The range of the contact interactions and the kinetics of the Go models of proteins

We consider two types of Go models of a protein (crambin) and study their kinetics through molecular dynamics simulations. In the first model, the residue – residue contact interactions are selected based on a cutoff distance, Rc, between the Cα atoms. The folding times depend on the value of Rc strongly and non-monotonically due to the interplay between frustration and the free energy barrier for folding. This indicates a need for a physically determined set of native contacts that takes into account all the residual atoms. This can be accomplished by considering the van der Waals radii of the atoms and checking if they are found within a proper range of the van der Waals attraction. In the second model, non-native attractive contacts are added to the system. This leads to bad foldability. However, for a small number of such extra contacts there is a slight acceleration in the kinetics of folding. keywords: protein folding; folding rate; molecular dynamics; chirality