Molecular Simulations of the Ribosome and Associated Translation Factors

TL;DR

This paper reviews recent computational studies using molecular dynamics simulations to understand the structure, dynamics, and energetics of the ribosome, complementing experimental structural data from cryo-EM and X-ray crystallography.

Contribution

It summarizes how molecular dynamics simulations have advanced understanding of ribosomal function and conformational changes.

Findings

Simulations reveal detailed ribosomal dynamics

Insights into energetics of translation

Bridging structural data with kinetic understanding

Abstract

The ribosome is a macromolecular complex which is responsible for protein synthesis in all living cells according to their transcribed genetic information. Using X-ray crystallography and, more recently, cryo-electron microscopy (cryo-EM), the structure of the ribosome was resolved at atomic resolution in many functional and conformational states. Molecular dynamics simulations have added information on dynamics and energetics to the available structural information, thereby have bridged the gap to the kinetics obtained from single-molecule and bulk experiments. Here, we review recent computational studies that brought notable insights into ribosomal structure and function.