Organic Solvent-Induced Structural Changes in a Protein Confined in a Giant Coordination Cage

Abstract We investigate the molecular mechanism of acetonitrile-induced structural changes in a cutinase-like enzyme in a giant coordination cage using molecular dynamics (MD) simulations. As the acetonitrile content within the cage increases, significant conformational changes of the caged protein occur due to acetonitrile binding to the specific sites, in line with protein denaturation events observed in previous nuclear magnetic resonance studies. Accordingly, employing MD simulations on caged proteins represents an effective strategy for investigating the dynamics of unstable protein structures.