Impact of Spin Label Rigidity on Extent and Accuracy of Distance Information from PRE Data

Overview

Journal J Biomol NMR

Publisher Springer

Specialties Molecular Biology
Nuclear Medicine

Date 2017 May 14

PMID 28500543

Citations 4

Authors

K A Schnorr

D B Gophane

C Helmling

E Cetiner

K Pasemann

B Furtig

A Wacker

N S Qureshi

M Granz

D Barthelmes

H R A Jonker

E Stirnal

S Th Sigurdsson

H Schwalbe

Affiliations

Soon will be listed here.

Abstract

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, 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 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 TEMPO as judged by comparison of the structural agreement with the I-A aptamer crystal structure (3SKI).

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References

Qin P, Hideg K, Feigon J, Hubbell W . Monitoring RNA base structure and dynamics using site-directed spin labeling. Biochemistry. 2003; 42(22):6772-83. DOI: 10.1021/bi027222p. View

Lebars I, Vileno B, Bourbigot S, Turek P, Wolff P, Kieffer B . A fully enzymatic method for site-directed spin labeling of long RNA. Nucleic Acids Res. 2014; 42(15):e117. PMC: 4150755. DOI: 10.1093/nar/gku553. View

Shelke S, Sandholt G, Sigurdsson S . Nitroxide-labeled pyrimidines for non-covalent spin-labeling of abasic sites in DNA and RNA duplexes. Org Biomol Chem. 2014; 12(37):7366-74. DOI: 10.1039/c4ob01095g. View

Macosko J, Pio M, Tinoco Jr I, Shin Y . A novel 5 displacement spin-labeling technique for electron paramagnetic resonance spectroscopy of RNA. RNA. 1999; 5(9):1158-66. PMC: 1369839. DOI: 10.1017/s1355838299990830. View

Steinert H, Rinnenthal J, Schwalbe H . Individual basepair stability of DNA and RNA studied by NMR-detected solvent exchange. Biophys J. 2012; 102(11):2564-74. PMC: 3368144. DOI: 10.1016/j.bpj.2012.03.074. View

Donaldson L, Skrynnikov N, Choy W, Muhandiram D, Sarkar B, Forman-Kay J . Structural characterization of proteins with an attached ATCUN motif by paramagnetic relaxation enhancement NMR spectroscopy. J Am Chem Soc. 2001; 123(40):9843-7. DOI: 10.1021/ja011241p. View

Muckstein U, Tafer H, Hackermuller J, Bernhart S, Stadler P, Hofacker I . Thermodynamics of RNA-RNA binding. Bioinformatics. 2006; 22(10):1177-82. DOI: 10.1093/bioinformatics/btl024. View

SCHMIDT P, Kuntz I . Distance measurements in spin-labeled lysozyme. Biochemistry. 1984; 23(18):4261-6. DOI: 10.1021/bi00313a038. View

Bertram K, Agafonov D, Liu W, Dybkov O, Will C, Hartmuth K . Cryo-EM structure of a human spliceosome activated for step 2 of splicing. Nature. 2017; 542(7641):318-323. DOI: 10.1038/nature21079. View

10.

Stoll S, Schweiger A . EasySpin, a comprehensive software package for spectral simulation and analysis in EPR. J Magn Reson. 2005; 178(1):42-55. DOI: 10.1016/j.jmr.2005.08.013. View

11.

Lorenz R, Bernhart S, Honer Zu Siederdissen C, Tafer H, Flamm C, Stadler P . ViennaRNA Package 2.0. Algorithms Mol Biol. 2011; 6:26. PMC: 3319429. DOI: 10.1186/1748-7188-6-26. View

12.

Buck J, Furtig B, Noeske J, Wohnert J, Schwalbe H . Time-resolved NMR methods resolving ligand-induced RNA folding at atomic resolution. Proc Natl Acad Sci U S A. 2007; 104(40):15699-704. PMC: 2000436. DOI: 10.1073/pnas.0703182104. View

13.

Madl T, Guttler T, Gorlich D, Sattler M . Structural analysis of large protein complexes using solvent paramagnetic relaxation enhancements. Angew Chem Int Ed Engl. 2011; 50(17):3993-7. DOI: 10.1002/anie.201007168. View

14.

Iwahara J, Schwieters C, Clore G . Characterization of nonspecific protein-DNA interactions by 1H paramagnetic relaxation enhancement. J Am Chem Soc. 2004; 126(40):12800-8. DOI: 10.1021/ja046246b. View

15.

Kamble N, Granz M, Prisner T, Sigurdsson S . Noncovalent and site-directed spin labeling of duplex RNA. Chem Commun (Camb). 2016; 52(100):14442-14445. DOI: 10.1039/c6cc08387k. View

16.

Blundell T, Fernandez-Recio J . Cell biology: brief encounters bolster contacts. Nature. 2006; 444(7117):279-80. DOI: 10.1038/nature05306. View

17.

Tang C, Iwahara J, Clore G . Visualization of transient encounter complexes in protein-protein association. Nature. 2006; 444(7117):383-6. DOI: 10.1038/nature05201. View

18.

Ubbink M, Worrall J, Canters G, Groenen E, Huber M . Paramagnetic resonance of biological metal centers. Annu Rev Biophys Biomol Struct. 2002; 31:393-422. DOI: 10.1146/annurev.biophys.31.091701.171000. View

19.

Wunderlich C, Huber R, Spitzer R, Liedl K, Kloiber K, Kreutz C . A novel paramagnetic relaxation enhancement tag for nucleic acids: a tool to study structure and dynamics of RNA. ACS Chem Biol. 2013; 8(12):2697-706. PMC: 3870906. DOI: 10.1021/cb400589q. View

20.

Hobartner C, Sicoli G, Wachowius F, Gophane D, Sigurdsson S . Synthesis and characterization of RNA containing a rigid and nonperturbing cytidine-derived spin label. J Org Chem. 2012; 77(17):7749-54. DOI: 10.1021/jo301227w. View