Temperature-Dependent Folding Pathways of Pin1 WW Domain: An All-Atom Molecular Dynamics Simulation of a Gō Model

Abstract

We study the folding thermodynamics and kinetics of the Pin1 WW domain, a three-stranded β-sheet protein, by using all-atom (except nonpolar hydrogens) discontinuous molecular dynamics simulations at various temperatures with a Gō model. The protein exhibits a two-state folding kinetics near the folding transition temperature. A good agreement between our simulations and the experimental measurements by the Gruebele group has been found, and the simulation sheds new insights into the structure of transition state, which is hard to be straightforwardly captured in experiments. The simulation also reveals that the folding pathways at approximately the transition temperature and at low temperatures are much different, and an intermediate state at a low temperature is predicted. The transition state of this small β-protein at its folding transition temperature has a well-established hairpin 1 made of β1 and β2 strands while its low-temperature kinetic intermediate has a formed hairpin 2 composed of β2 and β3 strands. Theoretical results are compared with other simulation results as well as available experimental data. This study confirms that specific side-chain packing in an all-atom Gō model can yield a reasonable prediction of specific folding kinetics for a given protein. Different folding behaviors at different temperatures are interpreted in terms of the interplay of entropy and enthalpy in folding process.