Elucidation of GB1 Protein Unfolding Mechanism via a Long-timescale Molecular Dynamics Simulation

This study investigates the unfolding mechanism of 1GB1 protein at various simulation temperatures using a long-timescale molecular dynamics simulation. Analysis of structural parameters of molecular dynamics simulation have indicated that the unfolding process of GB1 protein has started at 95 ns for 475 K simulation, and at 745 ps for 500 K simulation. The unfolding process in this simulation exhibit the feature of hydrophobic core collapse model, in which the beta-hairpin destruction precedes the alpha-helix to coil transition. The unfolding was started with the increasing flexibility of the beta-sheets and hydrophobic core region, continued with beta-hairpins destruction, and ended with alpha-helix to coil and turn transition. The final structures of GB1 protein after unfolding, suggest an unfinished denaturation of protein as seen from the small remains of alpha-helix structure.