Identifying Strategies to Experimentally Probe Multidimensional Dynamics in the Ribosome

The ribosome is a complex biomolecular machine that utilizes large-scale conformational rearrangements to synthesize proteins. For example, during the elongation cycle, the head domain of the ribosomal small subunit (SSU) is known to undergo transient rotation events that allow for movement of tRNA molecules (i.e., translocation). While the head may exhibit rigid-body-like properties, the precise relationship between experimentally accessible probes and multidimen-sional rotations has yet to be established. To address this gap, we perform molecular dynamics simulations of the translocation step of the elongation cycle in the ribosome, where the SSU head spontaneously undergoes rotation and tilt-like motions. With this data set (1250 simulated events), we used statistical and information-theory-based measures to identify possible single-molecule probes that can isolate SSU head rotation and head tilting. This analysis provides a molecular interpretation for previous single-molecule measurements, while establishing a framework for the design of next-generation experiments that may precisely probe the mechanistic and kinetic aspects of the ribosome.

Automated summary

In this study, molecular dynamics simulations were used to investigate the translocation step of the elongation cycle in the ribosome. The results reveal that the head domain of the ribosomal small subunit undergoes spontaneous rotation and tilt-like motions. Possible single-molecule probes that can isolate the rotation and tilt of the head domain were identified, providing insights into the mechanistic and kinetic aspects of the ribosome.