During the elongation cycle, ribosomes create peptides from an mRNA blueprint. To prime the ribosome for a new round of elongation after peptide bond formation, the transfer RNA (tRNA) bound to the aminoacyl site (A site) moves to the peptidyl site (P site) while the tRNA bound to the P site moves to the exit site (E site). In this work we investigated the driving forces and dynamics of this process called tRNA translocation. We found surprisingly large kinetic rates for 30S body and head as well as L1-stalk movements during translocation, while the tRNA are "road-blocks" for most individual transitions. Further, we find that tRNA movement is aided by three distinct interaction modes with ribosomal proteins L1, L5 and L16: pulling, sliding and stepping. In the context of this analysis we developed an analysis tool to efficiently find conacting atoms in biomolecular ensemble data.
Keywords: ribosome; cryo-EM; molecular dynamics; refinement; translocation; tRNA; range search; rate estimates; rate theory
