Simulation of protein misfolding using a lattice model

Misfolding during protein self-assembly is the cause of numerous human and animal diseases. Understanding of the mechanism that underlies the protein folding into a normal or abnormal form can enhance the search for pathogen inhibitors and drug design. We used Monte Carlo dynamics to study the folding of a 27-membered heteropolymer on a cubic lattice. This lattice protein had a stable compact (“latent”) state that competed with the native state. It appeared that the free-energy surface of the system studied consisted of three basins, which corresponded to the semicompact globule, latent, and native states. We determined the bifurcation regions in the protein kinetic trajectories where the protein took a native or a latent structure and the probabilities of these structures to be formed. The effects of mutations on the probability of native state and the rate of its formation were modeled.