Protein dynamic properties: essential dynamics method vs. NMR backbone dynamics

Proteins are dynamic systems whose internal motions and resulting conformational changes are essential for their functional skills. While the rigidity is required to maintain the structure, flexibility is needed to perform the function. The study of protein flexibility can be handled by both experimental, such as NMR backbone dynamics in solutions, and computational methods, such as molecular dynamics simulations. The major problem with molecular dynamics simulations is due to the conformational sampling efficiency that requires long times of calculation. In recent decades a new computational approach, based on the essential dynamics sampling (EDS) has been applied to the study of protein flexibility, folding etc. In essential dynamics sampling, an usual molecular dynamics simulation is performed, but only those steps, not increasing the distance from a target structure, are accepted. This method offers the possibility of representing protein dynamics in the essential subspace only, so reducing the complex protein dynamics to its essential degrees of freedom. In this work we apply ED simulations to identify flexible regions in two protein systems previously studied by NMR backbone dynamics.