Secondary Structure
Secondary structure is an important analytical tool which help us understand the structural preference of a protein throughout the simulation. Proteins during the folding process take up different structural conformations like alpha helix, beta sheets, turns etc. which plays significant role in defining protein functions in the underlying biological cascades [42]. Hence it is important to understand the secondary structure elements present in protein because, just as a particular structure can determine the protein function, any deviation from the normal structure, possibly due to misfolding or mutations, can lead to a pathological condition as well [43].
Analysis of PHF tau obtained from the brain of Alzheimer’s patients have revealed that tau is rich in beta sheet conformation in the microtubule binding region[35]. Indicating that tau protein when undergoing folding or aggregation tend to form secondary structure elements that are rich in beta sheet content [44, 45]. Hence, we performed secondary structure analysis of each of the systems using the DSSP [46] Algorithm and the time evolution of secondary structure throughout the trajectory is plotted in Figure S5 in supporting information.