Thermodynamics and Folding Pathways of Trpzip2: An Accelerated Molecular Dynamics Simulation Study

Abstract

In this paper, we apply an enhanced sampling method introduced earlier to study the folding mechanism of a beta-hairpin, trpzip2, using an all-atom potential for the protein and an implicit model for the solvent. The enhanced sampling method allows us to obtain multiple protein folding and unfolding trajectories in relatively short simulations. The sufficient sampling of folding and unfolding events of trpzip2 makes possible a more detailed investigation of its folding landscape and thermodynamics, leading to the identification of folding pathways. The analysis of the thermodynamics involved in the folding of trpzip2 showed that this polypeptide folds by two stages: a downhill hydrophobic collapse followed by formation of native hydrogen bonds. During the hydrogen bond formation, a transition state can be identified with only one native hydrogen bond being formed, which is more consistent with a 'zip-out' mechanism. To address the dynamics in a more reliable way, explicit solvent was used for the estimation of the diffusion constant, which was used in the Kramer's theory, together with the free energy profile calculated using the enhanced sampling and the implicit solvent, to calculate the folding rate. The calculated folding time agrees well with the experimental value of 2.5 micros.