Fig. 3: Unbinding of benzamidine from trypsin.
From: Multisecond ligand dissociation dynamics from atomistic simulations
a TMD snapshots of the structural evolution in trypsin along the dominant dissociation pathway, showing protein surface in gray, benzamidine as van der Waals spheres, Asp189 and water molecules as sticks. Benzamidine is bound to the protein in a cleft of the protein surface via a bidental salt bridge to Asp189. dcTMD calculations of b free energy ΔG(x), and c (Gaussian smoothed) friction Γ(x) together with the mean number of hydrogen bonds between benzamidine and water. Highlighted are the bound state 1, transition state 2, the state with maximal friction 3 and the unbound state 4. Error bars of free energy and friction estimates are given in Supplementary Fig. 2.
