Effective potentials for Folding Proteins

Nan-yow Chen, Zheng-Yao Su, Chung-Yu Mou

Published 2006-01-24, updated 2006-01-28Version 2

A coarse-grained off-lattice model that is not biased in any way to the native state is proposed to fold proteins. To predict the native structure in a reasonable time, the model has included the essential effects of water in an effective potential. Two new ingredients, the dipole-dipole interaction and the local hydrophobic interaction, are introduced and are shown to be as crucial as the hydrogen bonding. The model allows successful folding of the wild-type sequence of protein G and may have provided important hints to the study of protein folding.