Trp Cage Folding in Confinement

Abstract

While protein-folding studies are typically performed in bulk solution, the effects of confinement and crowding are poorly understood and in fact may alter the thermodynamics and kinetics of protein folding in a cellular environment. Here we have used all-atom simulations to examine the model Trp-cage mini-protein adsorbed to a purely hydrophobic surface and confined between hydrophobic walls. Replica exchange molecular dynamics simulations were performed to construct the folding free-energy landscape from which meta-stable states not seen in the bulk were indentified. In both cases, these states consist of different conformations of the protein adsorbed to the wall. The intermediates likely affect the free energy barriers to folding. Adsorption of the protein to a hydrophobic wall raises the energy barrier to folding, while lowering the barrier to folding of the confined protein. Although the confined protein is adsorbed to the wall, it appears that confinement stabilizes the α-helix, driving the protein toward the native state. Further, the presence of additional states likely changes the folding mechanism of the protein. Therefore we use multiple state transition path sampling to elucidate the differences between folding of Trp-cage in the bulk and confined between hydrophobic walls. Our simulation results can provide a realistic starting point for experiments on the effect of confinement on the folding behavior in Trp-cage and other small model proteins.