PMC

Minimum energy path connecting the active to Src-like inactive conformation.

(A) The proposed mechanism on the substrate-assisted glycosylation reaction in OfHex1.
(B) The chemical order parameters changes along the initial minimum energy path. Red: The CVs for the proton transfer process. Blue: The CVs for the nucleophilic substitution process.
(C) The chemical order parameters changes along the OTPRW optimized minimum free energy path. Red: The CVs for the proton transfer process. Blue: The CVs for the nucleophilic substitution process.
(D) The free energy changes along the initial minimum energy path (the dotted line) and along the OTPRW optimized minimum free energy path (the solid line).

End point structures used for determining the minimum energy path (MEP). A. Stacked conformation (pH 8.0 structure). B. Energy minimized U80 flipped-out conformation. Both structures are shown with A79 protonated.

Maximum flux transition path and minimum free energy path from C_7eq to C_7ax for alanine dipeptide in vacuum at 300 K. Triangles are images of the initial path; rectangles are the images of the maximum flux transition path; and circles are the images of the minimum free energy path. The contours are those for the zero-temperature free energy (adiabatic energy). The contour lines are separated by 0.6 kcal/mol.