Computational Investigation of RNA ConformationalChange

Non-coding RNAs (ncRNA) are RNAs that are not simply translated into protein but instead function as RNA and can be structured like proteins. Non-coding RNAs can perform biomolecular functions including catalysis and chemical reactions, and they can bind other RNAs and proteins. Conformational change of ncRNA is an important component in many of these functions. RNA conformational changes occur on small length and time scales that make their full detail unobservable directly by experimental techniques. Molecular mechanics, which uses classical mechanics to model structure and dynamics, can be used to model atomic and temporal details of biomolecular conformational change. Molecular mechanics requires a force field, which is a set of parameters that describe the potential energy of a molecule as a function of geometry. An RNA duplex previously studied by NMR in the lab of Dr. Doug Turner was investigated using computational techniques based on molecular mechanics, including molecular dynamics (MD), targeted molecular dynamics (TMD), nudged elastic band (NEB), molecular-mechanics Poisson-Boltzmann and Generalized Born solvent association (MM-PBSA/GBSA), and umbrella sampling free energy calculations. Potential conformational change pathways between the experimental NMR and X-ray structures of the 23S rRNA subunit helix 40 loop were also investigated with NEB. Molecular mechanics modeling of RNA conformational pathways provided detailed models of pathways; however, an improved force field was needed to accurately model RNA conformational space. Branch migration is a conformational change in RNA where bases of an invading acceptor nucleic acid strand displace bases of another donor strand already in a duplex. This process is hypothesized to occur as a random walk where exchange of base pairs between existing and invading strands proceeds forward and backwards stochastically. The Turner nearest neighbor free energy parameters were used to predict sequence dependent probabilities for forward and backward movement in a random walk branch migration model. A biochemical assay measuring completion of branch migration was used to measure branch migration for varying sequences. The hypothesis was that consecutive GC base pairs would slow migration. Experiments indicate faster branch migration with a GC barrier at the beginning of the sequence, contradicting predictions, possibly because of protein interactions.