Publication details
An RNA Molecular Switch: Intrinsic Flexibility of 23S rRNA Helices 40 and 68 5 '-UAA/5 '-GAN Internal Loops Studied by Molecular Dynamics Methods
| Authors | |
|---|---|
| Year of publication | 2010 |
| Type | Article in Periodical |
| Magazine / Source | Journal of Chemical Theory and Computation |
| MU Faculty or unit | |
| Citation | |
| Field | Biochemistry |
| Keywords | molecular dynamics; free energy; RNA |
| Description | Functional RNA molecules such as ribosomal RNAs (rRNAs) frequently contain highly conserved internal loops with a 5'-UAA/5'-GAN (UAA/GAN) consensus sequence. The UAA/GAN internal loops adopt a distinctive structure inconsistent with secondary structure predictions. The solution structure of an isolated UAA/GAA internal loop shows substantially rearranged base pairing with three consecutive non-Watson-Crick base pairs. Its A/U base pair adopts an incomplete cis Watson-Crick/Sugar edge (dWS) A/U conformation instead of the expected Watson-Crick arrangement. We performed 3.1 mu s of explicit solvent molecular dynamics (MD) simulations of the X-ray and NMR UAA/GAN structures, supplemented by molecular mechanics, Poisson-Boltzmann, and surface area free energy calculations; locally enhanced sampling (LES) runs; targeted MD (TMD); and nudged elastic band (NEB) analysis. As results, the simulations confirm that the UAA/GAN internal loop is a molecular switch RNA module that adopts its functional geometry upon specific tertiary contexts. |
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