Development of simulation models for protein folding in a thermal annealing process--I: A simulation of BPTI folding by the pearl necklace model.

A model system is proposed to simulate the folding processes of proteins during thermal annealing. This system consists of four subsystems: (i) the pearl necklace model with isotropic inter-residue interactions; (ii) the extended pearl necklace model with anisotropic interaction potentials; (iii) molten globule phase dynamics; and (iv) final generation of the three-dimensional structure of a given protein. In this paper results obtained with the pearl necklace model are reported. This model consists of spherical elements and virtual bonds of 3.8 A in length and is intended to simulate dynamical processes at relatively high temperature where entropic terms play a dominant role. Inter-residue interactions are composed of spherical soft repulsive potentials and hydrophobic interactions inherent to respective residues. A simulation of folding processes of BPTI starting from the fully extended conformation indicated that intermediates, even at early stages of folding, are not randomly coiled but assume organized structures that resemble, to some extent, the native conformation.