Protein Flexibility (4): Applications of NMA to Protein-Protein and Ligand-Protein Binding

The “lock-and-key” model emphasizes the importance of shape complementarity between two rigid structures. It can not be used to explain the conformation changes before and after binding. The “induced fit” model considers the conformation change due to non-rigid protein interactions. A geometric fit is ensured only after the structure rearrangement of the base protein. In the preexisting equilibrium model, an ensemble of closely related conformations in equilibrium is used to represent the native state of a protein, and for different substrates, there are different suitable conformations to be used for binding. The preexisting equilibrium model can be combined with the “induced fit” model to explain the protein binding.