A role for both conformational selection and induced fit in ligand binding by the LAO protein.

ABSTRACT: 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 ad

SUBMITTER: Silva DA 

PROVIDER: S-EPMC3102756 | biostudies-literature | 2011 May

REPOSITORIES: biostudies-literature