Undergraduate Researcher California State University, Long Beach Santa Ana, California, United States
Nguyet Nguyen (California State University, Long Beach)
The PK1 pseudoknot, a well-characterized super secondary structure, from Aquifex aeolicus is a transfer-messenger RNA (tmRNA) that participates in the ribosomal trans-translation rescue mechanism. Extensive all-atom molecular dynamics simulations were conducted across a worldwide distributed computing network to study the folding, unfolding, misfolding and conformational plasticity of the twenty-two nucleotides PK1 pseudoknot, yielded nearly 140 µs of cumulative sampling time. Complex K-means clustering was utilized to identify twenty-seven conformational microstates among forty starting structures spanning from the extended unfolded state to the native fold. Moreover, post equilibration data, established at 7.5 ns, provided detailed depictions the conformational free energy landscape that encompass the native states, numerous intermediate and misfolded states and intricate folding mechanism of the pseudoknot motif. The PK1 pseudoknot displays structural similarities to the class of frameshifting pseudoknots and suggests a parallel between the trans-translational mechanism and frameshifting mechanism of our previous study of the potato lead roll virus RNA pseudoknot.