Figure 3.

Representative MD simulations snapshots of Gdm⁺ and ClO₄⁻ binding to the EK and (AK)₆ peptides. (A) A Gdm⁺-ion (spheres) hydrogen bonded to the backbone (stick structure) amide and embedded by a nonpolar lysine and alanine methyl groups of the EK peptide. (B) Gdm⁺ binding to (AK)₆ in the coil state. (C) A ClO₄⁻ -ion hydrogen bonded to the backbone amide and embedded by lysine side chains in the (AK)₆ peptide. (D) ClO₄⁻ and Na⁺ displaying concerted binding to the backbone in a compact state of the EK-peptide. Snapshots in A and B were chosen using the kinetic criterion such that ion binding was longer than 0.1 ns. In D the ionic complex was bound for >1 ns.