The interplay between protein dynamics and frustration of non-bonded interactions as revealed by molecular dynamics simulations

The mechanism that allows proteins with the same fold to be different in their dynamic and stability properties is poorly understood. We report here the results of molecular dynamics (MD) simulations on rubredoxin (Rd) from hyperthermophilic and mesophilic bacteria that give new insights on this problem. In flexible proteins, the amino acid side chains can form multiple interchangeable non-bonded interaction networks, corresponding to iso-energetic minima in the energy landscape. Under these competing conditions, the system is said to be frustrated. A very stable fold instead, is poorly frustrated because it contains a well-defined and settled network of stabilizing non-bonded interactions.