Antimicrobial peptides of the uperin 3.x family, obtained from the skin secretions of Uperoleia mjobergii, have an inherent ability to form amyloid with possible functional roles and can serve as model peptides to understand mechanistic aspects of amyloidogenesis. The substitution of a positively charged amino acid with a nonpolar alanine residue increased aggregation, fibril content, and propensity for β-sheet formation for the uperin 3.5 R7A variant when compared with the uperin 3.5 wild-type peptides. We use molecular dynamics (MD) simulations and circular dichroism (CD) measurements on three uperin 3.x peptides and their corresponding seventh position alanine variants to understand the effect of substitution of a positively charged amino acid with a nonpolar alanine residue on the process of β-aggregation. Both CD experiments and simulations show that the uperin 3.x wild-type peptides demonstrated lower β-sheet content and propensity than with the corresponding alanine variants. Significantly, simulations of helix-to-coil transitions in individual peptides show an inverse relationship between the helical stability of peptides and their propensity to form structures rich in β-sheets as observed in CD experiments. A simulation scheme based on a conformational search of helix-to-coil transition trajectories to select peptide conformers was used to assemble propagating peptide oligomers. Whereas octamers consisting of lower helical stability peptide conformers evolve into compact aggregates with a large β-sheet component, octamers composed of high helical stability conformers disintegrate and show the least amounts of β-sheet components. The highlight of the current work is that MD simulations are able to predict the correct order of β-sheet propensity among the six peptides derived from the CD experiments and indicate the importance of helical intermediates in the amyloidogenesis pathway for uperin 3.x peptides.