Specific RNA-protein interactions detected with saturation transfer difference NMR

RNA Biology

Volumn 10, Issue 8, 2013, Pages 1307-1311

  Harris, Kimberly A ^a   Shekhtman, Alexander ^a   Agris, Paul F ^a  

^a STATE UNIVERSITY OF NEW YORK   (United States)

Author keywords

L7Ae; Lysyl tRNA; Modification enzymes; Nuclear magnetic resonance; RNA modification; SnoRNA; YrdC

Indexed keywords

NUCLEIC ACID; RIBOSOME PROTEIN; TRANSFER RNA;

ANTICODON; ARTICLE; MOLECULAR RECOGNITION; NONHUMAN; NUCLEAR MAGNETIC RESONANCE; PROTEIN RNA BINDING;

ARCHAEA;

L7AE; LYSYL-TRNA; MODIFICATION ENZYMES; NUCLEAR MAGNETIC RESONANCE; RNA MODIFICATION; SNORNA; YRDC;

ANTICODON; ARCHAEA; BINDING SITES; CIRCULAR DICHROISM; ESCHERICHIA COLI PROTEINS; MODELS, MOLECULAR; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; NUCLEIC ACID CONFORMATION; PROTEIN BINDING; PROTEINS; RNA; RNA, BACTERIAL; RNA, TRANSFER, LYS; RNA-BINDING PROTEINS;

EID: 84883131092     PISSN: 15476286     EISSN: 15558584     Source Type: Journal    
DOI: 10.4161/rna.25948     Document Type: Article

References (27)

1. Lane AN, Kelly G, Ramos A, Frenkiel TA. Determining binding sites in protein-nucleic acid complexes by cross-saturation. J Biomol NMR 2001; 21:127-39; PMID:11727976; http://dx.doi.org/10.1023/A:1012486527215
2. Ramos A, Kelly G, Hollingworth D, Pastore A, Frenkiel TA. Mapping the interfaces of protein-nucleic acid complexes using cross-saturation. J Am Chem Soc 2000; 122:11311-4; http://dx.doi.org/10.1021/ja002233w
3. Dominguez C, Schubert M, Duss O, Ravindranathan S, Allain FHT. Structure determination and dynamics of protein-RNA complexes by NMR spectroscopy. Prog Nucl Magn Reson Spectrosc 2011; 58:1-61; PMID:21241883; http://dx.doi.org/10. 1016/j.pnmrs.2010.10.001
4. Mayer M, Meyer B. Characterization of ligand binding by saturation transfer difference NMR spectroscopy. Angew Chem Int Ed 1999; 38:1784-8; http://dx.doi.org/10.1002/(SICI)1521-3773(19990614)38:12<1784:: AIDANIE1784>3.0.CO;2-Q
5. Mayer M, James TJ. Detecting Ligand Binding to a Small RNA Target via Saturation Transfer Difference NMR Experiments in D2O and H2O. J Am Chem Soc 2003; 124:13376-7; http://dx.doi.org/10.1021/ja027526z
6. Mayer M, James TL. NMR-based characterization of phenothiazines as a RNA binding scaffold. J Am Chem Soc 2004; 126:4453-60; PMID:15053636; http://dx.doi.org/10.1021/ja0398870
7. Mayer M, Lang PT, Gerber S, Madrid PB, Pinto IG, Guy RK, et al. Synthesis and testing of a focused phenothiazine library for binding to HIV-1 TAR RNA. Chem Biol 2006; 13:993-1000; PMID:16984889; http://dx.doi.org/10.1016/j. chembiol.2006.07.009
8. Szczygiel A, Timmermans L, Fritzinger B, Martins JC. Widening the view on dispersant-pigment interactions in colloidal dispersions with saturation transfer difference NMR spectroscopy. J Am Chem Soc 2009; 131:17756-8; PMID:19919034; http://dx.doi.org/10.1021/ja905637y
9. Xia Y, Zhu Q, Jun KY, Wang J, Gao X. Clean STDNMR spectrum for improved detection of ligand-protein interactions at low concentration of protein. Magn Reson Chem 2010; 48:918-24; PMID:20957656; http://dx.doi.org/10.1002/mrc.2687
10. Mayer M, Meyer B. Group epitope mapping by saturation transfer difference NMR to identify segments of a ligand in direct contact with a protein receptor. J Am Chem Soc 2001; 123:6108-17; PMID:11414845; http://dx.doi.org/10.1021/ ja0100120
11. Meyer B, Peters T. NMR spectroscopy techniques for screening and identifying ligand binding to protein receptors. Angew Chem Int Ed Engl 2003; 42:864-90; PMID:12596167; http://dx.doi.org/10.1002/anie.200390233
12. Deutsch C, El Yacoubi B, de Crécy-Lagard V, Iwata-Reuyl D. Biosynthesis of threonylcarbamoyl adenosine (t6A), a universal tRNA nucleoside. J Biol Chem 2012; 287:13666-73; PMID:22378793; http://dx.doi.org/10.1074/jbc. M112.344028
13. Harris KA, Jones V, Bilbille Y, Swairjo MA, Agris PF. YrdC exhibits properties expected of a subunit for a tRNA threonylcarbamoyl transferase. RNA 2011; 17:1678-87; PMID:21775474; http://dx.doi.org/10.1261/rna.2592411
14. 6-threonylcarbamoyladenonsine (t(6)A) biosynthesis: isolation and characterization of the intermediate threonylcarbamoyl-AMP. Biochemistry 2012; 51:8950-63; PMID:23072323; http://dx.doi.org/10.1021/bi301233d
15. Jühling F, Mörl M, Hartmann RK, Sprinzl M, Stadler PF, Pütz J. tRNAdb 2009: compilation of tRNA sequences and tRNA genes. Nucleic Acids Res 2009; 37(Database issue):D159-62; PMID:18957446; http://dx.doi.org/10. 1093/nar/gkn772
16. Yarian C, Marszalek M, Sochacka E, Malkiewicz A, Guenther R, Miskiewicz A, et al. Modified nucleoside dependent Watson-Crick and wobble codon binding by tRNALysUUU species. Biochemistry 2000; 39:13390-5; PMID:11063576; http://dx.doi.org/10.1021/bi001302g
17. Klein DJ, Schmeing TM, Moore PB, Steitz TA. The kink-turn: a new RNA secondary structure motif. EMBO J 2001; 20:4214-21; PMID:11483524; http://dx.doi.org/10.1093/emboj/20.15.4214
18. Henras AK, Dez C, Henry Y. RNA structure and function in C/D and H/ACA s(no)RNPs. Curr Opin Struct Biol 2004; 14:335-43; PMID:15193314; http://dx.doi.org/10.1016/j.sbi.2004.05.006
19. Durant PC, Davis DR. Stabilization of the anticodon stem-loop of tRNALys,3 by an A+-C base-pair and by pseudouridine. J Mol Biol 1999; 285:115-31; PMID:9878393; http://dx.doi.org/10.1006/jmbi.1998.2297
20. Teplova M, Tereshko V, Sanishvili R, Joachimiak A, Bushueva T, Anderson WF, et al. The structure of the yrdC gene product from Escherichia coli reveals a new fold and suggests a role in RNA binding. Protein Sci 2000; 9:2557-66; PMID:11206077; http://dx.doi.org/10.1110/ps.9.12.2557
21. El Yacoubi B, Lyons B, Cruz Y, Reddy R, Nordin B, Agnelli F, et al. The universal YrdC/Sua5 family is required for the formation of threonylcarbamoyladenosine in tRNA. Nucleic Acids Res 2009; 37:2894-909; PMID:19287007; http://dx.doi.org/10.1093/nar/gkp152
22. Kuhn JF, Tran EJ, Maxwell ES. Archaeal ribosomal protein L7 is a functional homolog of the eukaryotic 15.5kD/Snu13p snoRNP core protein. Nucleic Acids Res 2002; 30:931-41; PMID:11842104; http://dx.doi.org/10.1093/nar/30.4.931
23. Turner B, Melcher SE, Wilson TJ, Norman DG, Lilley DMJ. Induced fit of RNA on binding the L7Ae protein to the kink-turn motif. RNA 2005; 11:1192-200; PMID:15987806; http://dx.doi.org/10.1261/rna.2680605
24. Moore T, Zhang Y, Fenley MO, Li H. Molecular basis of box C/D RNA-protein interactions; cocrystal structure of archaeal L7Ae and a box C/D RNA. Structure 2004; 12:807-18; PMID:15130473; http://dx.doi.org/10.1016/j.str.2004.02.033
25. Hamma T, Ferré-D'Amaré AR. The box H/ACA ribonucleoprotein complex: interplay of RNA and protein structures in post-transcriptional RNA modification. J Biol Chem 2010; 285:805-9; PMID:19917616; http://dx.doi.org/10. 1074/jbc.R109.076893
26. Delaglio F, Grzesiek S, Vuister GW, Zhu G, Pfeifer J, Bax A. NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J Biomol NMR 1995; 6:277-93; PMID:8520220; http://dx.doi.org/10.1007/BF00197809
27. Goddard TD, Kneller DG. SPARKY 3. University of California, San Francisco, 2008.