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arXiv · 0711.0916

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

Pedro Ojeda·Aurora Londono·Nan-Yow Chen·Martin Garcia
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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.

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Pedro Ojeda, Aurora Londono, Nan-Yow Chen, Martin Garcia. 2008-08-04. Monte Carlo simulations of proteins in cages: influence of confinement on the stability of intermediate states. https://arxiv.org/abs/0711.0916

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