Monte Carlo simulations of proteins in cages: influence of confinement on the stability of intermediate states

TL;DR

This study uses Monte Carlo simulations to explore how confinement within cages affects protein folding pathways, stability of intermediate states, and thermodynamics, revealing that cage properties can significantly alter folding behavior.

Contribution

It introduces a theoretical model for protein folding inside confining potentials and demonstrates how cage interactions influence intermediate states and stability.

Findings

Confinement reduces the protein's phase space significantly.

Attractive walls can eliminate intermediate states, leading to two-state folding.

Slightly attractive walls enhance native state stability and promote intermediate configurations.

Abstract

We present a theoretical study of the folding of small proteins inside confining potentials. Proteins are described in the framework of an effective potential model which contains the Ramachandran angles as degrees of freedom and does not need any {\it a priori} information about the native state. Hydrogen bonds, dipole-dipole- and hydrophobic interactions are taken explicitly into account. An interesting feature displayed by this potential is the presence of some intermediates between the unfolded and native states. We consider different types of confining potentials in order to study the structural properties of proteins folding inside cages with repulsive or attractive walls. Using the Wang-Landau algorithm we determine the density of states (DOS) and analyze in detail the thermodynamical properties of the confined proteins for different sizes of the cages. We show that confinement dramatically reduces the phase space available to the protein and that the presence of intermediate states can be controlled by varying the properties of the confining potential. Cages with strongly attractive walls lead to the disappearance of the intermediate states and to a two-state folding into a less stable configuration. However, cages with slightly attractive walls make the native structure more stable than in the case of pure repulsive potentials, and the folding process occurs through intermediate configurations. In order to test the metastable states we analyze the free energy landscapes as a function of the configurational energy and of the end-to-end distance as an order parameter.