We present a theoretical investigation of the folding of small proteins assisted by chaperones. We describe the proteins in the framework of an effective potential model which contains the Ramachandran angles as degrees of freedom {\it   . The cage of chaperonins is modeled by an external confining potential which is also able to take into account hydrophobic and hydrophilic effects inside the cavity. Using the Wang-Landau algorithm Phys. Rev. Lett.%DIFDELCMD < {\bf %%% 86 , 2050 (2001) we determine the density of states g(E ) and analyze in detail the thermodynamical properties of the confined proteins for different sizes of the cage . We show how the confinement through the chaperon dramatically reduces the phase space available for the protein leading to a much faster folding process. Slightly hydrophobic cages seem to make the native structure more stable . However, not any confining potential helps folding . If the inner walls of the cage are strongly hydrophobic, a denaturation process is induced, in which the proteins partially unfold and stick to the walls .
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 %DIFDELCMD < {\bf %%% 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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investigation
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assisted by chaperones. We describe the proteins
inside confining potentials. Proteins are described
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and does not need any
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a priori
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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
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The cage of chaperonins is modeled by an external confining potential which is also able to take into account hydrophobic and hydrophilic effects inside the cavity.
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Phys. Rev. Lett.
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86
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, 2050 (2001)
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g(E
(DOS
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cage
cages
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how the confinement through the chaperon
that confinement
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for the protein leading to a much faster folding process. Slightly hydrophobic cages seem to
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
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. However, not any confining potential helps folding . If the inner walls of the cage are strongly hydrophobic, a denaturation process is induced, in which the proteins partially unfold and stick to the walls
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