Molecular Dynamics Simulation for Protein Unfolding

Protein folding research has always been a significant research topic in biological sciences. However, due to the diversity of protein structures and the unpredictability of folding pathways, the folding mechanism of the natural structure of proteins have not been clearly explained. In this work, ubiquitin is used as the research object to analyze the process of protein unfolding through molecular dynamics (MD) simulation. The aim to do protein unfolding is to enlighten the research on the issue about protein folding mechanism in reverse. Our simulation reveals the order of secondary structures to unfolding and the segmentation in the unfolding process. The results can confirm the difference in stability between various secondary structures. After that, the changes in the number of hydrogen bonds and energy during the unfolding process are focused on. It indicates that both of them also have the same step phenomenon. It is presumed that the protein folding may have the similar step phenomenon. It is hopeful for the results obtained from protein unfolding to guide and inspire protein folding mechanisms.