“Small ribonucleic acids in silico” (S-RNA-S) is a project funded by the European Research Council through a Starting Grant (No. 306662) and hosted by the International School for Advanced Studies (SISSA, Italy). The activities started on October the 1st 2012 and will last for five years. The goal is to understand small RNAs using computer simulations.
Ribonucleic acid (RNA) is acquiring a larger importance in cell biology, as more functions that it accomplishes are discovered. In particular, as it has emerged in the last decade, it has a crucial role in the post-transcriptional regulation of gene expression. The comprehension of these mechanisms and, in general, of RNA properties at a molecular level is a key issue in the study of many diseases and paves the way to possible applications in molecular medicine. Particularly interesting in this context are riboswitches, small portions of messenger RNAs which change their conformation in presence of specific metabolites and consequently inhibit or enhance gene transcription or translation. Another issue of paramount interest is RNA metabolism, crucial for viral replication, and in particular of the interaction of RNAs and the molecular motors devoted to its manipulation and unwinding. One of the goals of the present project is to develop new in silico approaches based on molecular dynamics for the study of small RNA molecules. Another goal is to apply these techniques, in combination with standard molecular dynamics and state-of-the-art rare-event methods, to the study of topics including riboswitch folding and dynamics, RNA-protein interaction and folding of non-coding RNAs.