Faculty Sponsor's Department(s):
One of the most remarkable nanomachines identified in biological systems is the ribosome. In particular, there exists an unidentified three-way junction (3WJ) in the ribosome that is highly conserved across biological kingdoms which appears to reflect some propensity for motion. This region is unique in that while its nucleotide secondary structure can be accurately determined, when in the context of the ribosome, it folds in a completely unprecedented manner, with unusual tertiary contacts guiding its stable, interned structure. We intend to use NVT dynamics with a CHARMM force field and explicit solvent to probe the conformational landscape of the 3WJ and its associated molecular motions. We hope to use these methods to guide future experiments and strengthen existing theories regarding this portion of the ribosome.