Elucidation of Conformational Switching Mechanisms of Sensing Proteins by Molecular Dynamics Perturbation Studies

Sensing proteins are a subclass of switchable proteins, which are biologically designed with multiple, purposeful, low-free-energy states and can interconvert between these states in the wake of some environmental perturbation. Note, that this phenomenon is no small feat. This is a preprogrammed response for regulatory purposes that requires no cognitive action and is reversible as the environment returns to normal. Sensing proteins often switch between active and non-active states, closed and open conformations or other particular dichotomous states. Therefore, understanding the mechanism by which these proteins sense a specific perturbation and how they switch between conformations is paramount. Addressing these issues can lead to the ability to control protein efficiency; by either direct manipulation of the protein itself to increase its sensitivity to the environment or by quantifying the optimum environmental condition for the desired function. Here molecular dynamics simulations and multi-scale analysis tools are used to elucidate the switching mechanisms of sensing proteins.