Unfolding energetics and pathways of peptides with varying secondary structure motifs
Bureau, Hailey Rhea
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The present body of work focuses on using computational techniques to characterize and predict the energetics and other observables of peptides unfolding under external forces. The energetics of stretching peptides can be obtained through the integration nonequilibrium molecular dynamics trajectories leading to a potential mean force. However, the computational challenge of such calculations makes them difficult to achieve. We have developed an enhanced sampling method, namely adaptive steered molecular dynamics (ASMD), which provides efficient convergence for the mechanical unfolding of peptides. The ASMD scheme also allows for the determination of other average observables such as hydrogen-bonding patterns and persistence of secondary structure motifs. The ASMD method has been used to determine the energetics and mechanical stretching pathways of several different types of helices, beta-hairpins, and multi-motif peptides.