  The protein-ligand residence time, tau, influences molecular function in
biological networks and has been recognized as an important determinant of drug
efficacy. To predict tau, computational methods must overcome the problem that
tau often exceeds the timescales accessible to conventional molecular dynamics
(MD) simulation. Here, we apply the tau-Random Acceleration Molecular Dynamics
(tauRAMD) method to a set of kinetically characterized complexes of T4 lysozyme
mutants with engineered binding cavities. tauRAMD yields relative ligand
dissociation rates in good accordance with experiments and thereby allows a
comprehensive characterization of the ligand egress routes and determinants of
tau. Although ligand dissociation by multiple egress routes is observed, we
find that egress via the predominant route determines the value of tau. We also
find that the presence of metastable states along egress pathways slows down
protein-ligand dissociation. These physical insights could be exploited in the
rational optimization of the kinetic properties of drug candidates.
