Research

Ribosomes

Over the past decade, we have performed large-scale molecular dynamics simulations of the ribosome to better understand its mechanism. Our goal is to produce an integrated picture of tRNA selection and translocation that ties together the large amount of existing crystallographic, cryo-EM and single molecule FRET data. By quantifying the energy landscapes of these processes, we are elucidating the underlying physics of protein synthesis.

Long non-coding RNAs

Long non-coding RNAs (lncRNAs) have emerged as an important class of RNAs in mammalian development and disease. We are performing the first structural studies of intact long non-coding RNAs (lncRNAs) to better understand their mechanism. Thousands of lncRNAs have been recently identified that are associated with stem cells, development, cancer, and brain disease. Since several lncRNA systems have been shown to recruit epigentic factors to their chromatin targets, lncRNAs are thought to play a key role in epigenetics.

Riboswitches

We are using a joint experiment/computation approach to understand the mechanism of riboswitch operation. Experimentally, we are performing biochemical probing experiments to understand the process of switching and the effect of ligand and magnesium on this process. Computationally, we are using molecular simulation to to understand the interplay between ligand binding, folding and magnesium interactions on riboswitch conformation.