Confinement Can Destabilize Alpha-Helix Folding Proteins by Stabilizing the Beta Structures

Protein folding in confined media has attracted wide attention over the past

decade due to its importance to both in-vivo and in-vitro applications.

It is generally believed that protein stability increases by decreasing the

size of the confining medium, if its interaction with the confining walls is

repulsive, and that maximum folding temperature occurs for a pore size only

slightly larger than the smallest dimension of protein folded state.

However, protein stability at pore sizes very close to the size of the folded

state has not received enough attention. Unfortunately, an in depth study of

this problem at atomistic level is not possible by the present experimental

apparatuses. Using 0.3 millisecond-long molecular dynamics simulations,

we show that proteins with alpha-helix native state can be destabilized at

high confinement due to entropic stabilization of the protein states that

contain the beta structures. In contradiction to the present theoretical

explanations, which do not consider entropy of the misfolded states, we find

that the folding temperature maximum occurs at larger pore sizes for smaller

alpha helices. These results shed light on many recent experimental

observations that could not be explained by the present theories.

Our work demonstrates the importance of entropic effects of proteins misfolded

states in highly confined environments. The results support the concept of

passive effect of GroEL on protein folding by preventing it from aggregation

in crowded environment of cells, and provide deeper clues to the \alpha-\beta

conformational transition, believed to contribute to Alzheimer's and

Parkinson's diseases. The strategy of protein and enzyme stabilization in

confined media may also have to be revisited in the case of high confinement.