Structural characterization of γ-repressor folding from all-atom molecular dynamics simulations

The five-helix bundle γ-repressor fragment is a fast-folding protein. A length of 80 amino acid residues puts it on the large end among all known microsecond folders, and its size poses a computational challenge for molecular dynamics (MD) studies. We simulated the folding of a novel γ-repressor fast-folding mutant (γ-HG) in explicit solvent using an all-atom description. By means of a recently developed tempering method, we observed reversible folding and unfolding of γ-repressor in a 10 μs trajectory. The folding kinetics was also investigated through a set of MD simulations run at different temperatures that together covered more than 125 μs. The protein was seen to fold into a native-like topology at intermediate temperature, and a slow-folding pathway was identified. The simulations suggest new experimental observables for better monitoring of the folding process, and a novel mutation is expected to accelerate γ-repressor folding.