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.