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A model of protein-ligand binding kinetics in which slow solvent dynamicsresults from hydrophobic drying transitions is investigated. Molecular dynamicssimulations show that solvent in the receptor pocket can fluctuate between wetand dry states with lifetimes in each state that are long enough for theextraction of a separable potential of mean force and wet-to-dry transitions.We introduce a Diffusive Surface Hopping Model that is represented by atwo-dimensional Markovian master equation. One dimension is the standardreaction coordinate, the ligand-pocket separation, and the other is the solventstate in the region between ligand and binding pocket which specifies whetherit is wet or dry. In our model, the ligand diffuses on a dynamic free energysurface which undergoes kinetic transitions between the wet and dry states. Themodel yields good agreement with results from explicit solvent moleculardynamics simulation and an improved description of the kinetics of hydrophobicassembly. Furthermore, it is consistent with a "non-Markovian Brownian theory"for the ligand-pocket separation coordinate alone.

How hydrophobic drying forces impact the kinetics of molecular recognition