetic metal binding tags [22][23][24][25][26] . The substitution of the paramagnetic center with a diamagnetic analogue has also been used to obtain NMR structures of metalloproteins 27,28 .…”

Section: Introductionmentioning

confidence: 99%

PRE‐driven protein NMR structures: an alternative approach in highly paramagnetic systems

et al. 2020

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The 20 conformers with the lowest target function constituting the final family obtained using the full set of NMR restraints were deposited to the Protein Data Bank (PDB ID: 6XYV). The 20 conformers with the lowest target function obtained using NOEs only (PDB ID: 7A58) and PREs only (PDB ID: 7A4L) were also deposited to the Protein Data Bank. The chemical shift assignments were deposited to the BMRB (code 34487).

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“…Compared to paramagnetic tagging methods relying on inorganic chelates, also currently under development for nucleic acids, [20–22] tags constructed around intrinsic sites would likely add a higher molecular‐weight burden to their targets, as well as, could potentially suffer reduced Δχ tensor magnitudes. On the other hand, using intrinsic sites for paramagnetic tagging is much more compatible with isotopic labeling of the target [55] and, as demonstrated here, can provide exceptionally rigid tags.…”

Section: Discussionmentioning

confidence: 82%

Solution Structure of a Lanthanide‐binding DNA Aptamer Determined Using High Quality pseudocontact shift restraints

Andrałojć

Wieruszewska

Pasternak

et al. 2022

Chemistry A European J

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In this contribution we report the high-resolution NMR structure of a recently identified lanthanide-binding aptamer (LnA). We demonstrate that the rigid lanthanide binding by LnA allows for the measurement of anisotropic paramagnetic NMR restraints which to date remain largely inaccessible for nucleic acids. One type of such restraintspseudocontact shifts (PCS) induced by four different para-magnetic lanthanides -was extensively used throughout the current structure determination study and the measured PCS turned out to be exceptionally well reproduced by the final aptamer structure. This finding opens the perspective for a broader application of paramagnetic effects in NMR studies of nucleic acids through the transplantation of the binding site found in LnA into other DNA/RNA systems.

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Paramagnetic-iterative relaxation matrix approach: extracting PRE-restraints from NOESY spectra for 3D structure elucidation of biomolecules

Cited by 10 publications

References 31 publications

Paramagnetic Chemical Probes for Studying Biological Macromolecules

Paramagnetic Chemical Probes for Studying Biological Macromolecules

PRE‐driven protein NMR structures: an alternative approach in highly paramagnetic systems

Solution Structure of a Lanthanide‐binding DNA Aptamer Determined Using High Quality pseudocontact shift restraints

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