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

ABSTRACT: We study the folding of small proteins inside confining potentials. Proteins are described using an effective potential model that contains the Ramachandran angles as degrees of freedom and does not need any 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 metastable intermediates between the unfolded and native states. We consider different types of confining potentials to describe proteins folding inside cages with repulsive or attractive walls. Using the Wang-Landau algorithm, we determine the density of states and analyze in detail the thermodynamical properties of the confined proteins for different sizes of the cages. We sho

SUBMITTER: Ojeda P 

PROVIDER: S-EPMC2716574 | biostudies-literature | 2009 Feb

REPOSITORIES: biostudies-literature