Physics – Condensed Matter
Scientific paper
2002-06-16
Physics
Condensed Matter
to appear in Int. J. Mod. Phys. C
Scientific paper
10.1142/S012918310200408X
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.
Cieplak Marek
Hoang Trinh Xuan
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