The interactions of a peptide with its local solvent environment affect many properties of the peptide, including the unfolding pathway. Understanding the energetics of unfolding offers insight into the relationship between the peptide structure and stability. Developing computationally efficient methods to obtain the potential of mean force (PMF) for the unfolding of a peptide is a significant challenge. One method for obtaining the PMF of the unfolding of a peptide is Steered Molecular Dynamics. SMD has been used for numerous applications and has been shown to obtain the PMF, although at significant computational cost. Adaptive Steered Molecular Dynamics (ASMD) is an alternative and more computationally efficient method for obtaining the PMF. ASMD has recently been used to compare the PMF and hydrogen bonding profiles of the unfolding of decaalanine in three different environments: vacuum, implicit, and explicit solvent. The use of implicit solvent was found to provide a reasonable estimate of the energetics and quantitative agreement with the hydrogen bonding profiles for unfolding the peptide.

Using computational methods to understand the energetics of small peptides

248th National Meeting (2014)

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