All-or-none folding of a flexible polymer chain in cylindrical nanoconfinement

Geometric confinement of a polymer chain results in a loss of conformational entropy. For a chain that can fold into a compact native state via a first-order-like transition, as is the case for many small proteins, confinement typically provides an entropic stabilization of the folded state, thereby shifting the location of the transition. This allows for the possibility of confinement (entropy) driven folding. Here, we investigate such confinement effects for a flexible square-well-sphere N-mer chain (monomer diameter σ) confined within a long cylindrical pore (diameter D) or a closed cylindrical box (height H = D). We carry out Wang-Landau simulations to construct the density of states, which provides access to the complete thermodynamics of the system. For a wide pore, an entropic stabilization of the folded state is observed. However, as the pore diameter approaches the size of the folded chain (D ∼ N^1/3σ), we find a destabilization effect. For pore diameters smaller than the native ground-state, the chain folds into a different, higher energy, ground state ensemble and the T vs D phase diagram displays non-monotonic behavior as the system is forced into different ground states for different ranges of D. In this regime, isothermal reduction of the confinement dimension can induce folding, unfolding, or crystallite restructuring. For the cylindrical box, we find a monotonic stabilization effect with decreasing D. Scaling laws for the confinement free energy in the athermal limit are also investigated.