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

TL;DR

This study investigates how the range of native contact interactions affects protein folding kinetics in Go models, highlighting the importance of physically accurate contact definitions and the impact of non-native interactions.

Contribution

It introduces a detailed analysis of contact range effects and the influence of non-native contacts on folding kinetics in protein Go models.

Findings

Folding times vary non-monotonically with contact cutoff distance.

Physically determined native contacts improve model accuracy.

Small amounts of non-native attractive contacts can slightly accelerate folding.

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.