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

Abstract

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, $R_c$, between the C${}_{\alpha }$ atoms. The folding times depend on the value of $R_c$ 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. %%. One may accomplish it This can be accomplished by considering the van der Waals radii of the atoms and checking if %%the atoms overlap. 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.

to appear in Int. J. Mod. Phys. C

References in corpus (1)

• Universality classes in folding times of proteins

Cited by in corpus (5)

• Chirality and Protein Folding
• Mechanical properties of the domains of titin in a Go-like model
• Protein escape at the ribosomal exit tunnel: Effects of native interactions, tunnel length and macromolecular crowding
• Cooperativity and Contact Order in Protein Folding
• The protein escape process at the ribosomal exit tunnel has conserved mechanisms across the domains of life