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Nucleic Acids Research Advance Access originally published online on August 31, 2009
Nucleic Acids Research 2009 37(19):6528-6539; doi:10.1093/nar/gkp664
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Nucleic Acids Research, 2009, Vol. 37, No. 19 6528-6539
© The Author [2009]. Published by Oxford University Press. All rights reserved.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

RNA

A mechanism for S-adenosyl methionine assisted formation of a riboswitch conformation: a small molecule with a strong arm

Wei Huang1, Joohyun Kim2, Shantenu Jha2,* and Fareed Aboul-ela1,*

1Department of Biological Sciences and 2Center for Computation and Technology, Louisiana State University, Baton Rouge, LA 70803, USA

*To whom correspondence should be addressed. Tel: +1 225 578 2791; Fax: +1 225 578 7258; Email: faboul{at}lsu.edu

Correspondence may also be addressed to Shantenu Jha. Email: sjha{at}cct.lsu.edu

Received May 13, 2009. Revised July 26, 2009. Accepted July 28, 2009.

The S-adenosylmethionine-1 (SAM-I) riboswitch mediates expression of proteins involved in sulfur metabolism via formation of alternative conformations in response to binding by SAM. Models for kinetic trapping of the RNA in the bound conformation require annealing of nonadjacent mRNA segments during a transcriptional pause. The entropic cost required to bring nonadjacent segments together should slow the folding process. To address this paradox, we performed molecular dynamics simulations on the SAM-I riboswitch aptamer domain with and without SAM, starting with the X-ray coordinates of the SAM-bound RNA. Individual trajectories are 200 ns, among the longest reported for an RNA of this size. We applied principle component analysis (PCA) to explore the global dynamics differences between these two trajectories. We observed a conformational switch between a stacked and nonstacked state of a nonadjacent dinucleotide in the presence of SAM. In the absence of SAM the coordination between a bound magnesium ion and the phosphate of A9, one of the nucleotides involved in the dinucleotide stack, is destabilized. An electrostatic potential map reveals a ‘hot spot’ at the Mg binding site in the presence of SAM. These results suggest that SAM binding helps to position J1/2 in a manner that is favorable for P1 helix formation.


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