Weekly RNA News - Week XI - March 2011

Jun Feng and Nils G. Walter and Charles L. Brooks, III @ University of Michigan
All-atom Go model study of preQ1 riboswitch aptamer domain folding.
Journal of the American Chemical Society, 133, 4196-4199 (2011)
Feng, Walter and Brooks present interesting results using a Go model for simulating the folding of an RNA sequence into a riboswitch aptamer in the presence of a metabolite called preQ1. The model used seems to favor a description of a funnel shaped free-energy landscape for the folding of this RNA riboswitch. It's interesting to see that what is described as a structure made of two helices called P1 and P2 could also be described as an "irregular" triple-helix:

Some very interesting thoughts come out from reading this article. The folding of this riboswitches must be pretty fast, pico, nano seconds? so, these are good cases for performing MD simulations. In general the folding of parts of mRNA into structured regions seem to be good targets for MD research. I also wonder if the methodology used can take into account the possibility of having a rugged RNA folding landscape and if such case would influence the sequential and cooperative folding mechanism results.
Other things which would be interesting to see are the electrostatics of the A-tract of the folded configuration, for example.

Martin Mann and Konstantin Klemm @ Freiburg & Leipzig
Efficient exploration of discrete energy landscapes
Physical Review E, 83, 1-7 (2011)
The authors use a so-called number partitioning problem, which is common in computer science, to be able to stochasically sample the free energy landscape of RNA secondary structures.