Ligand unbinding mechanisms and kinetics for T4 lysozyme mutants from tau RAMD simulations

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 (tau RAMD) method to a set of kinetically characterized complexes of T4 lysozyme mutants with small, engineered binding cavities. tau RAMD yields relative ligand dissociation rates in good accordance with experiments across this diverse set of complexes that differ with regard to measurement temperature, ligand identity, protein mutation and binding cavity. tau RAMD 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 a greater number of metastable states along egress pathways leads to slower proteinligand dissociation. These physical insights could be exploited in the rational optimization of the kinetic properties of drug candidates.