Molecular Dynamics Simulation of the Nascent Peptide Chain in the Ribosomal Exit Tunnel

Abstract

The ribosome is a large macromolecular complex which synthesizes all proteins in the cell according to the genetic code and thereby the central nanomachine of life. Nascent peptide chains are polymerized by the ribosome and exit through a tunnel in the large subunit. This tunnel is an important target for antibiotic action hindering the movement of the peptide chain. The recently solved structure of the ribosome led to a better understanding of the tunnel's geometry and the binding sites of the antibiotics. Yet the dynamics of the polypeptide's conformation and the interactions with the large subunit and the antibiotics remain unclear. We approach these questions with molecular dynamics simulations of the large subunit and the nascent chain in explicit water under physiological conditions. This allows us to investigate the dynamics the ribosome and the polypeptide at an atomistic level, which will lead to a huge improvement in the understanding of the translation process and the antibiotic action.