A mesoscopic model for molecular dynamics studies of RNA nanostructures

Maxim Paly*, Roderick Melnick, Bruce Shapiro

M2NeTLab, Wilfrid Laurier University, 75 University Avenue West, Waterloo, ON N2L 3C5, Canada. mpaliy@wlu.ca

Proc LSS Comput Syst Bioinform Conf. August, 2009. Vol. 8, p. 71-79. Full-Text PDF

*To whom correspondence should be addressed.

A series of 3-beads-per-nucleotide mesoscopic models is being developed for the study of the RNA nanostructures via a Molecular Dynamics simulation. Such coarse-grained treatment allows us to reach the microsecond time scale that is by three orders of magnitude larger than that achieved in the full atomistic computer simulations, and thus, to study the slowest conformational motions of the RNA, as well as to enable simulations of the larger RNA structures in the context of bionanotechnology. We find that the variant of the model described by a set of just a few universal parameters is able to describe different RNA conformations and is comparable in structural precision to the model variant where the detailed values of the backbone P-C4' dihedrals taken from a reference structure are included. Our findings demonstrate the importance of the RNA conformation classes based on these dihedrals.