Molecular dynamics study of mechanical extension of polyalanine by AFM cantilever

A series of molecular dynamics calculations have been performed mimicking the mechanical extension of α-helical polyalanine molecule in water on the AFM. Force profile has been evaluated as a function of extension. In an initial stage of the extension, ∼5%, the force was found to follow the Hooke’s law up to about 140 pN. At the extension of about 10%, however, the restoring force diminishes, indicating the rupture of α-helix. Then, α-helix region and β-strand region separate from each other in one molecule. Further extension causes stepwise breakages of hydrogen bonds to give the wholly β-stranded polyalanine.