Design and computational analysis of protein based nanoscale biomimetic actuators

A nanoscale biomolecular linear actuator taken from a virus is introduced, analyzed and methods to characterize and quantify its performance are discussed and applied. The HA2 domain of Influenza viral peptide is known to undergo a large conformational change in the cellular endosome upon a drop in pH. Targeted molecular dynamics techniques (TMD) are employed to study the opening/closing behavior of a hinge region that plays a critical role in the conformational change. Four different models of the peptide are subjected to TMD to trace a trajectory from closed (initial) to open (final) state and the differences between them are quantified using conformational energy and open state contacts to show the role of low pH as well as peptide mutations in order for such systems to act as nanoactuators. The results obtained are found to be in agreement with experimental findings that show that the protonated and mutated peptides are more likely to attain stable open state when compared to the wild type peptide.