Ab initio folding of helix bundle proteins using molecular dynamics simulations

The ab initio fast simulations at 400 K using a GB implicit solvent model with an all-atom based force field that could describe the spontaneous formation of nativelike structures for the 36-residue villin headpiece and the 46-residue fragment B of Staphylococcal protein A, is demonstrated. An implicit solvent model combined with high-temperature MD made it possible to perform direct folding simulations of small-to medium-sized proteins by reducing the computational requirements tremendously.