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Iron Responsive Element RNA Flexibility Described by NMR and Isotropic Reorientational Eigenmode Dynamics

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Abstract

The first example of the application of reorientational eigenmode dynamics (RED) to RNA is shown here for the small and floppy Iron Responsive Element (IRE) RNA hairpin. Order parameters calculated for bases and riboses from a 12 ns molecular dynamics trajectory are compared to experimentally determined order parameters from 13C-1H NMR relaxation experiments, and shown to be in qualitative agreement. Given the small size of the IRE hairpin and its very flexible loop, isotropic RED (iRED) was also used to analyze the trajectory in order to describe its dynamic motions. iRED analysis shows that the global and internal dynamics of the IRE are not rigorously separable, which will result in inaccurate experimental order parameters. In addition, the iRED analysis described the many correlated motions that comprise the dynamics of the IRE RNA. The combined use of NMR relaxation, RED, and iRED provide a uniquely detailed description of IRE RNA dynamics.

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References

  • K.J. Addess J.P. Basilion R.D. Klausner T.A. Rouault A. Pardi (1997) J. Mol. Biol. 274 72–83 Occurrence Handle10.1006/jmbi.1997.1377 Occurrence Handle9398517

    Article  PubMed  Google Scholar 

  • A. Amadei A.B.M. Linssen H.J.C. Berendsen (1993) Proteins 17 412–425 Occurrence Handle10.1002/prot.340170408 Occurrence Handle8108382

    Article  PubMed  Google Scholar 

  • H.A. Barton R.S. Eisenstein A. Bomford H.N. Munro (1990) J. Biol. Chem. 265 7000–7008 Occurrence Handle2324109

    PubMed  Google Scholar 

  • J.P. Basilion T.A. Rouault C.M. Massinople R.D. Klausner W.H. Burgess (1994) Proc. Natl. Acad. Sci. USA. 91 574–578 Occurrence Handle8290565

    PubMed  Google Scholar 

  • H.J.C. Berendsen J.P.M. Postma W.F. van Gunsteren A. Di Nola J.R. Haak (1984) J. Phys. Chem. 81 IssueID8 3684–3690 Occurrence Handle10.1063/1.448118

    Article  Google Scholar 

  • A.J. Bettany R.S. Eisenstein H.N. Munro (1992) J. Biol. Chem. 267 16531–16537 Occurrence Handle1644834

    PubMed  Google Scholar 

  • R. Brüschweiler (1995) J. Chem. Phys. 102 3396–3403 Occurrence Handle10.1063/1.469213

    Article  Google Scholar 

  • R. Brüschweiler P.E. Wright (1994) J. Am. Chem. Soc. 116 8426–8427 Occurrence Handle10.1021/ja00097a084

    Article  Google Scholar 

  • S.E. Butcher T. Dieckmann J. Feigon (1997) EMBO J. 16 7490–7499 Occurrence Handle10.1093/emboj/16.24.7490 Occurrence Handle9405377

    Article  PubMed  Google Scholar 

  • Case, D.A., Pearlman, D.A., Caldwell, J.W., Cheatham III, T.E., Wang, J., Ross, W.S., Simmerling, C., Darden, T., Merz, K.M., Stanton, R.V., Cheng, A., Vincent, J.J., Crowley, M., Tsui, V., Gohlke, H., Radmer, R., Duan, Y., Pitera, J., Massova, I., Siebel, G.L., Singh, U.C., Weiner, P. and Kollman, P.A. (2002) AMBER 7 User’s Manual. University of California

  • J.L. Casey M.W. Henze D.M. Koeller S.W. Caughman T.A. Rouault R.D. Klausner J.B. Harford (1988) Science 240 924–928 Occurrence Handle2452485

    PubMed  Google Scholar 

  • X. Cheng V. Hornak C. Simmerling (2004) J. Phys. Chem. B 108 426–437 Occurrence Handle10.1021/jp034505y

    Article  Google Scholar 

  • W.D. Cornell P. Cieplak C.I. Bayly I.R. Gould K.M. Merz D.M. Ferguson D.C. Spellmeyer T. Fox J.W. Caldwell P.A. Kollman (1995) J. Am. Chem. Soc. 117 5179–5197 Occurrence Handle10.1021/ja00124a002

    Article  Google Scholar 

  • T.A. Darden (2001) NoChapterTitle O.M. Becker A.D. Mackerell B. Roux M. Watanabe (Eds) Computational Biochemistry and Biophysics, Treatment of long-range forces and potential Marcel Dekker, Inc. New York 91

    Google Scholar 

  • K.T. Dayie A.S. Brodsky J.R. Williamson (2002) J. Mol. Biol. 317 263–278 Occurrence Handle10.1006/jmbi.2001.5424 Occurrence Handle11902842

    Article  PubMed  Google Scholar 

  • R. Fiala J. Czernek V. Sklenář (2000) J. Biomolec. NMR 16 291–302 Occurrence Handle10.1023/A:1008388400601

    Article  Google Scholar 

  • R. Fiala M.L. Munzarová V. Sklenář (2004) J. Biomol. NMR 29 477–490 Occurrence Handle10.1023/B:JNMR.0000034358.12599.d1 Occurrence Handle15243179

    Article  PubMed  Google Scholar 

  • K.B. Hall C. Tang (1998) Biochemistry 37 9323–9332 Occurrence Handle10.1021/bi9805285 Occurrence Handle9649313

    Article  PubMed  Google Scholar 

  • K.B. Hall D.J. Williams (2004) RNA 10 34–47

    Google Scholar 

  • H.A. Heus A. Pardi (1991) Science 253 191–194 Occurrence Handle1712983

    PubMed  Google Scholar 

  • H. Hirling B.R. Henderson L.C. Kuhn (1994) EMBO J. 13 453–461 Occurrence Handle7508861

    PubMed  Google Scholar 

  • C. Hoogstraten J.R. Wank A. Pardi (2000) Biochemistry 39 9951–9958

    Google Scholar 

  • S.R. Jaffrey D.J. Haile R.D. Klausner J.B. Harford (1993) Nucleic Acids Res. 21 4627–4631 Occurrence Handle8233801

    PubMed  Google Scholar 

  • W.L. Jorgensen J. Chandrasekhar J.D. Madura (1983) J. Chem. Phys. 79 926–935 Occurrence Handle10.1063/1.445869

    Article  Google Scholar 

  • P. Kaldy E. Menotti R. Moret L.C. Kuhn (1999) EMBO J. 18 6073–6083 Occurrence Handle10.1093/emboj/18.21.6073 Occurrence Handle10545118

    Article  PubMed  Google Scholar 

  • Z. Kikinis R.S. Eisenstein A.J.E. Bettany H.N. Munro (1995) Nucleic Acids Res. 23 4190–4195 Occurrence Handle7479083

    PubMed  Google Scholar 

  • G.C. King J.W. Harper Z. Xi (1995) Methods Enzymol. 261 436–450 Occurrence Handle8569506

    PubMed  Google Scholar 

  • A. Kitao F. Hirata N. Go (1991) Chem. Phys. 158 447–472 Occurrence Handle10.1016/0301-0104(91)87082-7

    Article  Google Scholar 

  • P.J. Kraulis (1991) J. Appl. Crystallogr. 24 946–950

    Google Scholar 

  • C.D. Kroenke M. Rance III, A.G. Palmer (1999) J. Am. Chem. Soc. 121 10119–10125

    Google Scholar 

  • L.G. Laing K.B. Hall (1996) Biochemistry 35 13586–13594 Occurrence Handle10.1021/bi961310q Occurrence Handle8885838

    Article  PubMed  Google Scholar 

  • E.A. Leibold A. Laudano Y. Yu (1990) Nucleic Acids Res. 18 1819–1824 Occurrence Handle2336358

    PubMed  Google Scholar 

  • G. Lipari A. Szabo (1982a) J. Am. Chem. Soc. 104 4546–4559 Occurrence Handle10.1021/ja00381a009

    Article  Google Scholar 

  • G. Lipari A. Szabo (1982b) J. Am. Chem. Soc. 104 4559–4570 Occurrence Handle10.1021/ja00381a010

    Article  Google Scholar 

  • A.M. Mandel M. Akke A.G. Palmer (1995) J. Mol. Biol 245 144–163 Occurrence Handle10.1006/jmbi.1994.0073

    Article  Google Scholar 

  • J.L. Miller P.A. Kollman (1997) J. Mol. Biol. 270 436–450 Occurrence Handle10.1006/jmbi.1997.1113 Occurrence Handle9237909

    Article  PubMed  Google Scholar 

  • E.P. Nikonowicz A. Sirr F.M. Legault P. Jucker L.M. Baer A. Pardi (1992) Nucleic Acids Res. 20 4507–4526 Occurrence Handle1383927

    PubMed  Google Scholar 

  • D.A. Pearlmann D.A. Case J.W. Caldwell W.S. Ross T.E. Cheatham S. DeBolt D. Ferguson G. Seibel P. Kollman (1995) Comput. Phys. Commun. 91 1–41 Occurrence Handle10.1016/0010-4655(95)00041-D

    Article  Google Scholar 

  • J.W. Ponder D.A. Case (2003) Adv. Protein Chem. 66 27–85 Occurrence Handle14631816

    PubMed  Google Scholar 

  • J.J. Prompers R. Brüschweiler (2001) J. Am. Chem. Soc. 123 7305–7313

    Google Scholar 

  • J.J. Prompers R. Brüschweiler (2002) J. Am. Chem. Soc. 124 4522–4534

    Google Scholar 

  • J.D. Puglisi R. Tan B.J. Calnan A.D. Frankel J.R. Williamson (1992) Science 257 76–80 Occurrence Handle1621097

    PubMed  Google Scholar 

  • N.J. Reiter H. Blad F. Abildgaard S.E. Butcher (2004) Biochemistry 43 13739–13747 Occurrence Handle10.1021/bi048815y Occurrence Handle15504036

    Article  PubMed  Google Scholar 

  • A.H. Robbins C.D. Stout (1989) Proc. Natl. Acad. Sci. USA 86 3639–3643 Occurrence Handle2726740

    PubMed  Google Scholar 

  • J.-P. Ryckaert G. Ciccotti W.F. van Gunsteren (1977) J.␣Comput. Phys. 23 327–341 Occurrence Handle10.1016/0021-9991(77)90098-5

    Article  Google Scholar 

  • S.A. Showalter K.B. Hall (2002) J. Mol. Biol. 322 533–542 Occurrence Handle10.1016/S0022-2836(02)00804-5 Occurrence Handle12225747

    Article  PubMed  Google Scholar 

  • Showalter S.A. and Hall, K.B. (2005) Methods Enzymol.394, in press

  • D. Sitkoff D.A. Case (1998) Prog. NMR Spectrosc. 32 165–229 Occurrence Handle10.1016/S0079-6565(98)00013-2

    Article  Google Scholar 

  • D. Stueber D.M. Grant (2002) J. Am. Chem. Soc. 124 10539–10551

    Google Scholar 

  • A. Vitalis N.A. Baker J.A. McCammon (2004) Mol. Simulation 30 45–61 Occurrence Handle10.1080/08927020310001597862

    Article  Google Scholar 

  • L. Vugmeyster D.P. Raleigh III A.G. Palmer B.E. Vugmeister (2003) J. Am. Chem. Soc. 125 8400–8404

    Google Scholar 

  • T. Yamazaki R. Muhandiram L.E. Kay (1994) J. Am. Chem. Soc. 116 8266–8278

    Google Scholar 

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Correspondence to Kathleen B. Hall.

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Showalter, S.A., Baker, N.A., Tang, C. et al. Iron Responsive Element RNA Flexibility Described by NMR and Isotropic Reorientational Eigenmode Dynamics. J Biomol NMR 32, 179–193 (2005). https://doi.org/10.1007/s10858-005-7948-2

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