Impact of spin label rigidity on extent and accuracy of distance information from PRE data

• Published in: Journal of biomolecular NMR Vol. 68; no. 1; pp. 53 - 63
• Main Authors: Schnorr, K. A., Gophane, D. B., Helmling, C., Cetiner, E., Pasemann, K., Fürtig, B., Wacker, A., Qureshi, N. S., Gränz, M., Barthelmes, D., Jonker, H. R. A., Stirnal, E., Sigurdsson, S. Th, Schwalbe, H.
• Format: Journal Article
• Language: English
• Published: Dordrecht Springer Netherlands 01.05.2017; Springer Nature B.V
• Subjects: Accuracy; Aptamers; Aptamers, Nucleotide; Biochemistry; Biological and Medical Physics; Biophysics; Constraints; Construction; Crystal structure; Cyclic N-Oxides; Fragmentation; Fragments; Hybridization; Labels; Macromolecules; NMR; Nuclear magnetic resonance; Nuclear Magnetic Resonance, Biomolecular - methods; Physics; Physics and Astronomy; Pliability; Protons; Quality; Ribonucleic acid; Riboswitch; Rigidity; RNA; Spectroscopic analysis; Spectroscopy/Spectrometry; Spin Labels; Paramagnetic relaxation enhancement (PRE); Spin labeling; RNA; Paramagnetic NMR; EPR
• ISSN: 0925-2738; 1573-5001
• DOI: 10.1007/s10858-017-0114-9

Paramagnetic relaxation enhancement (PRE) is a versatile tool for NMR spectroscopic structural and kinetic studies in biological macromolecules. Here, we compare the quality of PRE data derived from two spin labels with markedly different dynamic properties for large RNAs using the I-A riboswitch aptamer domain (78 nt) from Mesoplamsa florum as model system. We designed two I-A aptamer constructs that were spin-labeled by noncovalent hybridization of short spin-labeled oligomer fragments. As an example of a flexible spin label, Ureido U-TEMPO was incorporated into the 3′ terminal end of helix P1 while, the recently developed rigid spin-label Çm was incorporated in the 5′ terminal end of helix P1. We determined PRE rates obtained from aromatic 13 C bound proton intensities and compared these rates to PREs derived from imino proton intensities in this sizeable RNA (~78 nt). PRE restraints derived from both imino and aromatic protons yielded similar data quality, and hence can both be reliably used for PRE determination. For NMR, the data quality derived from the rigid spin label Çm is slightly better than the data quality for the flexible Ureido TEMPO as judged by comparison of the structural agreement with the I-A aptamer crystal structure (3SKI).