Protein escape at the ribosomal exit tunnel: Effects of native interactions, tunnel length and macromolecular crowding

TL;DR

This study uses molecular dynamics simulations to investigate how native interactions, tunnel length, and crowding influence the escape time of nascent proteins from the ribosomal exit tunnel, revealing factors that optimize folding and escape efficiency.

Contribution

It demonstrates that native interactions and tunnel length significantly affect escape times, and introduces a diffusion model to predict escape behavior under various conditions.

Findings

Native interactions decrease escape time.

Longer tunnels increase escape time, especially beyond 90-110 Å.

Macromolecular crowding slows down protein escape.

Abstract

How fast a post-translational nascent protein escapes from the ribosomal exit tunnel is relevant to its folding and protection against aggregation. Here, by using Langevin molecular dynamics, we show that non-local native interactions help decreasing the escape time, and foldable proteins generally escape much faster than same-length self-repulsive homopolymers at low temperatures. The escape process, however, is slowed down by the local interactions that stabilize the {\alpha}-helices. The escape time is found to increase with both the tunnel length and the concentration of macromolecular crowders outside the tunnel. We show that a simple diffusion model described by the Smoluchowski equation with an effective linear potential can be used to map out the escape time distribution for various tunnel lengths and various crowder concentrations. The consistency between the simulation data and the diffusion model however is found only for the tunnel length smaller than a cross-over length of 90 {\AA} to 110 {\AA}, above which the escape time increases much faster with the tunnel length. It is suggested that the length of ribosomal exit tunnel has been selected by evolution to facilitate both the efficient folding and efficient escape of single domain proteins. We show that macromolecular crowders lead to an increase of the escape time, and attractive crowders are unfavorable for the folding of nascent polypeptide.