The energetics of two small peptides, as represented though their potential of mean force along a chosen coordinate, has been obtained using a stage-wise implementation of steered molecular dynamics. Specifically, adaptive steered molecular dynamics (ASMD) has been used to obtain and compare the energetics of the mechanical stretching of two small, stable β- hairpins, chignolin and trpzip1. The two β-hairpins are of comparable size and structure, yet have vastly different energetics and stability observed both computationally and experimentally. We have obtained the potentials of mean force for the stretching of the two peptides at slow pulling velocities with high sampling in explicit water solvent conditions. In addition to energetics, we have obtained quantitative insight into the peptide stability though analysis of the hydrogen-bonding profiles and several residue pair interactions within each peptide along the stretching coordinate. The comparison of the energetics and pathways between these peptides, and to those of helical peptides, reveal differences in the relative stability of specific contacts and local geometric features of the peptide motif.

Probing the energetics of β-hairpins using adaptive steered molecular dynamics

251st National Meeting (2016)

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