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Journal of Biomolecular NMR

, Volume 32, Issue 3, pp 179–193 | Cite as

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

  • Scott A. Showalter
  • Nathan A. Baker
  • Changguo Tang
  • Kathleen B. Hall
Article

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.

Keywords

IRE RNA molecular dynamics NMR structure and dynamics RED analysis 

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Copyright information

© Springer 2005

Authors and Affiliations

  • Scott A. Showalter
    • 1
  • Nathan A. Baker
    • 1
    • 2
  • Changguo Tang
    • 1
  • Kathleen B. Hall
    • 1
  1. 1.Department of Biochemistry & Molecular BiophysicsUSA
  2. 2.Center for Computational BiologyWashington University School of MedicineSt LouisUSA

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