Protein Folding

Questions addressed: Mechanisms for protein folding under confining potentials (chaperons)? Accurate models for the description of the folding of specific proteins

We carried out a theoretical investigation of the folding of small proteins assisted by chaperons. We describe the proteins in the framework of an effective potential model which contains the Ramachandran angles as degrees of freedom. The cage of chaperonins is modelled 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. 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.

Methods: Different kinds of Monte Carlo simulations

Publications: [75] (see list of publications)