Ribosome Tunnel Environment Drives the Formation of α-Helix during Cotranslational Folding

Protein conformations in cells are not solely determined by amino acid sequences; they also depend on cellular environments. For instance, the ribosome tunnel induces its specific alpha-helix formation during cotranslational folding. Owing to the link between these temporally alpha-helix and biological functions, the mechanism of alpha-helix formation inside the ribosome tunnel has been previously explored. Consequently, the conformational restrictions of the tunnel were considered one of the driving forces of alpha-helix formation. Conversely, the ribosomal tunnel environment, including its chemical properties, appears to influence the alpha-helix formation. However, a comprehensive analysis of the ribosome tunnel environment's impact on the alpha-helix formation has not been conducted yet due to challenges in experimentally controlling it. Therefore, as a new computational approach, we proposed a ribosome environment-mimicking model (REMM) based on the radius and components of the experimentally determined ribosome tunnel structures. Using REMM, we assessed the impact of the ribosome tunnel environment on alpha-helix formation. Herein, we employed carbon nanotubes (CNT) as a reference model alongside REMM because CNT reproduce conformational restrictions rather than the ribosome tunnel environment. Quantitatively, the ability to reproduce the alpha-helix of nascent peptides in the experimental structure was compared between the CNT and REMM using enhanced all-atom molecular dynamics simulations. Consequently, the REMM more accurately reproduced the alpha-helix of the nascent peptides than the CNT, highlighting the significance of the ribosome tunnel environment in alpha-helix formation. Additionally, we analyzed the properties of the peptide inside each model to reveal the mechanism of ribosome tunnel-specific alpha-helix formation. Consequently, we revealed that the chemical diversities of the tunnel are essential for the formation of backbone-to-backbone hydrogen bonds in the peptides. In conclusion, the ribosome tunnel environment, with the diverse chemical properties, drives its specific alpha-helix formation. By proposing REMM, we newly provide the technical basis for investigating the protein conformations in various cellular environments.