Eur. Phys. J. B 30, 381-391 (2002)
https://doi.org/10.1140/epjb/e2002-00393-4

Folding of lattice protein chains with modified Gō potential

National Laboratory of Solid State Microstructure and Department of Physics, Nanjing University, Nanjing 210093, PR China

Corresponding author: ^a wangwei@nju.edu.cn

Received: 10 April 2002
Revised: 20 August 2002
Published online: 19 December 2002

Abstract

We propose a modified Gō model in which the pairwise interaction energies vary as local environment changes. The stability difference between the surface and the core is also well considered in this model. Thermodynamic and kinetic studies suggest that this model has improved folding cooperativity and foldability in contrast with the Gō model. The free energy landscape of this model has broad barriers and narrow denatured states, which is consistent with that of the two-state folding proteins and is lacked for the Gō model. The role of non-native interactions in protein folding is also studied. We find that appropriate consideration of the contribution of the non-native interactions may increase the folding rate around the transition temperature. Our results show that conformation-dependent interaction between the residues is a realistic representation of potential functions in protein folding.