DNA Recognition Process of the Lactose Repressor Protein Studied via Metadynamics and Umbrella Sampling Simulations

The lactose repressor, LacI, finds its DNA target sites via a process that is faster than what it is expected from a diffusion-driven mechanism. This is possible thanks to nonspecific binding of LacI to DNA, followed by diffusion along the DNA molecule. The diffusion of the protein along DNA might lead to a fast-searching mechanism only if LacI binds with comparable strength to different nonspecific sequences and if, in addition, the value of the binding energy remarkably decreases in the presence of a binding site. The first condition would be favored by loose interactions with the base edges, while the second would take advantage from the opposite situation. In order to understand how the protein satisfies these two opposing requirements, the DNA recognition process was studied by a combination of umbrella sampling and metadynamics simulations. The simulations revealed that when aligned with a specific sequence, LacI establishes polar interactions with the base edges that require ∼4 kcal/mol to be disrupted. In contrast, these interactions are not stable when the protein is aligned with nonspecific sequences. These results confirm that LacI is able to efficiently recognize a specific sequence while sliding along DNA before any structural change of the protein–DNA complex occurs.