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 th eir dynamic and stability properties is poorly understood. We report here t he results of molecular dynamics (MD) simulations on rubredoxin (Rd) from h yperthermophilic and mesophilic bacteria that give new insights on this pro blem. In flexible proteins, the amino acid side chains can form multiple in terchangeable non-bonded interaction networks, corresponding to iso-energet ic minima in the energy landscape. Under these competing conditions, the sy stem is said to be frustrated. A very stable fold instead, is poorly frustr ated because it contains a well-defined and settled network of stabilizing non-bonded interactions. (C) 2001 Elsevier Science B.V. All rights reserved .