Figure 5.

Alternative scenarios for lysine acetylation. The maximum common substructure of lysine (left) and its acetylated form (right). (A) This perturbation topology is generated in the case when removing bonded interactions is allowed (improper dihedral angle around the nitrogen atom) and one of the following two options is used: either change in the multiplicity of dihedral angles is allowed or the procedure for matching dihedral angles uses only the middle atoms. (B) This definition of the perturbation path is obtained if the conditions from case A are not fulfilled or if perturbing bonds is not allowed. Note, however, that in this solution, the carbon atom of the acetyl group has five bonded interactions (one bond, two angles, one proper, and one improper dihedrals) with the unperturbed atoms, i.e., two redundant terms. Unperturbed atoms are highlighted in blue, perturbed atoms in red, and dummy atoms in gray.