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

Journal of Biomolecular NMR
K A SchnorrH Schwalbe

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, (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 cry...Continue Reading

References

Jan 1, 1976·Nucleic Acids Research·M Caron, H Dugas
Jan 1, 1989·Methods in Enzymology·P A Kosen
Aug 28, 1984·Biochemistry·P G Schmidt, I D Kuntz
May 5, 1999·Current Opinion in Chemical Biology·I Bertini, C Luchinat
Mar 15, 2000·Protein Science : a Publication of the Protein Society·V GaponenkoP R Rosevear
May 4, 2002·Annual Review of Biophysics and Biomolecular Structure·M UbbinkM Huber
Sep 26, 2002·FEBS Letters·Alex DvoretskyPaul R Rosevear
Jun 5, 2003·Biochemistry·Peter Z QinWayne L Hubbell
Oct 30, 2003·Journal of the American Chemical Society·Jens WöhnertHarald Schwalbe
Jun 24, 2004·Journal of Biomolecular NMR·Guido PintacudaGottfried Otting
Oct 8, 2004·Journal of the American Chemical Society·Junji IwaharaG Marius Clore
Sep 29, 2005·Journal of Magnetic Resonance·Stefan Stoll, Arthur Schweiger
Feb 1, 2006·Bioinformatics·Ulrike MücksteinIvo L Hofacker
Oct 20, 2006·Nature·Tom L Blundell, Juan Fernández-Recio
Nov 7, 2006·Journal of Magnetic Resonance·Junji IwaharaG Marius Clore
Dec 6, 2006·Proceedings of the National Academy of Sciences of the United States of America·Alexander N VolkovMarcellus Ubbink
Apr 25, 2007·Nucleic Acids Research·Nelly PitonJoachim W Engels
Aug 19, 2007·Nature Protocols·Thomas E Edwards, Snorri Th Sigurdsson
Sep 27, 2007·Proceedings of the National Academy of Sciences of the United States of America·Janina BuckHarald Schwalbe
Oct 4, 2007·Proceedings of the National Academy of Sciences of the United States of America·Jane N KimRonald R Breaker
Mar 5, 2008·Journal of the American Chemical Society·Chun TangG Marius Clore
Jul 17, 2008·Dalton Transactions : an International Journal of Inorganic Chemistry·Ivano BertiniRoberta Pierattelli
May 14, 2010·Annual Review of Biophysics·Gottfried Otting
Jul 29, 2010·Angewandte Chemie·Giuseppe SicoliClaudia Höbartner
Sep 17, 2010·Angewandte Chemie·Sandip A Shelke, Snorri Th Sigurdsson
Dec 25, 2010·Journal of the American Chemical Society·Katja BarthelmesHarald Schwalbe
Sep 20, 2011·Molecular Cell·Ronald R Breaker
Nov 26, 2011·Algorithms for Molecular Biology : AMB·Ronny LorenzIvo L Hofacker
Dec 14, 2011·Topics in Current Chemistry·Ivan KrstićThomas F Prisner
May 25, 2012·Physical Chemistry Chemical Physics : PCCP·Ivano BertiniEnrico Ravera
Jun 21, 2012·Biophysical Journal·Hannah S SteinertHarald Schwalbe
Aug 14, 2012·The Journal of Organic Chemistry·Claudia HöbartnerSnorri Th Sigurdsson
Jan 22, 2013·Cell·Alexander Serganov, Evgeny Nudler
Mar 21, 2013·Journal of the American Chemical Society·Jia-Ying GuanGregg Siegal
May 15, 2013·Bioorganic & Medicinal Chemistry·Lea BüttnerClaudia Höbartner
Jul 16, 2013·Current Opinion in Structural Biology·Wayne L HubbellZhongyu Yang

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Citations

Jul 18, 2018·Beilstein Journal of Organic Chemistry·Timo WeinrichMichael W Göbel
May 24, 2018·Journal of the American Chemical Society·Henry W Orton, Gottfried Otting

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