Abstract
Molecular chaperonins, such as GroEL/ES, are considered to assist in protein folding through both the confinement effect and chemical interactions provided by chaperonins themselves. Although the confinement effect on protein folding has been extensively investigated, the role of the chemical properties within chaperonins remains underexplored. To address this, we propose a Chaperonin Environment-Mimicking Model (CEMM) based on the effective radii and components of the GroEL/ES structure. Using enhanced molecular dynamics simulations, we compared the ability of CEMM with non-polar, polar uniform models and dilute environment to stabilize the experimental conformations of model substrate proteins. Consequently, the CEMM most effectively stabilized each experimental protein conformation, highlighting the importance of chemical properties within chaperonins in assisting protein folding. Furthermore, the analyses of the substrate proteins within each model suggest that the chemical diversity within chaperonins contributes to their ability to assist in protein folding.
