Book of Abstracts: Albany 2007

category image Albany 2007
Conversation 15
June 19-23 2007

Study of Structure, Dynamics and Local Elasticity of 16S rRNA Helix 44 Using Molecular Dynamics Methods

Molecular dynamics (MD) simulations were carried out to investigate the structure, dynamics, and local base-pair step deformability of the free 16S ribosomal helix 44 from Thermus thermophilus and of a canonical A-RNA double helix. While helix 44 is bent in the crystal structure of the small ribosomal subunit, the simulated helix 44 is intrinsically straight. It shows, however, substantial instantaneous bends that are isotropic. The spontaneous motions seen in simulations achieve large degrees of bending seen in the X-ray structure and would be entirely sufficient to allow the dynamics of the upper part of helix 44 evidenced by cryo-electron microscopic studies (1). Analysis of local base-pair step deformability reveals a patch of flexible steps in the upper part of helix 44 and in the area proximal to the bulge bases, suggesting that the upper part of helix 44 has enhanced flexibility. The simulations identify two conformational substates of the second bulge area (bottom part of the helix) with distinct base pairing that can be commonly seen in atomic resolution structures. In agreement with nuclear magnetic resonance (NMR) and X-ray studies, a flipped out conformational substate of conserved 1492A is seen in the first bulge area. Molecular dynamics (MD) simulations reveal a number of reversible α-γ backbone flips that correspond to transitions between two known A-RNA backbone families. The flipped substates do not cumulate along the trajectory and lead to a modest transient reduction of helical twist with no significant influence on the overall geometry of the duplexes. Despite their considerable flexibility, the simulated structures are very stable with no indication of substantial force field inaccuracies.

References and Footnotes
  1. VanLoock, M. S., Agrawal, R. K., Gabashvili, I. R., Qi, L., Frank, J., and Harvey S. C. Journal of Molecular Biology 304, 507-515 (2000).

Kamila Réblová1, *
Filip Lankas2
Jirí Sponer1

1Institute of Biophysics
Academy of Sciences of the Czech Republic
Kralovopolska 135
61265 Brno, Czech Republic
2Institute for Mathematics B
EPFL (Swiss Federal Institute of Technology)
Station 8, CH-1015 Lausanne, Switzerland

*Phone: +420 541 517 250
Fax: +420 541 211 293
Email: kristina@physics.muni.cz