Polar Zipper on a Peptide Nanomembrane: A Characterization by Potential of Mean Force

Abstract

In this work, nanomembranes formed by the I3 XGK (X = Q, S, or N) polar peptides are studied to characterize the average force and energy required to separate two neighboring β-sheets laterally joined by polar zippers. The results presented are obtained using a methodology (state of the art) involving the pulling umbrella method to generate the samples (umbrella sampling) and the potential of mean force (PMF) to evaluate the energetic variation evolved in the process of separating the polar zipper. It was observed that the maximum force required to separate the regions linked by polar zippers is 1.48 kJ/mol nm for the I3 NGK nanomembrane and 1.22 kJ/mol nm [1.30 kJ/mol nm] for the I3 QGK [I3 SGK] nanomembranes, emphasizing that polar zippers play an important role in the interaction that interconnects β-sheets in broad and robust two-dimensional structures (tapes and membranes), offering an agile route to the construction of distinct nanomaterials from β-sheets. Also, negative values were obtained for energy as a function of the reaction coordinate for the regions where the formation of polar zippers occurs, showing that the lateral union of neighboring β-sheets is energetically favorable, with a value up to −3.0 kJ/mol, in the case of I3 NGK nanomembranes.