A Role for Both Conformational Selection and Induced Fit in Ligand Binding by the LAO Protein

Molecular recognition is determined by the structure and dynamics of both a protein and its ligand, but it is difficult to directly assess the role of each of these players. In this study, we use Markov State Models (MSMs) built from atomistic simulations to elucidate the mechanism by which the Lysine-, Arginine-, Ornithine-binding (LAO) protein binds to its ligand. We show that our model can predict the bound state, binding free energy, and association rate with reasonable accuracy and then use the model to dissect the binding mechanism. In the past, this binding event has often been assumed to occur via an induced fit mechanism because the protein's binding site is completely closed in the bound state, making it impossible for the ligand to enter the binding site after the protein has adopted the closed conformation. More complex mechanisms have also been hypothesized, but these have remained controversial. Here, we are able to directly observe roles for both the conformational selection and induced fit mechanisms in LAO binding. First, the LAO protein tends to form a partially closed encounter complex via conformational selection (that is, the apo protein can sample this state), though the induced fit mechanism can also play a role here. Then, interactions with the ligand can induce a transition to the bound state. Based on these results, we propose that MSMs built from atomistic simulations may be a powerful way of dissecting ligand-binding mechanisms and may eventually facilitate a deeper understanding of allostery as well as the prediction of new protein-ligand interactions, an important step in drug discovery. Author Summary: Protein-ligand interactions are crucial to chemistry, biology and medicine. Many studies have been conducted to probe the mechanism of protein-ligand binding, leading to the development of the induced fit and conformational selection models. Unfortunately, experimentally probing the atomistic details of protein-ligand binding mechanisms is challenging. Computer simulations have the potential to provide a detailed picture of molecular recognition events. In this study, we construct kinetic network models from atomistic simulations to elucidate the mechanism by which the LAO protein binds to its ligand. Because the LAO protein completely encompasses its substrate in the bound state, it has generally been assumed that it operates via an induced fit mechanism. We find that both the conformational selection and induced fit mechanisms play important roles in LAO binding. Furthermore, we have identified a number of parallel pathways for binding, all of which pass through a single gatekeeper state, which we refer to as the encounter complex state because the protein is partially closed and only weakly interacting with its substrate.