The electrostatic probe: a tool for the investigation of the Aβ(1–16) peptide deformations using the static modes

Abstract

We investigate the conformational changes of the Amyloid β(1–16) peptide induced by moving Zn²⁺ ions in the solvent, which we call the electrostatic probe. We use our recently developed approach of static modes which allows treating the flexibility of biological molecules at the atomic scale. Starting from an experimental apostructure, we find that several ion impacts allow the transition of the peptide toward its folded conformation, observed experimentally in the presence of Zn²⁺ ions. This result shows the ability of our model and its associated software tool to describe properly the conformational changes and opens a new path toward the molecule/molecule docking problem.