Folding of Top7 in unbiased all-atom Monte Carlo simulations

For computational studies of protein folding, proteins with both helical and -sheet secondary structure elements are very challenging, as they expose subtle biases of the physical models. Here, we present reproducible folding of a 92 residue / protein (residues 3-94 of Top7, PDB ID: 1QYS) in computer simulations starting from random initial conformations using a transferable physical model which has been previously shown to describe the folding and thermodynamic properties of about 20 other smaller proteins of different folds. Top7 is a de novo designed protein with two -helices and a five stranded -sheet. Experimentally, it is known to be unusually stable for its size, and its folding transition distinctly deviates from the two-state behavior commonly seen in natural single domain proteins. In our all-atom implicit solvent parallel tempering Monte Carlo simulations, Top7 shows a rapid transition to a group of states with high native-like secondary structure, and a much slower subsequent transition to the native state with a root mean square deviation of about 3.5 angstrom from the experimentally determined structure. Consistent with experiments, we find Top7 to be thermally extremely stable, although the simulations also find a large number of very stable non-native states with high native-like secondary structure. Proteins 2013; 81:1446-1456. (c) 2013 Wiley Periodicals, Inc.