Folding and Unfolding Simulations of a Three-Stranded Beta-Sheet Protein

Understanding the folding processes of a protein into its three-dimensional native structure only with its amino-acid sequence information is a long-standing challenge in modern science. Twohundred independent folding simulations (starting from non-native conformations) and twohundred independent unfolding simulations (starting from the folded native structure) are performed using the united-residue force field and Metropolis Monte Carlo algorithm for betanova (three-stranded antiparallel beta-sheet protein). From these extensive computer simulations, two representative folding pathways and two representative unfolding pathways are obtained in the reaction coordinates such as the fraction of native contacts, the radius of gyration, and the rootmean-square deviation. The folding pathways and the unfolding pathways are similar each other. The largest deviation between the folding pathways and the unfolding pathways results from the root-mean-square deviation near the folded native structure. In general, unfolding computer simulations could capture the essentials of folding simulations.