Molecular Dynamics Simulations of Ribosomes: Integrating Theory and Experiment

Abstract

We will report results from the first molecular simulations of eukaryotic ribosomes. Using an integrated approach, we combine data from X-ray crystallography, cryo-EM and SHAPE chemical probing. Over the past decade, we have developed a pipeline that begins with X-ray crystallographic structures and uses molecular simulation to produce all-atom models consistent with cryo-EM reconstructions. Theses models are then used as beginning and end points for simulations of large-scale conformational changes. Our strategy has been highly successful in the case of the accommodation conformational change during tRNA selection in bacteria. Here, we correctly predicted the universally conserved accommodation corridor, which has been verified in several independent experimental studies. We have also recently identified the hybrid corridor, responsible for tRNA hybrid state formation during translocation. Our latest addition to our pipeline is the incorporation of SHAPE probing data describing the mobility of the RNA backbone in solution. We have developed a novel algorithm to generate molecular dynamics simulations highly consistent with SHAPE probing data. We have applied these techniques to eukaryotic ribosomes to investigate their dynamics and conformational changes.